Psyllid ID: psy8507

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------
Protein Sequence
MRVPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYKLLVQTGRVDNPVDKSLIKHNRLVSRDGIINPKLLLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQFILRIFFYMLFGIVLVGLLYMVLL
Secondary Structure (PSIPRED)
cccccEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHccccHHHHHHHHHHHccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccEEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHccccccccccccccEEEEEcccccccHHHHHHHHHHHccccHHHHHHHHHHccccccccEEEEEcHccccccccccHHHHHHHHccHHHccHHHHHHHHHEEEccHHHHHHHHHHHHHHHHHHHHHHHcccc
Coil and Loop (DISEMBL)
mrvpnivknddgglpgnFWLELFRDWLLGLQEsfdkdyaagcitqerwfpnasesSILAYKLLVQTgrvdnpvdkslikhnrlvsrdgiinpKLLLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQFILRIFFYMLFGIVLVGLLYMVLL
Flexible Loop (DISEMBL)
mrvpnivknddgglpgNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYKLLVQTGRvdnpvdkslikhnrlvsrdgiinPKLLLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQFILRIFFYMLFGIVLVGLLYMVLL
Low Complexity Region (SEG)
MRVPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYKLLVQTGRVDNPVDKSLIKHNRLVSRDGIINPKLLLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQFILRIFFYMLFGIVLVGLLYMVLL
Disordered region (IsUnstruct)
***********GGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYKLLVQTGRVDNPVDKSLIKHNRLVSRDGIINPKLLLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQFILRIFFYMLFGIVLVGLLYMVL*
Disordered Region (DISOPRED)
*RVPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYKLLVQTGRVDNPVDKSLIKHNRLVSRDGIINPKLLLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQFILRIFFYMLFGIVLVGLLYMVLL
Disordered Region (DISEMBL)
MRVPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYKLLVQTGRVDNPVDKSLIKHNRLVSRDGIINPKLLLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQFILRIFFYMLFGIVLVGLLYMVLL
Disordered Region (DISPRO)
*RVPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYKLLVQTGRVDNPVDKSLIKHNRLVSRDGIINPKLLLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQFILRIFFYMLFGIVLVGLLYMVLL
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiHHHHHHHHHHHHHHHHHHHHHHHo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooHHHHHHHHHHHHHHHHHHHi
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHooHHHHHHHHHHHHHHHHHHHiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHoooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHoooooooHHHHHHHHHHHHHHHHHHiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHoooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooHHHHHHHHHHHHHHHHHHHHHHHi
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRVPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYKLLVQTGRVDNPVDKSLIKHNRLVSRDGIINPKLLLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQFILRIFFYMLFGIVLVGLLYMVLL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	197	2.2.26 [Sep-21-2011]
P18502	1286	Protein patched OS=Drosop	yes	N/A	0.467	0.071	0.623	3e-28
Q90693	1442	Protein patched homolog 1	yes	N/A	0.492	0.067	0.444	4e-17
Q13635	1447	Protein patched homolog 1	no	N/A	0.532	0.072	0.411	4e-17
Q61115	1434	Protein patched homolog 1	yes	N/A	0.532	0.073	0.411	5e-17
Q9Y6C5	1203	Protein patched homolog 2	no	N/A	0.451	0.073	0.411	7e-15
Q09614	1408	Protein patched homolog 1	yes	N/A	0.532	0.074	0.327	9e-15
Q98864	1220	Protein patched homolog 1	no	N/A	0.492	0.079	0.393	2e-14
O35595	1182	Protein patched homolog 2	no	N/A	0.451	0.075	0.4	7e-14
P56941	1277	Niemann-Pick C1 protein O	no	N/A	0.492	0.075	0.363	6e-06
O35604	1277	Niemann-Pick C1 protein O	no	N/A	0.492	0.075	0.343	2e-05

>sp|P18502|PTC_DROME Protein patched OS=Drosophila melanogaster GN=ptc PE=2 SV=2

 Score =  125 bits (313), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 58/93 (62%), Positives = 75/93 (80%), Gaps = 1/93 (1%)

Query: 1   MRVPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAY 60
           +RVP+++KND+GGLP +FWL LF +WL  LQ+ FD++Y  G +T+E WFPNAS  +ILAY
Sbjct: 758 VRVPHVIKNDNGGLP-DFWLLLFSEWLGNLQKIFDEEYRDGRLTKECWFPNASSDAILAY 816

Query: 61  KLLVQTGRVDNPVDKSLIKHNRLVSRDGIINPK 93
           KL+VQTG VDNPVDK L+  NRLV+ DGIIN +
Sbjct: 817 KLIVQTGHVDNPVDKELVLTNRLVNSDGIINQR 849

Segmentation polarity protein. Acts as a receptor for the hedgehog protein (HH). Associates with the smoothened protein (SMO) to transduce the hedgehog signal leading to the activation of wingless, decapentaplegic and patched itself. Participates in cell interactions that establish pattern within the segment and the imaginal disks during development. In the absence of HH, represses the constitutive signaling activity of smo through fused (FU).
Drosophila melanogaster (taxid: 7227)

>sp|Q90693|PTC1_CHICK Protein patched homolog 1 OS=Gallus gallus GN=PTCH1 PE=1 SV=1

 Score = 87.8 bits (216), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 44/99 (44%), Positives = 58/99 (58%), Gaps = 2/99 (2%)

Query: 11  DGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYKLLVQTGRVD 70
           D  LP   WL  FRDWL GLQ++FD D+  G IT    + N S+ ++LAYKLLVQTG   
Sbjct: 836 DRQLP-KMWLHYFRDWLQGLQDAFDSDWETGKITYSN-YKNGSDDAVLAYKLLVQTGNRA 893

Query: 71  NPVDKSLIKHNRLVSRDGIINPKLLLVMYLMNIKLNPIS 109
            P+D S +   RLV  DGIINP    +     +  +P++
Sbjct: 894 KPIDISQLTKQRLVDADGIINPNAFYIYLTAWVSNDPVA 932

Acts as a receptor for sonic hedgehog (SHH), indian hedgehog (IHH) and desert hedgehog (DHH). Associates with the smoothened protein (SMO) to transduce the hedgehog's proteins signal.

Gallus gallus (taxid: 9031)

>sp|Q13635|PTC1_HUMAN Protein patched homolog 1 OS=Homo sapiens GN=PTCH1 PE=1 SV=2

 Score = 87.8 bits (216), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 44/107 (41%), Positives = 61/107 (57%), Gaps = 2/107 (1%)

Query: 3   VPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYKL 62
           V  ++  ++  LP   WL  FRDWL GLQ++FD D+  G I     + N S+  +LAYKL
Sbjct: 829 VKYVMLEENKQLP-KMWLHYFRDWLQGLQDAFDSDWETGKIMPNN-YKNGSDDGVLAYKL 886

Query: 63  LVQTGRVDNPVDKSLIKHNRLVSRDGIINPKLLLVMYLMNIKLNPIS 109
           LVQTG  D P+D S +   RLV  DGIINP    +     +  +P++
Sbjct: 887 LVQTGSRDKPIDISQLTKQRLVDADGIINPSAFYIYLTAWVSNDPVA 933

Acts as a receptor for sonic hedgehog (SHH), indian hedgehog (IHH) and desert hedgehog (DHH). Associates with the smoothened protein (SMO) to transduce the hedgehog's proteins signal. Seems to have a tumor suppressor function, as inactivation of this protein is probably a necessary, if not sufficient step for tumorigenesis.

Homo sapiens (taxid: 9606)

>sp|Q61115|PTC1_MOUSE Protein patched homolog 1 OS=Mus musculus GN=Ptch1 PE=2 SV=1

 Score = 87.8 bits (216), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 44/107 (41%), Positives = 61/107 (57%), Gaps = 2/107 (1%)

Query: 3   VPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYKL 62
           V  ++  ++  LP   WL  FRDWL GLQ++FD D+  G I     + N S+  +LAYKL
Sbjct: 815 VKYVMLEENKQLP-QMWLHYFRDWLQGLQDAFDSDWETGRIMPNN-YKNGSDDGVLAYKL 872

Query: 63  LVQTGRVDNPVDKSLIKHNRLVSRDGIINPKLLLVMYLMNIKLNPIS 109
           LVQTG  D P+D S +   RLV  DGIINP    +     +  +P++
Sbjct: 873 LVQTGSRDKPIDISQLTKQRLVDADGIINPSAFYIYLTAWVSNDPVA 919

Acts as a receptor for sonic hedgehog (SHH), indian hedgehog (IHH) and desert hedgehog (DHH). Associates with the smoothened protein (SMO) to transduce the hedgehog's proteins signal. Seems to have a tumor suppressor function, as inactivation of this protein is probably a necessary, if not sufficient step for tumorigenesis.

Mus musculus (taxid: 10090)

>sp|Q9Y6C5|PTC2_HUMAN Protein patched homolog 2 OS=Homo sapiens GN=PTCH2 PE=2 SV=2

 Score = 80.5 bits (197), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 37/90 (41%), Positives = 58/90 (64%), Gaps = 1/90 (1%)

Query: 19  WLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYKLLVQTGRVDNPVDKSLI 78
           WL  +R+WL G+Q +FD+D+A+G IT+   + N SE   LAYKLL+QTG    P+D S +
Sbjct: 781 WLHYYRNWLQGIQAAFDQDWASGRITRHS-YRNGSEDGALAYKLLIQTGDAQEPLDFSQL 839

Query: 79  KHNRLVSRDGIINPKLLLVMYLMNIKLNPI 108
              +LV R+G+I P+L  +   + +  +P+
Sbjct: 840 TTRKLVDREGLIPPELFYMGLTVWVSSDPL 869

May have a role in epidermal development. May act as a receptor for Sonic hedgehog (SHH).

Homo sapiens (taxid: 9606)

>sp|Q09614|PTC1_CAEEL Protein patched homolog 1 OS=Caenorhabditis elegans GN=ptc-1 PE=1 SV=2

 Score = 80.1 bits (196), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 36/110 (32%), Positives = 70/110 (63%)

Query: 88   GIINPKLLLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGNRDRRVRLSIE 147
            GI+  +L   M L+ IKLNP+S V ++ + GI + F  ++ +SFLT +G R +R   +++
Sbjct: 1216 GIMTCELAGFMGLVGIKLNPVSAVTLITAVGIGVEFTVHVVVSFLTALGTRSQRTSSAVD 1275

Query: 148  HMYSVVLHAGLILLVAISILAFSEFQFILRIFFYMLFGIVLVGLLYMVLL 197
             ++  V+H     L+ I +L FSEF+F+++ FF ++  ++ +G++  ++L
Sbjct: 1276 RVFVPVIHGSFSTLLGILMLGFSEFEFVVKYFFIVMTALICIGIINGLIL 1325

Required but not essential for cytokinesis of mitotically proliferating germ cells.

Caenorhabditis elegans (taxid: 6239)

>sp|Q98864|PTC1_DANRE Protein patched homolog 1 OS=Danio rerio GN=ptch1 PE=2 SV=1

 Score = 79.3 bits (194), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 39/99 (39%), Positives = 65/99 (65%)

Query: 93   KLLLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGNRDRRVRLSIEHMYSV 152
            +L  +M L+ IKL+ I  V+++ S GI + F  +I L FLT IG+R+ R  +++EHM++ 
Sbjct: 1055 ELFGIMGLIGIKLSAIPVVILIASVGIGVEFTVHIALGFLTAIGDRNTRSAVAMEHMFAP 1114

Query: 153  VLHAGLILLVAISILAFSEFQFILRIFFYMLFGIVLVGL 191
            V+   +  L+ + +LA SEF FI+R FF +L  + L+G+
Sbjct: 1115 VIDGAISTLLGVLMLAGSEFDFIMRYFFAVLAILTLLGI 1153

Acts as a receptor for sonic hedgehog (SHH), indian hedgehog (IHH) and desert hedgehog (DHH). Associates with the smoothened protein (SMO) to transduce the hedgehog's proteins signal.

Danio rerio (taxid: 7955)

>sp|O35595|PTC2_MOUSE Protein patched homolog 2 OS=Mus musculus GN=Ptch2 PE=2 SV=2

 Score = 77.0 bits (188), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 36/90 (40%), Positives = 56/90 (62%), Gaps = 1/90 (1%)

Query: 19  WLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYKLLVQTGRVDNPVDKSLI 78
           WL  +R WL G+Q +FD+D+A+G IT    + N SE   LAYKLL+QTG    P+D S +
Sbjct: 781 WLHYYRSWLQGIQAAFDQDWASGRITCHS-YRNGSEDGALAYKLLIQTGNAQEPLDFSQL 839

Query: 79  KHNRLVSRDGIINPKLLLVMYLMNIKLNPI 108
              +LV ++G+I P+L  +   + +  +P+
Sbjct: 840 TTRKLVDKEGLIPPELFYMGLTVWVSSDPL 869

May have a role in epidermal development. May act as a receptor for Sonic hedgehog (SHH).

Mus musculus (taxid: 10090)

>sp|P56941|NPC1_PIG Niemann-Pick C1 protein OS=Sus scrofa GN=NPC1 PE=2 SV=1

 Score = 50.8 bits (120), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 36/99 (36%), Positives = 52/99 (52%), Gaps = 2/99 (2%)

Query: 97   VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSF-LTCIGNRDRRVRLSIEHMYSVVLH 155
            VM+L  I LN +S V +V S GI + F S+I  +F L+  G+R  R   ++ HM S V  
Sbjct: 1140 VMWLWGISLNAVSLVNLVMSCGISVEFCSHITRAFTLSTKGSRVDRAEEALAHMGSSVFS 1199

Query: 156  A-GLILLVAISILAFSEFQFILRIFFYMLFGIVLVGLLY 193
               L     I +LAF++ Q     +F M   IVL+G  +
Sbjct: 1200 GITLTKFGGIVVLAFAKSQIFQIFYFRMYLAIVLLGATH 1238

Involved in the intracellular trafficking of cholesterol. May play a role in vesicular trafficking in glia, a process that may be crucial for maintaining the structural and functional integrity of nerve terminals.

Sus scrofa (taxid: 9823)

>sp|O35604|NPC1_MOUSE Niemann-Pick C1 protein OS=Mus musculus GN=Npc1 PE=1 SV=2

 Score = 49.3 bits (116), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 34/99 (34%), Positives = 52/99 (52%), Gaps = 2/99 (2%)

Query: 97   VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSF-LTCIGNRDRRVRLSIEHMYSVVLH 155
            VM+L  I LN +S V +V S GI + F S+I  +F ++  G+R  R   ++ HM S V  
Sbjct: 1140 VMWLWGISLNAVSLVNLVMSCGISVEFCSHITRAFTMSTKGSRVSRAEEALAHMGSSVFS 1199

Query: 156  A-GLILLVAISILAFSEFQFILRIFFYMLFGIVLVGLLY 193
               L     I +LAF++ Q     +F M   +VL+G  +
Sbjct: 1200 GITLTKFGGIVVLAFAKSQIFEIFYFRMYLAMVLLGATH 1238

Involved in the intracellular trafficking of cholesterol. May play a role in vesicular trafficking in glia, a process that may be crucial for maintaining the structural and functional integrity of nerve terminals.

Mus musculus (taxid: 10090)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	197
321479419	1285	putative hedgehog receptor patched [Daph	0.461	0.070	0.739	5e-35
383849191	1327	PREDICTED: LOW QUALITY PROTEIN: protein	0.467	0.069	0.698	1e-34
380011471	1327	PREDICTED: LOW QUALITY PROTEIN: protein	0.467	0.069	0.698	1e-34
307191579	1191	Protein patched [Harpegnathos saltator]	0.467	0.077	0.698	3e-34
340727459	1292	PREDICTED: protein patched-like [Bombus	0.467	0.071	0.677	4e-34
322790929	952	hypothetical protein SINV_80439 [Solenop	0.467	0.096	0.709	1e-33
350421906	1011	PREDICTED: protein patched-like [Bombus	0.467	0.090	0.677	3e-33
242015824	1320	patched 1, putative [Pediculus humanus c	0.467	0.069	0.698	4e-33
332030584	1114	Protein patched [Acromyrmex echinatior]	0.467	0.082	0.698	5e-33
241027837	1172	patched-2 protein, putative [Ixodes scap	0.456	0.076	0.659	4e-32

>gi|321479419|gb|EFX90375.1| putative hedgehog receptor patched [Daphnia pulex]

 Score =  152 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 68/92 (73%), Positives = 77/92 (83%), Gaps = 1/92 (1%)

Query: 2   RVPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYK 61
           RV  I+KNDDGGLP  FWL LFRDWL+GLQ +FD+D +AGCI QERWF NAS+ +ILAYK
Sbjct: 755 RVSTIIKNDDGGLP-EFWLSLFRDWLIGLQRAFDRDQSAGCINQERWFSNASDDAILAYK 813

Query: 62  LLVQTGRVDNPVDKSLIKHNRLVSRDGIINPK 93
           LLVQTG VDNP+DKSL+ H RLV  DGIINPK
Sbjct: 814 LLVQTGHVDNPIDKSLVGHVRLVDGDGIINPK 845

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383849191|ref|XP_003700229.1| PREDICTED: LOW QUALITY PROTEIN: protein patched-like [Megachile rotundata]

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 65/93 (69%), Positives = 78/93 (83%), Gaps = 1/93 (1%)

Query: 1   MRVPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAY 60
           MR+ N++KND+GGLP  FWL LFRDWL GLQ +FDKDY +GCITQERW+ NAS+ +ILAY
Sbjct: 805 MRIKNVIKNDNGGLP-EFWLSLFRDWLKGLQSAFDKDYNSGCITQERWYKNASDEAILAY 863

Query: 61  KLLVQTGRVDNPVDKSLIKHNRLVSRDGIINPK 93
           KLLVQTG VDNP+DKSL+   RLV  +GIINP+
Sbjct: 864 KLLVQTGHVDNPIDKSLVTQVRLVDSEGIINPR 896

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380011471|ref|XP_003689826.1| PREDICTED: LOW QUALITY PROTEIN: protein patched-like [Apis florea]

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 65/93 (69%), Positives = 78/93 (83%), Gaps = 1/93 (1%)

Query: 1   MRVPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAY 60
           MR+ N++KND+GGLP  FWL LFRDWL GLQ +FDKDY+ GCITQERW+ NAS+ +ILAY
Sbjct: 804 MRIKNVIKNDNGGLP-EFWLSLFRDWLKGLQSAFDKDYSNGCITQERWYKNASDDAILAY 862

Query: 61  KLLVQTGRVDNPVDKSLIKHNRLVSRDGIINPK 93
           KLLVQTG VDNP+DKSL+   RLV  +GIINP+
Sbjct: 863 KLLVQTGHVDNPIDKSLVTQVRLVDSEGIINPR 895

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307191579|gb|EFN75077.1| Protein patched [Harpegnathos saltator]

 Score =  150 bits (378), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 65/93 (69%), Positives = 79/93 (84%), Gaps = 1/93 (1%)

Query: 1   MRVPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAY 60
           +R+ N++KND+GGLP  FWL LFRDWL GLQ +FDKDY++GCITQERW+ NAS+ +ILAY
Sbjct: 670 VRIKNVIKNDNGGLP-EFWLGLFRDWLKGLQTAFDKDYSSGCITQERWYQNASDEAILAY 728

Query: 61  KLLVQTGRVDNPVDKSLIKHNRLVSRDGIINPK 93
           KLLVQTG VDNP+DK+LI   RLV  DGIINP+
Sbjct: 729 KLLVQTGYVDNPIDKTLITQVRLVDSDGIINPR 761

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340727459|ref|XP_003402061.1| PREDICTED: protein patched-like [Bombus terrestris]

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 63/93 (67%), Positives = 78/93 (83%), Gaps = 1/93 (1%)

Query: 1   MRVPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAY 60
           MR+ N++KND+GGLP  FWL LFRDWL GLQ +FD+DY+ GCITQERW+ NAS+ +ILAY
Sbjct: 770 MRIKNVIKNDNGGLP-EFWLSLFRDWLKGLQNAFDRDYSNGCITQERWYKNASDEAILAY 828

Query: 61  KLLVQTGRVDNPVDKSLIKHNRLVSRDGIINPK 93
           KLLVQTG VDNP+DKSL+   RL+  +GIINP+
Sbjct: 829 KLLVQTGHVDNPIDKSLVTQVRLIDSEGIINPR 861

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322790929|gb|EFZ15595.1| hypothetical protein SINV_80439 [Solenopsis invicta]

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 66/93 (70%), Positives = 78/93 (83%), Gaps = 1/93 (1%)

Query: 1   MRVPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAY 60
           MR+ N++KND+GGLP  FWL LFRDWL GLQ +FDKDY +GCITQERWF NAS+ +ILAY
Sbjct: 475 MRIKNVIKNDNGGLP-EFWLGLFRDWLKGLQTAFDKDYHSGCITQERWFQNASDEAILAY 533

Query: 61  KLLVQTGRVDNPVDKSLIKHNRLVSRDGIINPK 93
           KLLVQTG VDNP+DK+LI   RLV  +GIINP+
Sbjct: 534 KLLVQTGHVDNPIDKTLITQVRLVDSEGIINPR 566

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350421906|ref|XP_003492995.1| PREDICTED: protein patched-like [Bombus impatiens]

 Score =  146 bits (369), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 63/93 (67%), Positives = 78/93 (83%), Gaps = 1/93 (1%)

Query: 1   MRVPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAY 60
           MR+ N++KND+GGLP  FWL LFRDWL GLQ +FD+DY+ GCITQERW+ NAS+ +ILAY
Sbjct: 489 MRIKNVIKNDNGGLP-EFWLSLFRDWLKGLQNAFDRDYSNGCITQERWYKNASDEAILAY 547

Query: 61  KLLVQTGRVDNPVDKSLIKHNRLVSRDGIINPK 93
           KLLVQTG VDNP+DKSL+   RL+  +GIINP+
Sbjct: 548 KLLVQTGHVDNPIDKSLVTQVRLIDSEGIINPR 580

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242015824|ref|XP_002428547.1| patched 1, putative [Pediculus humanus corporis] gi|212513181|gb|EEB15809.1| patched 1, putative [Pediculus humanus corporis]

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 65/93 (69%), Positives = 78/93 (83%), Gaps = 1/93 (1%)

Query: 1   MRVPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAY 60
           ++V NI+KND+GGLP  FWLE+FRDWL+GLQ++FD+D+A GCITQERW  NAS+  ILAY
Sbjct: 789 IKVSNIMKNDNGGLP-EFWLEMFRDWLIGLQKAFDRDWANGCITQERWCANASDEGILAY 847

Query: 61  KLLVQTGRVDNPVDKSLIKHNRLVSRDGIINPK 93
           KLLVQTG VDNP+DKSL+   RLV   GIINPK
Sbjct: 848 KLLVQTGHVDNPIDKSLVHQVRLVDSKGIINPK 880

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332030584|gb|EGI70272.1| Protein patched [Acromyrmex echinatior]

 Score =  146 bits (368), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 65/93 (69%), Positives = 77/93 (82%), Gaps = 1/93 (1%)

Query: 1   MRVPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAY 60
           MR+ N++KND+GGLP  FWL LFR+WL GLQ +FDKDY  GCITQERWFPNAS+ +ILAY
Sbjct: 596 MRIKNVIKNDNGGLP-EFWLSLFREWLKGLQAAFDKDYENGCITQERWFPNASDEAILAY 654

Query: 61  KLLVQTGRVDNPVDKSLIKHNRLVSRDGIINPK 93
           KLLVQTG VDNP+DK+LI   RL+  DGIIN +
Sbjct: 655 KLLVQTGHVDNPIDKTLITSVRLIDGDGIINSR 687

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|241027837|ref|XP_002406320.1| patched-2 protein, putative [Ixodes scapularis] gi|215491922|gb|EEC01563.1| patched-2 protein, putative [Ixodes scapularis]

 Score =  143 bits (361), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 60/91 (65%), Positives = 77/91 (84%), Gaps = 1/91 (1%)

Query: 3   VPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYKL 62
           V +++KNDDGGLP +FWL LFRDWLL LQ +FD+D+  GCIT+E+WFPNAS+  +LAYKL
Sbjct: 754 VEHVIKNDDGGLP-DFWLTLFRDWLLELQAAFDQDWEGGCITREQWFPNASDEGVLAYKL 812

Query: 63  LVQTGRVDNPVDKSLIKHNRLVSRDGIINPK 93
           LVQTGRVDNP+DK+L+   RLV  +G++NPK
Sbjct: 813 LVQTGRVDNPIDKTLVLKGRLVDAEGLVNPK 843

Source: Ixodes scapularis

Species: Ixodes scapularis

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	197
FB|FBgn0003892	1286	ptc "patched" [Drosophila mela	0.467	0.071	0.623	9.8e-41
UNIPROTKB|F1NYG9	1303	PTCH1 "Protein patched homolog	0.517	0.078	0.457	5.5e-34
WB|WBGene00004208	1408	ptc-1 [Caenorhabditis elegans	0.558	0.078	0.327	5.3e-23
WB|WBGene00004210	1367	ptc-3 [Caenorhabditis elegans	0.477	0.068	0.372	6.6e-18
ZFIN|ZDB-GENE-980526-196	1475	ptch1 "patched 1" [Danio rerio	0.507	0.067	0.467	1.4e-17
WB|WBGene00004209	667	ptc-2 [Caenorhabditis elegans	0.421	0.124	0.349	1.1e-16
UNIPROTKB|F1MVV4	584	PTCH1 "Uncharacterized protein	0.532	0.179	0.411	1.8e-16
UNIPROTKB|Q90693	1442	PTCH1 "Protein patched homolog	0.532	0.072	0.420	4.2e-16
UNIPROTKB|Q6UY90	1434	Ptch1 "Protein Ptch1" [Rattus	0.532	0.073	0.411	6.8e-16
MGI|MGI:105373	1434	Ptch1 "patched homolog 1" [Mus	0.532	0.073	0.411	6.8e-16

FB|FBgn0003892 ptc "patched" [Drosophila melanogaster (taxid:7227)]

 Score = 313 (115.2 bits), Expect = 9.8e-41, Sum P(2) = 9.8e-41
 Identities = 58/93 (62%), Positives = 75/93 (80%)

Query:     1 MRVPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAY 60
             +RVP+++KND+GGLP +FWL LF +WL  LQ+ FD++Y  G +T+E WFPNAS  +ILAY
Sbjct:   758 VRVPHVIKNDNGGLP-DFWLLLFSEWLGNLQKIFDEEYRDGRLTKECWFPNASSDAILAY 816

Query:    61 KLLVQTGRVDNPVDKSLIKHNRLVSRDGIINPK 93
             KL+VQTG VDNPVDK L+  NRLV+ DGIIN +
Sbjct:   817 KLIVQTGHVDNPVDKELVLTNRLVNSDGIINQR 849

GO:0008158 "hedgehog receptor activity" evidence=IMP;TAS

GO:0005887 "integral to plasma membrane" evidence=NAS;TAS

GO:0007224 "smoothened signaling pathway" evidence=IGI;NAS;IMP;TAS

GO:0005886 "plasma membrane" evidence=IDA

GO:0045169 "fusome" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0048477 "oogenesis" evidence=IMP

GO:0048471 "perinuclear region of cytoplasm" evidence=IDA

GO:0045879 "negative regulation of smoothened signaling pathway" evidence=IGI;TAS

GO:0048099 "anterior/posterior lineage restriction, imaginal disc" evidence=TAS

GO:0007350 "blastoderm segmentation" evidence=NAS

GO:0001746 "Bolwig's organ morphogenesis" evidence=IMP

GO:0030707 "ovarian follicle cell development" evidence=TAS

GO:0007422 "peripheral nervous system development" evidence=TAS

GO:0016021 "integral to membrane" evidence=IEA;TAS

GO:0009880 "embryonic pattern specification" evidence=TAS

GO:0007346 "regulation of mitotic cell cycle" evidence=IMP

GO:0004888 "transmembrane signaling receptor activity" evidence=NAS

GO:0048100 "wing disc anterior/posterior pattern formation" evidence=TAS

GO:0007455 "eye-antennal disc morphogenesis" evidence=IMP

GO:0016311 "dephosphorylation" evidence=TAS

GO:0006508 "proteolysis" evidence=TAS

GO:0009952 "anterior/posterior pattern specification" evidence=NAS

GO:0048103 "somatic stem cell division" evidence=TAS

GO:0042078 "germ-line stem cell division" evidence=TAS

GO:0042306 "regulation of protein import into nucleus" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0035225 "determination of genital disc primordium" evidence=IMP

GO:0007411 "axon guidance" evidence=IMP

GO:0007476 "imaginal disc-derived wing morphogenesis" evidence=IMP

GO:0030139 "endocytic vesicle" evidence=IDA

GO:0055088 "lipid homeostasis" evidence=IMP

GO:0030228 "lipoprotein particle receptor activity" evidence=IDA

GO:0008406 "gonad development" evidence=IMP

UNIPROTKB|F1NYG9 PTCH1 "Protein patched homolog 1" [Gallus gallus (taxid:9031)]

 Score = 216 (81.1 bits), Expect = 5.5e-34, Sum P(2) = 5.5e-34
 Identities = 48/105 (45%), Positives = 60/105 (57%)

Query:     3 VPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYKL 62
             V  ++   D  LP   WL  FRDWL GLQ++FD D+  G IT    + N S+ ++LAYKL
Sbjct:   697 VTYVLLEGDRQLP-KMWLHYFRDWLQGLQDAFDSDWETGKITYSN-YKNGSDDAVLAYKL 754

Query:    63 LVQTGRVDNPVDKSLIKHNRLVSRDGIINPKLLLVMYLMNIKLNP 107
             LVQTG    P+D S +   RLV  DGIINP    + YL     NP
Sbjct:   755 LVQTGNRAKPIDISQLTKQRLVDADGIINPNAFYI-YLTAWVSNP 798

GO:0008158 "hedgehog receptor activity" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0001658 "branching involved in ureteric bud morphogenesis" evidence=IEA

GO:0001843 "neural tube closure" evidence=IEA

GO:0003007 "heart morphogenesis" evidence=IEA

GO:0005113 "patched binding" evidence=IEA

GO:0005119 "smoothened binding" evidence=IEA

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0005901 "caveola" evidence=IEA

GO:0007224 "smoothened signaling pathway" evidence=IEA

GO:0007346 "regulation of mitotic cell cycle" evidence=IEA

GO:0007420 "brain development" evidence=IEA

GO:0008201 "heparin binding" evidence=IEA

GO:0008544 "epidermis development" evidence=IEA

GO:0008589 "regulation of smoothened signaling pathway" evidence=IEA

GO:0010157 "response to chlorate" evidence=IEA

GO:0010875 "positive regulation of cholesterol efflux" evidence=IEA

GO:0015485 "cholesterol binding" evidence=IEA

GO:0016485 "protein processing" evidence=IEA

GO:0021904 "dorsal/ventral neural tube patterning" evidence=IEA

GO:0021997 "neural plate axis specification" evidence=IEA

GO:0030326 "embryonic limb morphogenesis" evidence=IEA

GO:0030332 "cyclin binding" evidence=IEA

GO:0030496 "midbody" evidence=IEA

GO:0032403 "protein complex binding" evidence=IEA

GO:0032880 "regulation of protein localization" evidence=IEA

GO:0035137 "hindlimb morphogenesis" evidence=IEA

GO:0040015 "negative regulation of multicellular organism growth" evidence=IEA

GO:0042593 "glucose homeostasis" evidence=IEA

GO:0043433 "negative regulation of sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0043616 "keratinocyte proliferation" evidence=IEA

GO:0045668 "negative regulation of osteoblast differentiation" evidence=IEA

GO:0048471 "perinuclear region of cytoplasm" evidence=IEA

GO:0050680 "negative regulation of epithelial cell proliferation" evidence=IEA

GO:0051782 "negative regulation of cell division" evidence=IEA

GO:0060037 "pharyngeal system development" evidence=IEA

GO:0060603 "mammary gland duct morphogenesis" evidence=IEA

GO:0060644 "mammary gland epithelial cell differentiation" evidence=IEA

GO:0061005 "cell differentiation involved in kidney development" evidence=IEA

GO:0061053 "somite development" evidence=IEA

GO:0071397 "cellular response to cholesterol" evidence=IEA

GO:0072203 "cell proliferation involved in metanephros development" evidence=IEA

GO:0072661 "protein targeting to plasma membrane" evidence=IEA

GO:0097108 "hedgehog family protein binding" evidence=IEA

WB|WBGene00004208 ptc-1 [Caenorhabditis elegans (taxid:6239)]

 Score = 201 (75.8 bits), Expect = 5.3e-23, Sum P(2) = 5.3e-23
 Identities = 36/110 (32%), Positives = 70/110 (63%)

Query:    88 GIINPKLLLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGNRDRRVRLSIE 147
             GI+  +L   M L+ IKLNP+S V ++ + GI + F  ++ +SFLT +G R +R   +++
Sbjct:  1216 GIMTCELAGFMGLVGIKLNPVSAVTLITAVGIGVEFTVHVVVSFLTALGTRSQRTSSAVD 1275

Query:   148 HMYSVVLHAGLILLVAISILAFSEFQFILRIFFYMLFGIVLVGLLYMVLL 197
              ++  V+H     L+ I +L FSEF+F+++ FF ++  ++ +G++  ++L
Sbjct:  1276 RVFVPVIHGSFSTLLGILMLGFSEFEFVVKYFFIVMTALICIGIINGLIL 1325

GO:0008158 "hedgehog receptor activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0019915 "lipid storage" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0018991 "oviposition" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

GO:0006898 "receptor-mediated endocytosis" evidence=IMP

GO:0018996 "molting cycle, collagen and cuticulin-based cuticle" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0005887 "integral to plasma membrane" evidence=IDA

WB|WBGene00004210 ptc-3 [Caenorhabditis elegans (taxid:6239)]

 Score = 188 (71.2 bits), Expect = 6.6e-18, Sum P(2) = 6.6e-18
 Identities = 35/94 (37%), Positives = 60/94 (63%)

Query:    98 MYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGNRDRRVRLSIEHMYSVVLHAG 157
             M LM IK+NPIS V ++ + GI + F +++ L+FLT +G  D+R+   ++HM+  V H  
Sbjct:  1187 MGLMGIKMNPISAVTLICAVGIGVEFTAHVELAFLTALGTIDQRLESCLQHMFVPVYHGA 1246

Query:   158 LILLVAISILAFSEFQFILRIFFYMLFGIVLVGL 191
             +   + + +L FSEF F++  FFY +  +V +G+
Sbjct:  1247 ISTFLGVVMLVFSEFDFVVTYFFYTMTLLVALGV 1280

GO:0008158 "hedgehog receptor activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0002119 "nematode larval development" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0018996 "molting cycle, collagen and cuticulin-based cuticle" evidence=IMP

GO:0040018 "positive regulation of multicellular organism growth" evidence=IMP

GO:0016324 "apical plasma membrane" evidence=IDA

GO:0031410 "cytoplasmic vesicle" evidence=IDA

ZFIN|ZDB-GENE-980526-196 ptch1 "patched 1" [Danio rerio (taxid:7955)]

 Score = 229 (85.7 bits), Expect = 1.4e-17, P = 1.4e-17
 Identities = 50/107 (46%), Positives = 67/107 (62%)

Query:     3 VPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYKL 62
             V  I++ ++G LP   WL  FRDWLLGLQE+FDKD+ AG ITQ   + N S+  +LAYKL
Sbjct:   848 VKYILREENGQLP-RMWLHYFRDWLLGLQEAFDKDWQAGRITQGN-YRNGSDDGVLAYKL 905

Query:    63 LVQTGRVDNPVDKSLIKHNRLVSRDGIINPKLLLVMYLMNIKLNPIS 109
             LVQTGR +  + +      RLVS DGIINP    +     +  +P++
Sbjct:   906 LVQTGRREKTITRQ-----RLVSADGIINPNAFYIYLSAWVSNDPVA 947

GO:0016020 "membrane" evidence=IEA

GO:0008158 "hedgehog receptor activity" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0048635 "negative regulation of muscle organ development" evidence=IGI

GO:0010002 "cardioblast differentiation" evidence=IGI

GO:0060042 "retina morphogenesis in camera-type eye" evidence=IMP

GO:0001957 "intramembranous ossification" evidence=IMP

GO:0001649 "osteoblast differentiation" evidence=IMP

GO:0060041 "retina development in camera-type eye" evidence=IMP

GO:0045879 "negative regulation of smoothened signaling pathway" evidence=IMP

WB|WBGene00004209 ptc-2 [Caenorhabditis elegans (taxid:6239)]

 Score = 146 (56.5 bits), Expect = 1.1e-16, Sum P(2) = 1.1e-16
 Identities = 29/83 (34%), Positives = 50/83 (60%)

Query:    88 GIINPKLLLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGNRDRRVRLSIE 147
             GI+  +L   M L+ IKLNP+S V ++ + GI + F  ++ +SFLT +G R +R   +++
Sbjct:   584 GIMTCELAGFMGLVGIKLNPVSAVTLITAVGIGVEFTVHVVVSFLTALGTRSQRTSSAVD 643

Query:   148 HMYSVVLHAGLILLVAISILAFS 170
              ++  V+H     L+ I +L FS
Sbjct:   644 RVFVPVIHGSFSTLLGILMLGFS 666

GO:0008158 "hedgehog receptor activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0019915 "lipid storage" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0018991 "oviposition" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

GO:0006898 "receptor-mediated endocytosis" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

UNIPROTKB|F1MVV4 PTCH1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 213 (80.0 bits), Expect = 1.8e-16, P = 1.8e-16
 Identities = 44/107 (41%), Positives = 61/107 (57%)

Query:     3 VPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYKL 62
             V  ++  ++  LP   WL  FRDWL GLQ++FD D+  G I     + N S+  +LAYKL
Sbjct:   264 VKYVMLEENKQLP-KMWLHYFRDWLQGLQDAFDSDWETGKIMPNN-YKNGSDDGVLAYKL 321

Query:    63 LVQTGRVDNPVDKSLIKHNRLVSRDGIINPKLLLVMYLMNIKLNPIS 109
             LVQTG  D P+D S +   RLV  DGIINP    +     +  +P++
Sbjct:   322 LVQTGSRDKPIDISQLTKRRLVDADGIINPSAFYIYLTAWVSNDPVA 368

GO:0016020 "membrane" evidence=IEA

GO:0008158 "hedgehog receptor activity" evidence=IEA

UNIPROTKB|Q90693 PTCH1 "Protein patched homolog 1" [Gallus gallus (taxid:9031)]

 Score = 215 (80.7 bits), Expect = 4.2e-16, P = 4.2e-16
 Identities = 45/107 (42%), Positives = 61/107 (57%)

Query:     3 VPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYKL 62
             V  ++   D  LP   WL  FRDWL GLQ++FD D+  G IT    + N S+ ++LAYKL
Sbjct:   828 VTYVLLEGDRQLP-KMWLHYFRDWLQGLQDAFDSDWETGKITYSN-YKNGSDDAVLAYKL 885

Query:    63 LVQTGRVDNPVDKSLIKHNRLVSRDGIINPKLLLVMYLMNIKLNPIS 109
             LVQTG    P+D S +   RLV  DGIINP    +     +  +P++
Sbjct:   886 LVQTGNRAKPIDISQLTKQRLVDADGIINPNAFYIYLTAWVSNDPVA 932

GO:0008158 "hedgehog receptor activity" evidence=IEA

GO:0007224 "smoothened signaling pathway" evidence=NAS

GO:0005887 "integral to plasma membrane" evidence=NAS

UNIPROTKB|Q6UY90 Ptch1 "Protein Ptch1" [Rattus norvegicus (taxid:10116)]

 Score = 213 (80.0 bits), Expect = 6.8e-16, P = 6.8e-16
 Identities = 44/107 (41%), Positives = 61/107 (57%)

Query:     3 VPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYKL 62
             V  ++  ++  LP   WL  FRDWL GLQ++FD D+  G I     + N S+  +LAYKL
Sbjct:   815 VKYVMLEENKQLP-QMWLHYFRDWLQGLQDAFDSDWETGRIMPNN-YKNGSDDGVLAYKL 872

Query:    63 LVQTGRVDNPVDKSLIKHNRLVSRDGIINPKLLLVMYLMNIKLNPIS 109
             LVQTG  D P+D S +   RLV  DGIINP    +     +  +P++
Sbjct:   873 LVQTGSRDKPIDISQLTKQRLVDADGIINPSAFYIYLTAWVSNDPVA 919

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0001658 "branching involved in ureteric bud morphogenesis" evidence=IEA

GO:0001843 "neural tube closure" evidence=IEA

GO:0003007 "heart morphogenesis" evidence=IEA

GO:0005113 "patched binding" evidence=IEA

GO:0005119 "smoothened binding" evidence=IEA

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0005901 "caveola" evidence=IEA

GO:0007224 "smoothened signaling pathway" evidence=ISS

GO:0007346 "regulation of mitotic cell cycle" evidence=IEA

GO:0007420 "brain development" evidence=IEA

GO:0008158 "hedgehog receptor activity" evidence=IEA

GO:0008201 "heparin binding" evidence=IEA

GO:0008544 "epidermis development" evidence=IEA

GO:0008589 "regulation of smoothened signaling pathway" evidence=ISS

GO:0009887 "organ morphogenesis" evidence=ISS

GO:0009953 "dorsal/ventral pattern formation" evidence=ISS

GO:0010157 "response to chlorate" evidence=IEA

GO:0010875 "positive regulation of cholesterol efflux" evidence=IEA

GO:0015485 "cholesterol binding" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0016485 "protein processing" evidence=ISS

GO:0021904 "dorsal/ventral neural tube patterning" evidence=IEA

GO:0021997 "neural plate axis specification" evidence=IEA

GO:0030326 "embryonic limb morphogenesis" evidence=ISS

GO:0030332 "cyclin binding" evidence=IEA

GO:0030496 "midbody" evidence=IEA

GO:0032403 "protein complex binding" evidence=IEA

GO:0032880 "regulation of protein localization" evidence=IEA

GO:0035137 "hindlimb morphogenesis" evidence=IEA

GO:0040015 "negative regulation of multicellular organism growth" evidence=ISS

GO:0042593 "glucose homeostasis" evidence=IEA

GO:0043433 "negative regulation of sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0043616 "keratinocyte proliferation" evidence=IEA

GO:0045668 "negative regulation of osteoblast differentiation" evidence=IEA

GO:0048471 "perinuclear region of cytoplasm" evidence=IEA

GO:0050680 "negative regulation of epithelial cell proliferation" evidence=IEA

GO:0051782 "negative regulation of cell division" evidence=IEA

GO:0060037 "pharyngeal system development" evidence=IEA

GO:0060603 "mammary gland duct morphogenesis" evidence=IEA

GO:0060644 "mammary gland epithelial cell differentiation" evidence=IEA

GO:0061005 "cell differentiation involved in kidney development" evidence=IEA

GO:0061053 "somite development" evidence=IEA

GO:0071397 "cellular response to cholesterol" evidence=IEA

GO:0072203 "cell proliferation involved in metanephros development" evidence=IEA

GO:0072661 "protein targeting to plasma membrane" evidence=IEA

GO:0097108 "hedgehog family protein binding" evidence=IEA

MGI|MGI:105373 Ptch1 "patched homolog 1" [Mus musculus (taxid:10090)]

 Score = 213 (80.0 bits), Expect = 6.8e-16, P = 6.8e-16
 Identities = 44/107 (41%), Positives = 61/107 (57%)

Query:     3 VPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYKL 62
             V  ++  ++  LP   WL  FRDWL GLQ++FD D+  G I     + N S+  +LAYKL
Sbjct:   815 VKYVMLEENKQLP-QMWLHYFRDWLQGLQDAFDSDWETGRIMPNN-YKNGSDDGVLAYKL 872

Query:    63 LVQTGRVDNPVDKSLIKHNRLVSRDGIINPKLLLVMYLMNIKLNPIS 109
             LVQTG  D P+D S +   RLV  DGIINP    +     +  +P++
Sbjct:   873 LVQTGSRDKPIDISQLTKQRLVDADGIINPSAFYIYLTAWVSNDPVA 919

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0001658 "branching involved in ureteric bud morphogenesis" evidence=IMP

GO:0001841 "neural tube formation" evidence=IDA

GO:0001843 "neural tube closure" evidence=IMP

GO:0003007 "heart morphogenesis" evidence=IMP

GO:0005113 "patched binding" evidence=IDA

GO:0005119 "smoothened binding" evidence=ISO

GO:0005515 "protein binding" evidence=IPI

GO:0005576 "extracellular region" evidence=TAS

GO:0005886 "plasma membrane" evidence=ISO;IDA

GO:0005887 "integral to plasma membrane" evidence=TAS

GO:0005901 "caveola" evidence=ISO

GO:0007165 "signal transduction" evidence=IDA;TAS

GO:0007224 "smoothened signaling pathway" evidence=IGI;IDA

GO:0007346 "regulation of mitotic cell cycle" evidence=IMP

GO:0007389 "pattern specification process" evidence=IMP

GO:0007420 "brain development" evidence=IMP

GO:0008158 "hedgehog receptor activity" evidence=TAS

GO:0008201 "heparin binding" evidence=IDA

GO:0008270 "zinc ion binding" evidence=NAS

GO:0008285 "negative regulation of cell proliferation" evidence=IMP

GO:0008544 "epidermis development" evidence=IMP

GO:0008589 "regulation of smoothened signaling pathway" evidence=IGI;IMP

GO:0009887 "organ morphogenesis" evidence=IMP

GO:0009953 "dorsal/ventral pattern formation" evidence=IGI

GO:0010157 "response to chlorate" evidence=IDA

GO:0010875 "positive regulation of cholesterol efflux" evidence=ISO

GO:0014069 "postsynaptic density" evidence=ISO

GO:0015485 "cholesterol binding" evidence=ISO;TAS

GO:0016020 "membrane" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0016485 "protein processing" evidence=IMP

GO:0021522 "spinal cord motor neuron differentiation" evidence=IGI

GO:0021532 "neural tube patterning" evidence=ISO

GO:0021904 "dorsal/ventral neural tube patterning" evidence=IMP

GO:0021997 "neural plate axis specification" evidence=IMP

GO:0030326 "embryonic limb morphogenesis" evidence=IGI;IMP

GO:0030332 "cyclin binding" evidence=ISO;IPI

GO:0030496 "midbody" evidence=IDA

GO:0030879 "mammary gland development" evidence=IMP

GO:0032403 "protein complex binding" evidence=IDA

GO:0032880 "regulation of protein localization" evidence=IDA;IMP

GO:0035108 "limb morphogenesis" evidence=ISO

GO:0035137 "hindlimb morphogenesis" evidence=IMP

GO:0040008 "regulation of growth" evidence=IMP

GO:0040015 "negative regulation of multicellular organism growth" evidence=IMP

GO:0042127 "regulation of cell proliferation" evidence=IMP

GO:0042593 "glucose homeostasis" evidence=IMP

GO:0043231 "intracellular membrane-bounded organelle" evidence=ISO

GO:0043433 "negative regulation of sequence-specific DNA binding transcription factor activity" evidence=ISO

GO:0043616 "keratinocyte proliferation" evidence=IMP

GO:0044294 "dendritic growth cone" evidence=ISO

GO:0044295 "axonal growth cone" evidence=ISO

GO:0045668 "negative regulation of osteoblast differentiation" evidence=ISO

GO:0045879 "negative regulation of smoothened signaling pathway" evidence=IGI;NAS;IMP

GO:0048471 "perinuclear region of cytoplasm" evidence=ISO

GO:0050680 "negative regulation of epithelial cell proliferation" evidence=IMP

GO:0051782 "negative regulation of cell division" evidence=IMP

GO:0060037 "pharyngeal system development" evidence=ISO

GO:0060603 "mammary gland duct morphogenesis" evidence=IMP

GO:0060644 "mammary gland epithelial cell differentiation" evidence=IMP

GO:0060831 "smoothened signaling pathway involved in dorsal/ventral neural tube patterning" evidence=IMP

GO:0061005 "cell differentiation involved in kidney development" evidence=IGI

GO:0061053 "somite development" evidence=ISO;IMP

GO:0071397 "cellular response to cholesterol" evidence=ISO

GO:0072203 "cell proliferation involved in metanephros development" evidence=IMP

GO:0072372 "primary cilium" evidence=IDA

GO:0072661 "protein targeting to plasma membrane" evidence=ISO

GO:0097108 "hedgehog family protein binding" evidence=ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P18502	PTC_DROME	No assigned EC number	0.6236	0.4670	0.0715	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	197
TIGR00918	1145	TIGR00918, 2A060602, The Eukaryotic (Putative) Ste	3e-36
TIGR00918	1145	TIGR00918, 2A060602, The Eukaryotic (Putative) Ste	2e-21
TIGR00917	1204	TIGR00917, 2A060601, Niemann-Pick C type protein f	2e-10

>gnl|CDD|233185 TIGR00918, 2A060602, The Eukaryotic (Putative) Sterol Transporter (EST) Family

 Score =  133 bits (336), Expect = 3e-36
 Identities = 51/99 (51%), Positives = 66/99 (66%), Gaps = 3/99 (3%)

Query: 2   RVPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYK 61
            V  ++K D+G LP   WL  FRDWL GLQ++FD+D+  G IT+E +  N S+ ++LAYK
Sbjct: 768 SVKYVLKEDNGQLP-RMWLHYFRDWLQGLQKAFDEDWRDGRITKENYR-NGSDDAVLAYK 825

Query: 62  LLVQTGRVDNPVDKSLIKHNRLVSRDGIINPKLLLVMYL 100
           LLVQTG  D PVDK  +   RLV+ DGIINP     +YL
Sbjct: 826 LLVQTGHRDKPVDKEQLTTQRLVNADGIINPNAFY-IYL 863

Length = 1145

>gnl|CDD|233185 TIGR00918, 2A060602, The Eukaryotic (Putative) Sterol Transporter (EST) Family

 Score = 90.7 bits (225), Expect = 2e-21
 Identities = 44/105 (41%), Positives = 69/105 (65%)

Query: 93   KLLLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGNRDRRVRLSIEHMYSV 152
            +L  +M L+ IKL+ I  V+++ S GI + F  +I L FLT IG+R+RR  L++EHM++ 
Sbjct: 1005 ELFGMMGLLGIKLSAIPVVILIASVGIGVEFTVHIALGFLTAIGDRNRRAVLALEHMFAP 1064

Query: 153  VLHAGLILLVAISILAFSEFQFILRIFFYMLFGIVLVGLLYMVLL 197
            VL   L  L+ + +LA SEF FI+R FF +L  +  +G+L  ++L
Sbjct: 1065 VLDGALSTLLGVLMLAGSEFDFIVRYFFAVLAVLTCLGVLNGLVL 1109

Length = 1145

>gnl|CDD|233184 TIGR00917, 2A060601, Niemann-Pick C type protein family

 Score = 58.7 bits (142), Expect = 2e-10
 Identities = 39/109 (35%), Positives = 61/109 (55%), Gaps = 4/109 (3%)

Query: 88   GIINPKLLLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCI-GNRDRRVRLSI 146
            G+I   L+ +M+L NI LN +S V +V + GI I F S+I   F T    +R+ R + ++
Sbjct: 1084 GMIVVNLVGIMHLWNISLNAVSVVNLVMAKGISIEFCSHINAQFSTSKHFSRNHRAKEAL 1143

Query: 147  EHMYSVVLHAGLIL--LVAISILAFSEFQFILRIFFYMLFGIVLVGLLY 193
              M S V  +G+ L  LV + +L FS+ +     +F M   IVL+G L+
Sbjct: 1144 GGMGSSVF-SGITLTKLVGVVVLGFSKSEIFQVYYFRMYLAIVLLGALH 1191

The model describes Niemann-Pick C type protein in eukaryotes. The defective protein has been associated with Niemann-Pick disease which is described in humans as autosomal recessive lipidosis. It is characterized by the lysosomal accumulation of unestrified cholesterol. It is an integral membrane protein, which indicates that this protein is most likely involved in cholesterol transport or acts as some component of cholesterol homeostasis [Transport and binding proteins, Other]. Length = 1204

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	197
KOG1935|consensus	1143		100.0
TIGR00918	1145	2A060602 The Eukaryotic (Putative) Sterol Transpor	100.0
KOG1934|consensus	868		100.0
PF02460	798	Patched: Patched family; InterPro: IPR003392 The t	100.0
TIGR00917	1204	2A060601 Niemann-Pick C type protein family. The m	99.96
KOG1933|consensus	1201		99.7
TIGR00921	719	2A067 The (Largely Archaeal Putative) Hydrophobe/A	99.21
TIGR00921	719	2A067 The (Largely Archaeal Putative) Hydrophobe/A	99.06
COG1033	727	Predicted exporters of the RND superfamily [Genera	99.01
TIGR00916	192	2A0604s01 protein-export membrane protein, SecD/Se	98.83
COG1033	727	Predicted exporters of the RND superfamily [Genera	98.66
PF03176	333	MMPL: MMPL family; InterPro: IPR004869 Proteins of	98.63
TIGR03480	862	HpnN hopanoid biosynthesis associated RND transpor	98.56
PRK09579	1017	multidrug efflux protein; Reviewed	98.45
TIGR00966	246	3a0501s07 protein-export membrane protein SecF. Th	98.41
PRK10614	1025	multidrug efflux system subunit MdtC; Provisional	98.39
TIGR03480	862	HpnN hopanoid biosynthesis associated RND transpor	98.35
PRK10555	1037	aminoglycoside/multidrug efflux system; Provisiona	98.32
TIGR00915	1044	2A0602 The (Largely Gram-negative Bacterial) Hydro	98.3
PRK15127	1049	multidrug efflux system protein AcrB; Provisional	98.27
PRK09577	1032	multidrug efflux protein; Reviewed	98.24
TIGR00833	910	actII Transport protein. Characterized members of	98.23
TIGR01129	397	secD protein-export membrane protein SecD. SecD fr	98.16
PRK10503	1040	multidrug efflux system subunit MdtB; Provisional	98.14
PRK13022	289	secF preprotein translocase subunit SecF; Reviewed	98.11
PF00873	1021	ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR0010	98.02
PRK13023	758	bifunctional preprotein translocase subunit SecD/S	97.99
PF12349	153	Sterol-sensing: Sterol-sensing domain of SREBP cle	97.94
PRK08578	292	preprotein translocase subunit SecF; Reviewed	97.91
PRK05812	498	secD preprotein translocase subunit SecD; Reviewed	97.87
PRK13024	755	bifunctional preprotein translocase subunit SecD/S	97.83
TIGR00914	1051	2A0601 heavy metal efflux pump (cobalt-zinc-cadmiu	97.68
TIGR00914	1051	2A0601 heavy metal efflux pump (cobalt-zinc-cadmiu	97.67
PRK08343	417	secD preprotein translocase subunit SecD; Reviewed	97.64
PRK14726	855	bifunctional preprotein translocase subunit SecD/S	97.64
COG0841	1009	AcrB Cation/multidrug efflux pump [Defense mechani	97.59
PF02355	189	SecD_SecF: Protein export membrane protein; InterP	97.58
TIGR00917	1204	2A060601 Niemann-Pick C type protein family. The m	97.53
TIGR00833	910	actII Transport protein. Characterized members of	97.47
PRK15127	1049	multidrug efflux system protein AcrB; Provisional	97.44
PF02460	798	Patched: Patched family; InterPro: IPR003392 The t	97.42
PRK12933	604	secD preprotein translocase subunit SecD; Reviewed	97.27
TIGR00918	1145	2A060602 The Eukaryotic (Putative) Sterol Transpor	97.27
TIGR00915	1044	2A0602 The (Largely Gram-negative Bacterial) Hydro	97.24
PRK13024	755	bifunctional preprotein translocase subunit SecD/S	97.18
PRK12911	1403	bifunctional preprotein translocase subunit SecD/S	97.08
PRK10503	1040	multidrug efflux system subunit MdtB; Provisional	97.08
PRK10555	1037	aminoglycoside/multidrug efflux system; Provisiona	96.91
PRK13021	297	secF preprotein translocase subunit SecF; Reviewed	96.63
PRK09577	1032	multidrug efflux protein; Reviewed	96.37
PRK14726	855	bifunctional preprotein translocase subunit SecD/S	96.25
PRK09579	1017	multidrug efflux protein; Reviewed	96.07
PF00873	1021	ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR0010	95.86
PRK10614	1025	multidrug efflux system subunit MdtC; Provisional	95.55
COG0342	506	SecD Preprotein translocase subunit SecD [Intracel	94.35
KOG1934|consensus	868		94.32
KOG1935|consensus	1143		93.61
COG0341	305	SecF Preprotein translocase subunit SecF [Intracel	90.96
COG4258	788	Predicted exporter [General function prediction on	88.04
COG0841	1009	AcrB Cation/multidrug efflux pump [Defense mechani	87.84
PRK13023	758	bifunctional preprotein translocase subunit SecD/S	83.6

>KOG1935|consensus

Probab=100.00  E-value=5.9e-50  Score=385.71  Aligned_cols=193  Identities=41%  Similarity=0.717  Sum_probs=188.4

Q ss_pred             CCcCceeeCCCCCCccccchHHHHHHHHhhhhhhhHhhhcccccccccCCCCChhhHHHhhhhhhccCCCCCcchhhHhh
Q psy8507           1 MRVPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYKLLVQTGRVDNPVDKSLIKH   80 (197)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~WL~~~~~wl~~lq~~fD~~~~~~~i~~~~w~~n~~~~~ila~r~~iqt~~~~~~~~~~~~~~   80 (197)
                      .++||||||+|+++| +|||++|||||+++|++||+||++|+|+.+.|-+|+|+|+++||||+||||..+|  |.+++.+
T Consensus       726 ~s~k~vik~~n~~l~-~~Wl~~~r~WL~~lq~~fded~a~G~~~~~~~v~n~S~d~~lA~kL~~qtG~~~~--~~~~l~k  802 (1143)
T KOG1935|consen  726 GSSKYVIKNENEQLP-KYWLHLFRDWLQSLQRAFDEDWAKGRFTLTSGVSNGSEDARLAYKLLCQTGSLDN--DAGRLGK  802 (1143)
T ss_pred             ccCceeecCCCCCCc-hHHHHHHHHHHHHHHHHHHHHHhcCccccccCCCCCChHHHHHHHHHHhcCCccc--hhHhhhh
Confidence            378999999999999 9999999999999999999999999999999889999999999999999999998  7778999


Q ss_pred             hhhhhcCCCcChhHHH----------------------------------------------------------------
Q psy8507          81 NRLVSRDGIINPKLLL----------------------------------------------------------------   96 (197)
Q Consensus        81 ~r~v~~~~~i~p~~f~----------------------------------------------------------------   96 (197)
                      +|+||+ |+|||++||                                                                
T Consensus       803 ~rlVd~-giInp~~FYnyLTaW~~~D~~~y~aSQa~~yP~pP~w~h~~~~~~~iP~aePl~yaQmPFyL~gL~dTa~Ivk  881 (1143)
T KOG1935|consen  803 IRLVDA-GIINPEAFYNYLTAWFNNDPMAYYASQASFYPTPPEWEHDNDYAKEIPAAEPLEYAQMPFYLNGLTDTADIVK  881 (1143)
T ss_pred             hhhhhc-cccCHHHHHHhhhhhcccchHHhhhhccCCCCCCccccccccccccccccccchhccCchHHhhhhhHHHHHH
Confidence            999998 999999999                                                                


Q ss_pred             --------------------------------------------------------------------------------
Q psy8507          97 --------------------------------------------------------------------------------   96 (197)
Q Consensus        97 --------------------------------------------------------------------------------   96 (197)
                                                                                                      
T Consensus       882 ~I~~iR~~c~~~~s~Gl~nyPsGiPF~FWEQYl~Lrg~l~~~IcIil~~vf~vcs~ll~npWaA~Liv~sL~~mt~eL~G  961 (1143)
T KOG1935|consen  882 AIESIRASCEEYTSLGLPNYPSGIPFTFWEQYLTLRGNLLQAICIILLAVFCVCSVLLLNPWAAGLIVCSLAIMTVELFG  961 (1143)
T ss_pred             HHHHHHHHHhhcccCCCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHH
Confidence                                                                                            


Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcccCChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccchhH
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQFIL  176 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~~~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~~~~  176 (197)
                      +|++.||+||+|+.|.|+.+||+.|||++|+..+|+++.|+|++|+..|++++..|+.+|++||++|++||++|+++++.
T Consensus       962 ~Mgl~GIKlS~i~aViLi~sVGigveFtvhv~l~FlTs~G~rs~R~s~al~~~F~Pv~hG~lST~lgv~MLs~S~FdFvV 1041 (1143)
T KOG1935|consen  962 FMGLLGIKLSAIPAVILIASVGIGVEFTVHVALGFLTALGTRSQRASSALQHMFVPVSHGALSTLLGVLMLSFSEFDFVV 1041 (1143)
T ss_pred             HHHhhceeeccchhHHHHHHhhhchhhhHHHHHHHHHhhccchhHhHHhhhhcchhhhhhHHHHHhhHheeccCchhHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhhhcC
Q psy8507         177 RIFFYMLFGIVLVGLLYMVLL  197 (197)
Q Consensus       177 ~~FF~~~~~vi~~G~~hGLvl  197 (197)
                      +|||.++.+++++|++|||++
T Consensus      1042 ryFf~~ltvl~~lGv~ngL~~ 1062 (1143)
T KOG1935|consen 1042 RYFFAVLTVLTCLGVLNGLVV 1062 (1143)
T ss_pred             HHHHHHHHHHHHHHHhccchH
Confidence            999999999999999999984

>TIGR00918 2A060602 The Eukaryotic (Putative) Sterol Transporter (EST) Family

Probab=100.00  E-value=1.9e-44  Score=362.34  Aligned_cols=194  Identities=47%  Similarity=0.822  Sum_probs=181.4

Q ss_pred             CcCceeeCCCCCCccccchHHHHHHHHhhhhhhhHhhhcccccccccCCCCChhhHHHhhhhhhccCCCCCcchhhHhhh
Q psy8507           2 RVPNIVKNDDGGLPGNFWLELFRDWLLGLQESFDKDYAAGCITQERWFPNASESSILAYKLLVQTGRVDNPVDKSLIKHN   81 (197)
Q Consensus         2 ~~~~~~~~~~~~~~~~~WL~~~~~wl~~lq~~fD~~~~~~~i~~~~w~~n~~~~~ila~r~~iqt~~~~~~~~~~~~~~~   81 (197)
                      +++|+++++|+++| +|||++|++||+.+|.+||++|+.|+++.+. +.|+++++.+||++++|||+.++|.|++++.+.
T Consensus       768 ~~~~i~~~~~~~~~-~~WLddf~~wL~~lq~~~d~~~~~g~~~~~~-~~n~s~~~~~~~~l~~qtg~~~~p~~~~~~~~~  845 (1145)
T TIGR00918       768 SVKYVLKEDNGQLP-RMWLHYFRDWLQGLQKAFDEDWRDGRITKEN-YRNGSDDAVLAYKLLVQTGHRDKPVDKEQLTTQ  845 (1145)
T ss_pred             cCceeecCCCCCcc-chHHHHHHHHHHHhhhhhhhhhhhccccccc-ccCCccccchhhhhcccccccCCcccccccccc
Confidence            67899999999989 9999999999999999999999999998876 679999999999999999999999999888888


Q ss_pred             hhhhcCCCcChhHHH-----------------------------------------------------------------
Q psy8507          82 RLVSRDGIINPKLLL-----------------------------------------------------------------   96 (197)
Q Consensus        82 r~v~~~~~i~p~~f~-----------------------------------------------------------------   96 (197)
                      |+|+.+|.+||+.||                                                                 
T Consensus       846 r~v~~~g~~~~~~F~~yL~~wl~~~~~~y~~sq~~~~p~~~~~~~~~~~~~~~~~~I~as~~i~~~~F~fy~~~L~~~~d  925 (1145)
T TIGR00918       846 RLVNADGIINPNAFYIYLSAWVSNDPVAYAASQANIYPHPPEWLHDKNDYDPENLRIPAAEPLEYAQFPFYLNGLRETSQ  925 (1145)
T ss_pred             ccccccCCCCHHHHHHHHHHHHcCCcchhhcccccccCCcchhcccccccccccccccccccchhheeeEEEcCCCCHHH
Confidence            988888777664332                                                                 


Q ss_pred             --------------------------------------------------------------------------------
Q psy8507          97 --------------------------------------------------------------------------------   96 (197)
Q Consensus        97 --------------------------------------------------------------------------------   96 (197)
                                                                                                      
T Consensus       926 ~i~al~~~R~Ia~~~~~~~~~vf~~g~~fvf~eQy~~i~~~~~~~l~~al~~~fvV~~lll~~~~~a~iv~l~v~~i~v~ 1005 (1145)
T TIGR00918       926 FVEAIEHVRAICNNYEGFGLPSYPSGYPFLFWEQYMGLRHWLLLSISVVLACTFLVCALLLLNPWTAGLIVLVLALMTVE 1005 (1145)
T ss_pred             HHHHHHHHHHHHHhhhhcCceeccCCCceeHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcchHHHHHHHHHHHHHHHH
Confidence                                                                                            


Q ss_pred             ---HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcccCChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccc
Q psy8507          97 ---VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQ  173 (197)
Q Consensus        97 ---~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~~~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~  173 (197)
                         +|++|||+||+||++||+||||+|||||+||+|+|+++.++|++|+++||+++|+||++|++||++|+++|+|+++.
T Consensus      1006 v~G~M~lwgI~LnaVS~vnLimsIGisVefsaHI~~~F~~~~~~r~eR~~~AL~~~G~pVl~g~lTT~lGvlvLafs~s~ 1085 (1145)
T TIGR00918      1006 LFGMMGLLGIKLSAIPVVILIASVGIGVEFTVHIALGFLTAIGDRNRRAVLALEHMFAPVLDGALSTLLGVLMLAGSEFD 1085 (1145)
T ss_pred             HHHHHHHHcCCccHHHHHHHHHHHhhhhhhhHHHHHHHHhcCCCHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhCCcH
Confidence               99999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hhHHHHHHHHHHHHHHHhhhhhcC
Q psy8507         174 FILRIFFYMLFGIVLVGLLYMVLL  197 (197)
Q Consensus       174 ~~~~~FF~~~~~vi~~G~~hGLvl  197 (197)
                      ++.+||||++++++++|++||||+
T Consensus      1086 ~~~~~Ffk~~~l~V~~g~lHgLv~ 1109 (1145)
T TIGR00918      1086 FIVRYFFAVLAVLTCLGVLNGLVL 1109 (1145)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            888899999999999999999985

>KOG1934|consensus

Probab=100.00  E-value=1.5e-36  Score=298.88  Aligned_cols=189  Identities=20%  Similarity=0.363  Sum_probs=156.1

Q ss_pred             eCCCCCCccccchHHHHHHHHhhh---hhhhHhhhccc----ccc---ccc------C-CCCChhhHHHhhhhhhccCCC
Q psy8507           8 KNDDGGLPGNFWLELFRDWLLGLQ---ESFDKDYAAGC----ITQ---ERW------F-PNASESSILAYKLLVQTGRVD   70 (197)
Q Consensus         8 ~~~~~~~~~~~WL~~~~~wl~~lq---~~fD~~~~~~~----i~~---~~w------~-~n~~~~~ila~r~~iqt~~~~   70 (197)
                      +...|...-+|||+.|.++++..+   ...|++|....    +..   ..|      + .+..+..+.++|+.++-.|..
T Consensus       556 ~~~~G~~sT~~wlr~y~~~~~~~~~~~~~~~~~~~~~~~~~fl~~~~~~~~~~di~~~~~~~~~~~i~~f~f~~~~~~~~  635 (868)
T KOG1934|consen  556 PYSMGRESTKFWLREYLNFLFEKNAELEDNDDEFYDHLYESFLKSPEFSFWRNDIVFDNKSDEETIIFAFRFTIGLTNLT  635 (868)
T ss_pred             CcccCcccchhHHHHHHHHHhhhcccccCCCcchhhhhHHHHhcccccccCccceEeccCCCCCceEEEEEEEEEEeccC
Confidence            444555555899999999864432   22233454442    111   113      1 235677899999999999999


Q ss_pred             CCcchh-hHhhhhhhhcCC-Cc-----ChhHHH-----------------------------------------------
Q psy8507          71 NPVDKS-LIKHNRLVSRDG-II-----NPKLLL-----------------------------------------------   96 (197)
Q Consensus        71 ~~~~~~-~~~~~r~v~~~~-~i-----~p~~f~-----------------------------------------------   96 (197)
                      ++.++. ++.++|.++++. ..     +|.+.|                                               
T Consensus       636 ~~~~~~~~~~~~R~ia~~~~~fnvtvf~~~~~f~Dq~~~v~~~ti~~~~~a~i~M~~v~~lfIp~~~~~~~it~si~SI~  715 (868)
T KOG1934|consen  636 KWNERTRLLETWRKIADEYSDFNVTVFDPSFVFLDQYLSVVPVTIQSIVIALICMFLVCFLFIPNPLCVFWITLSIVSIN  715 (868)
T ss_pred             CHHHHHHHHHHHHHHHhhccCCCeEEecCchHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHhhee
Confidence            999884 899999999765 22     777655                                               


Q ss_pred             -----HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcccC--ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhc
Q psy8507          97 -----VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIG--NRDRRVRLSIEHMYSVVLHAGLILLVAISILAF  169 (197)
Q Consensus        97 -----~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~~--~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~f  169 (197)
                           +|++||++||||||++++|||||||||+|||||||+.+.+  ++++|+++||+.+||||+||++||+||++||++
T Consensus       716 ~GV~G~lslW~V~LDpISmi~iiMsIGFSVD~~AHi~yhy~~~~~~~t~~~Rv~~aL~~vgwPv~Qa~lSTiL~v~pL~~  795 (868)
T KOG1934|consen  716 IGVFGFLSLWGVDLDPISMITIIMSIGFSVDFSAHVAYHYYQSRKSSTPRERLRSALSAVGWPVLQAGLSTILGVLPLLF  795 (868)
T ss_pred             ehHhhhhHHhcCCccHHHHHHHHHhCCceeeehhheeeeeEecCCCCCHHHHHHHHHHhhhhHHHhhhhHHHHHHHHHHh
Confidence                 9999999999999999999999999999999999999998  566999999999999999999999999999999


Q ss_pred             cccchhHHHHHHHHHHHHHHHhhhhhcC
Q psy8507         170 SEFQFILRIFFYMLFGIVLVGLLYMVLL  197 (197)
Q Consensus       170 s~s~~~~~~FF~~~~~vi~~G~~hGLvl  197 (197)
                      +++|++++| ||++++++.+|++|||++
T Consensus       796 V~sYmv~vF-~KTv~LVv~~GllHGLv~  822 (868)
T KOG1934|consen  796 VPSYMVQVF-FKTVVLVVTLGLLHGLVF  822 (868)
T ss_pred             chHHHHHHH-HHHHHHHHHHHHHHHHHH
Confidence            999999986 799999999999999985

>PF02460 Patched: Patched family; InterPro: IPR003392 The transmembrane protein, patched, is a receptor for the morphogene Sonic Hedgehog

Probab=100.00  E-value=1.9e-35  Score=288.35  Aligned_cols=182  Identities=25%  Similarity=0.424  Sum_probs=150.3

Q ss_pred             ccccchHHHHHHHHhhhhhhhHhhh----cc----cccc-cc--c------C-CCCChhhHHHhhhhhhccCCCCCcch-
Q psy8507          15 PGNFWLELFRDWLLGLQESFDKDYA----AG----CITQ-ER--W------F-PNASESSILAYKLLVQTGRVDNPVDK-   75 (197)
Q Consensus        15 ~~~~WL~~~~~wl~~lq~~fD~~~~----~~----~i~~-~~--w------~-~n~~~~~ila~r~~iqt~~~~~~~~~-   75 (197)
                      +.++||+.|.+|++.++....++.+    ..    +++. +.  |      . .+.....|-|+|+.+|..+..++.++ 
T Consensus       530 ~t~~WL~~y~~~l~~~~~~~~~~~~~~~~~~~l~~FL~~~~~~~~~~di~~~~~~~~~~~I~a~rf~~~~~~~~~~~~~~  609 (798)
T PF02460_consen  530 STSFWLRDYLNFLNSINSSFQDDNDKEFFYNLLPEFLNSPEYRHYSNDIKFDDSDNDTTQISAFRFTTQLKNLSDWSDRI  609 (798)
T ss_pred             cchhhHHHHHHHHhhccccccccccceeeeccchhhhccccccccccccccccccCCccceeeEEEEEEccCCCCHHHHH
Confidence            3389999999999765544444333    11    1211 11  3      1 23557789999999998888888777 


Q ss_pred             hhHhhhhhhhcCCC-c-----ChhHHH----------------------------------------------------H
Q psy8507          76 SLIKHNRLVSRDGI-I-----NPKLLL----------------------------------------------------V   97 (197)
Q Consensus        76 ~~~~~~r~v~~~~~-i-----~p~~f~----------------------------------------------------~   97 (197)
                      +++.+.|.++++.+ .     +|.+.|                                                    +
T Consensus       610 ~~~~~~R~i~~~~~~~~~~~~~~~~~~~dq~~~i~~~~~~~~~~a~~~~~~v~~l~~~~~~~~~~~~~~i~~i~~~v~G~  689 (798)
T PF02460_consen  610 EAMKDWRQIADKYSDFNVFVFSPFFIFYDQYLSIVPETIQNIGIALVCMFVVCLLFIPNPRSSLIVTLSILSIDVGVIGF  689 (798)
T ss_pred             HHHHHHHHhhhcceecceEeeccchhhHhhhhhcchHHHHHHHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHHHHh
Confidence            58899999988552 2     554433                                                    9


Q ss_pred             HHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcccC-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccchhH
Q psy8507          98 MYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIG-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQFIL  176 (197)
Q Consensus        98 M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~~~~  176 (197)
                      |++||++||++|+++++||||+|||||+||+|+|+.+.+ ++++|+++||+++|+||+||++||++|++||+|+++|+++
T Consensus       690 m~~~g~~l~~vs~v~l~~~iG~sVd~~~Hi~~~f~~~~~~~~~~r~~~al~~~g~pv~~~~~st~l~~~~l~f~~~~~~~  769 (798)
T PF02460_consen  690 MSLWGVDLDPVSMVNLIMSIGFSVDFSAHIAYAFVHSQGSTRDERVAEALSSMGWPVLQGALSTFLGVLPLAFSPSYIFR  769 (798)
T ss_pred             hhccccCcchHHHHHHHHHhchhhHHHHHHHHHheecccchHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhHHHHH
Confidence            999999999999999999999999999999999999998 6679999999999999999999999999999999999998


Q ss_pred             HHHHHHHHHHHHHHhhhhhcC
Q psy8507         177 RIFFYMLFGIVLVGLLYMVLL  197 (197)
Q Consensus       177 ~~FF~~~~~vi~~G~~hGLvl  197 (197)
                      + |||++++++++|++||||+
T Consensus       770 ~-ff~~~~l~~~~~~~hglv~  789 (798)
T PF02460_consen  770 V-FFKTVFLVIIFGLLHGLVF  789 (798)
T ss_pred             H-HHHHHHHHHHHHHHHHHHH
Confidence            6 5799999999999999985

In Drosophila melanogaster, this protein associates with the smoothened protein to transduce hedgehog signals, leading to the activation of wingless, decapentaplegic and patched itself. It participates in cell interactions that establish pattern within the segment and imaginal disks during development. The mouse homologue may play a role in epidermal development. The human Niemann-Pick C1 protein, defects in which cause Niemann-Pick type II disease, is also a member of this family. This protein is involved in the intracellular trafficking of cholesterol, and may play a role in vesicular trafficking in glia, a process that may be crucial for maintaining the structural functional integrity of nerve terminals.; GO: 0008158 hedgehog receptor activity, 0016020 membrane

>TIGR00917 2A060601 Niemann-Pick C type protein family

Probab=99.96  E-value=1.4e-30  Score=264.35  Aligned_cols=142  Identities=28%  Similarity=0.368  Sum_probs=125.9

Q ss_pred             hHHHhhhhhhccCCCCCcch-hhHhhhhhhhcC----CCc-----ChhH-HH----------------------------
Q psy8507          56 SILAYKLLVQTGRVDNPVDK-SLIKHNRLVSRD----GII-----NPKL-LL----------------------------   96 (197)
Q Consensus        56 ~ila~r~~iqt~~~~~~~~~-~~~~~~r~v~~~----~~i-----~p~~-f~----------------------------   96 (197)
                      .|.|+||..++.+..+..|. +++++.|.++++    ..+     +|.+ ||                            
T Consensus       989 ~I~aS~f~~~h~~l~~~~d~i~a~~~~R~ia~~i~~~~~~~vfpys~~~vf~eQY~~i~~~~~~~l~~a~~~v~~V~~l~ 1068 (1204)
T TIGR00917       989 IIQASYFMTYHTPLNTQADFINALRAAREISANVTRSLKMEVFPYSVFYVFFEQYLTIWSDALINLGISLGAIFIVTLVL 1068 (1204)
T ss_pred             eEEEEEEEEeccCCCCHHHHHHHHHHHHHHHHHhhhccCCccccCcCceehhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            38899999999998888777 589999999872    211     2222 22                            


Q ss_pred             ------------------------HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhccc-CChhHHHHHHHHHHhH
Q psy8507          97 ------------------------VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCI-GNRDRRVRLSIEHMYS  151 (197)
Q Consensus        97 ------------------------~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~-~~~~~R~~~aL~~~G~  151 (197)
                                              +|++||++||+||+++|+||||+||||++||+|+|..+. +++++|+++||++||+
T Consensus      1069 l~l~~~~aliv~l~I~~i~~~~~g~M~~~gisLN~vSlv~Li~avGisV~f~~hI~~~f~~~~~~~~~~ra~~al~~vg~ 1148 (1204)
T TIGR00917      1069 LGLNALSAVNVVISVGMIVVNLVGIMHLWNISLNAVSVVNLVMAKGISIEFCSHINAQFSTSKHFSRNHRAKEALGGMGS 1148 (1204)
T ss_pred             hcccchhHHHHHHHHHHHHHHHHHHHHHhCCCHhHHHHHHHHHHhhhHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHH
Confidence                                    899999999999999999999999999999999999874 4677999999999999


Q ss_pred             HHHHH-HHHHHHHHHHhhccccchhHHHHHHHHHHHHHHHhhhhhcC
Q psy8507         152 VVLHA-GLILLVAISILAFSEFQFILRIFFYMLFGIVLVGLLYMVLL  197 (197)
Q Consensus       152 pVl~g-a~ST~lgv~~L~fs~s~~~~~~FF~~~~~vi~~G~~hGLvl  197 (197)
                      ||++| .+||++|++||+|++||+|++|||+|+++++++|++|||||
T Consensus      1149 ~v~~g~tlT~~~g~~~L~f~~s~if~vfff~m~l~iv~~g~~HGLvf 1195 (1204)
T TIGR00917      1149 SVFSGITLTKLVGVVVLGFSKSEIFQVYYFRMYLAIVLLGALHGLVF 1195 (1204)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999 57889999999999999999999999999999999999985

The model describes Niemann-Pick C type protein in eukaryotes. The defective protein has been associated with Niemann-Pick disease which is described in humans as autosomal recessive lipidosis. It is characterized by the lysosomal accumulation of unestrified cholesterol. It is an integral membrane protein, which indicates that this protein is most likely involved in cholesterol transport or acts as some component of cholesterol homeostasis.

>KOG1933|consensus

Probab=99.70  E-value=1.2e-18  Score=175.83  Aligned_cols=101  Identities=35%  Similarity=0.485  Sum_probs=97.1

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcccCC-hhHHHHHHHHHHhHHHHHH-HHHHHHHHHHhhccccch
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGN-RDRRVRLSIEHMYSVVLHA-GLILLVAISILAFSEFQF  174 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~~~-~~~R~~~aL~~~G~pVl~g-a~ST~lgv~~L~fs~s~~  174 (197)
                      +|++|||.+|++|++|++|++|++|||++||.++|.++.+. +.+|+++++.++|+.++.| .++.+.|+++|+|+++.+
T Consensus      1064 ~m~~~~I~~NavS~vNlvm~vgi~vef~~hi~~sf~~s~~~~~~~ra~~~l~s~Gs~v~sgitlt~~~~~~vl~fa~s~i 1143 (1201)
T KOG1933|consen 1064 FMYLWGISLNAVSLVNLVMSVGIAVEFCVHITHSFATSSGPDATERAEEALNSIGSSVFSGITLTKFGGIIVLSFAKSQI 1143 (1201)
T ss_pred             HHHhhceeehhhhhhhhhhhcchhhhHHHHhhcceeeccCCchhHHHHHHHhccCcceecceeehhcCceEEEeeccccE
Confidence            99999999999999999999999999999999999999985 4599999999999999999 777899999999999999


Q ss_pred             hHHHHHHHHHHHHHHHhhhhhcC
Q psy8507         175 ILRIFFYMLFGIVLVGLLYMVLL  197 (197)
Q Consensus       175 ~~~~FF~~~~~vi~~G~~hGLvl  197 (197)
                      +.+|||+|++..++.|++||+|+
T Consensus      1144 ~~~~~f~~~l~~~l~~a~hGlif 1166 (1201)
T KOG1933|consen 1144 FQVFYFRMYLGIVLVGALHGLIF 1166 (1201)
T ss_pred             EEEEeehHHHHHHHHHheeeeee
Confidence            99999999999999999999875

>TIGR00921 2A067 The (Largely Archaeal Putative) Hydrophobe/Amphiphile Efflux-3 (HAE3) Family

Probab=99.21  E-value=3.9e-11  Score=115.59  Aligned_cols=100  Identities=15%  Similarity=0.080  Sum_probs=89.4

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcccC--ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccch
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIG--NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQF  174 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~~--~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~~  174 (197)
                      +|+++|+++|..+++.+.+.+|++|||+.|+.++|....+  +.++++++|+++.|.||+.+++++.+|..+|.+|+.+.
T Consensus       611 ~~~~~gi~l~~~~~~~~~i~lGigvDy~i~~~~r~~~~~~~~~~~~ai~~a~~~~g~ai~~s~lt~~~gf~~l~~s~~~~  690 (719)
T TIGR00921       611 LMGLRGIPSFLAMATTISIILGLGMDYSIHLAERYFEERKEHGPKEAITHTMERTGPGILFSGLTTAGGFLSLLLSHFPI  690 (719)
T ss_pred             HHHHHcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhccCHH
Confidence            9999999999999999999999999999999999986543  45589999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHHhhhhhcC
Q psy8507         175 ILRIFFYMLFGIVLVGLLYMVLL  197 (197)
Q Consensus       175 ~~~~FF~~~~~vi~~G~~hGLvl  197 (197)
                      ++.|. .++.+.+++++++.|++
T Consensus       691 ~~~~g-~~~~~~i~~~~~~~l~l  712 (719)
T TIGR00921       691 MRNFG-LVQGIGVLSSLTAALVV  712 (719)
T ss_pred             HHHHH-HHHHHHHHHHHHHHHHH
Confidence            98864 56666677888888763

Characterized members of the RND superfamily all probably catalyze substrate efflux via an H+ antiport mechanism. These proteins are found ubiquitously in bacteria, archaea and eukaryotes. They fall into seven phylogenetic families, this family (2.A.6.7) consists of uncharacterised putative transporters, largely in the Archaea.

>TIGR00921 2A067 The (Largely Archaeal Putative) Hydrophobe/Amphiphile Efflux-3 (HAE3) Family

Probab=99.06  E-value=6.4e-10  Score=107.22  Aligned_cols=99  Identities=19%  Similarity=0.195  Sum_probs=84.7

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc--cC-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC--IG-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQ  173 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s--~~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~  173 (197)
                      +|+++|+++|.++++..++.+|++|||+.|+...|...  .| ++++++++|+++.|.|++.+++||.+|.++|.++++.
T Consensus       237 ~~~~~g~~l~~~~~~~~~l~lgi~vd~~ihl~~r~~~~~~~g~~~~~ai~~a~~~~g~~i~~t~~t~~~gf~~l~~s~~~  316 (719)
T TIGR00921       237 IMGWLGIPLYATTLLAVPMLIGVGIDYGIQTLNRYEEERDIGRAKGEAIVTAVRRTGRAVLIALLTTSAGFAALALSEFP  316 (719)
T ss_pred             HHHHhCCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHcCCCHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHhccCh
Confidence            99999999999999999999999999999999999753  33 4559999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHHhhhhhc
Q psy8507         174 FILRIFFYMLFGIVLVGLLYMVL  196 (197)
Q Consensus       174 ~~~~~FF~~~~~vi~~G~~hGLv  196 (197)
                      .++.+- ....+-+++++++.+.
T Consensus       317 ~~~~~g-~~~~~gv~~~~l~~l~  338 (719)
T TIGR00921       317 MVSEFG-LGLVAGLITAYLLTLL  338 (719)
T ss_pred             HHHHHH-HHHHHHHHHHHHHHHH
Confidence            888764 4444445556666543

Characterized members of the RND superfamily all probably catalyze substrate efflux via an H+ antiport mechanism. These proteins are found ubiquitously in bacteria, archaea and eukaryotes. They fall into seven phylogenetic families, this family (2.A.6.7) consists of uncharacterised putative transporters, largely in the Archaea.

>COG1033 Predicted exporters of the RND superfamily [General function prediction only]

Probab=99.01  E-value=9.6e-10  Score=107.98  Aligned_cols=99  Identities=20%  Similarity=0.217  Sum_probs=84.9

Q ss_pred             HHHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcccCC--hhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccc
Q psy8507          96 LVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGN--RDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQ  173 (197)
Q Consensus        96 ~~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~~~--~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~  173 (197)
                      .+|++.||++|+.++..-.+.+|++|||+.|+.+.|....+.  .+|-...|.++.|.+|+.+++||..|.+.|.||++.
T Consensus       611 ~~M~l~gI~~~~~ta~v~ai~lGiGvDYsIh~~ery~eer~~~~~~eAi~~t~~~~G~ail~s~ltt~~GF~aLi~S~f~  690 (727)
T COG1033         611 GLMGLLGIPLTPATATLGAIILGIGVDYSIHITERYREERKKGGPKEAIETTVERTGKAILASALTTAIGFLALIFSPFP  690 (727)
T ss_pred             HHHHHhCCchhHHHHHHHHHhhhccchhhhHHHHHHHHHHhcCCchHHHHHHHHhhchHHHHHHHHHHHHHHHHHhcCCH
Confidence            399999999999999999999999999999999999966543  558889999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHHhhhhh
Q psy8507         174 FILRIFFYMLFGIVLVGLLYMV  195 (197)
Q Consensus       174 ~~~~~FF~~~~~vi~~G~~hGL  195 (197)
                      ++..|- .+....++++++-.|
T Consensus       691 i~snfG-ll~~~~il~sl~asl  711 (727)
T COG1033         691 IISNFG-LLTVIGILLSLLASL  711 (727)
T ss_pred             HHHHHH-HHHHHHHHHHHHHHH
Confidence            987754 444444555555444

>TIGR00916 2A0604s01 protein-export membrane protein, SecD/SecF family

Probab=98.83  E-value=1.5e-08  Score=84.76  Aligned_cols=83  Identities=17%  Similarity=0.088  Sum_probs=73.4

Q ss_pred             HHHHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc----cC-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhc
Q psy8507          95 LLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC----IG-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAF  169 (197)
Q Consensus        95 f~~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s----~~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~f  169 (197)
                      +.+|+++|+++|..+++-+++.+|++||++.|+...|.+.    ++ ++++-+.++..+.+.|++...++|++|.+||.+
T Consensus        88 ~g~m~l~G~~ln~~s~~glil~iGi~Vd~aIvv~e~~~~~~~~~~g~~~~~Av~~a~~~~~~~il~ttlTtii~f~pl~~  167 (192)
T TIGR00916        88 LGVLSLFGATLTLPGIAGLLTIIGYSVDDTVVIFDRIREELRKYKGRTFREAINLGINQTLSRIIDTNVTTLLAVLALYV  167 (192)
T ss_pred             HHHHHHHCCcccHHHHHHHHHHHHHhhcCeEEehHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5699999999999999999999999999999999888753    22 344778999999999999999999999999999


Q ss_pred             cccchhHH
Q psy8507         170 SEFQFILR  177 (197)
Q Consensus       170 s~s~~~~~  177 (197)
                      ++...++.
T Consensus       168 ~~~~~~~~  175 (192)
T TIGR00916       168 FGGGAIKG  175 (192)
T ss_pred             HhhhhHHH
Confidence            98766544

The SecA,SecB,SecD,SecE,SecF,SecG and SecY proteins form the protein translocation appartus in prokaryotes. This family is specific for the SecD and SecF proteins.

>COG1033 Predicted exporters of the RND superfamily [General function prediction only]

Probab=98.66  E-value=7.2e-08  Score=94.96  Aligned_cols=88  Identities=19%  Similarity=0.087  Sum_probs=79.0

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcccCC---hhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGN---RDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQ  173 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~~~---~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~  173 (197)
                      +|++.|++|+..|+....+-||++.||.+|+-.+|....+.   .+|.+++|+++.|.|++-+++||.+|.+-|.++...
T Consensus       240 ~m~llG~plt~~s~~~~~llIgiGidy~vh~~nr~~ee~~~~~~~~eAv~~ai~~~g~avl~a~lTT~~GF~Sl~~s~i~  319 (727)
T COG1033         240 AMGLLGIPLTITTSAVPPLLIGIGIDYGVHFHNRYEEERRKGRTVEEAVVEAIKHTGPAVLIAALTTAAGFLSLLTSSIP  319 (727)
T ss_pred             HHHHhCCCchhHHHHHHHHHhhhhhhHHHHHHHHHHHHHhcCCCHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHcccH
Confidence            99999999999999999999999999999999999865433   348999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHH
Q psy8507         174 FILRIFFYMLF  184 (197)
Q Consensus       174 ~~~~~FF~~~~  184 (197)
                      .++.+-.-+..
T Consensus       320 ~i~~~Gi~~si  330 (727)
T COG1033         320 AIKEFGILLSI  330 (727)
T ss_pred             HHHHHHHHHHH
Confidence            99886533333

>PF03176 MMPL: MMPL family; InterPro: IPR004869 Proteins of this entry are putative integral membrane proteins from bacteria

Probab=98.63  E-value=4.7e-08  Score=86.27  Aligned_cols=94  Identities=20%  Similarity=0.239  Sum_probs=73.3

Q ss_pred             HHHhccccchhhH-HHHhhhhcceeeehHHHHhHhhcccC---ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccc
Q psy8507          98 MYLMNIKLNPISC-VLIVNSSGIYIHFISYICLSFLTCIG---NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQ  173 (197)
Q Consensus        98 M~l~gi~Ln~iS~-v~Li~sIG~sVDFtaHI~~~F~~s~~---~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~  173 (197)
                      +..+|+++|.++. +..++.+|+++||+.|+...|.....   ++++.+++++.+.|.|++.++++|.+|...|.++++.
T Consensus       192 ~~~~~~~~~~~~~~l~~~l~lgvgidy~i~l~~r~ree~~~g~~~~~ai~~a~~~~g~~i~~s~ltt~~gf~~L~~s~~~  271 (333)
T PF03176_consen  192 MGLLGIPLSWITPALVFVLLLGVGIDYSIHLINRYREELRRGMSRKEAIRRAVRSTGRAILLSALTTAIGFGSLLFSPFP  271 (333)
T ss_pred             HHhhccccceeehHhhhhhHHHhhhhhHHHHHHHHHHHHHhccchHHHHHHHHhccCchhHHHHHHHHHHHHHHHHhhhh
Confidence            4566778887654 45578899999999999999976542   3347899999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHHhh
Q psy8507         174 FILRIFFYMLFGIVLVGLL  192 (197)
Q Consensus       174 ~~~~~FF~~~~~vi~~G~~  192 (197)
                      .++.+- .+..+-++++++
T Consensus       272 ~~~~~G-~~~~~gi~~~~l  289 (333)
T PF03176_consen  272 PLRQFG-LLAAIGILIALL  289 (333)
T ss_pred             HHHHHH-HHHHHHHHHHHH
Confidence            888764 333333344443

Several of the members are mycobacterial proteins. Many of the proteins contain two copies of this aligned region. The function of these proteins is not known, although it has been suggested that they may be involved in lipid transport [].; GO: 0016020 membrane

>TIGR03480 HpnN hopanoid biosynthesis associated RND transporter like protein HpnN

Probab=98.56  E-value=2.1e-07  Score=92.59  Aligned_cols=79  Identities=16%  Similarity=0.158  Sum_probs=67.6

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcccCChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccchhH
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQFIL  176 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~~~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~~~~  176 (197)
                      +|+++|++||..+++.+.+.+|++|||+.|+.++|....+...  .  .-.+.|.+|+.+++||.+|...|+||+...+.
T Consensus       756 ~m~~~gi~l~~~~~~~~~l~lGigVDy~I~~~~r~~~~~~~~~--~--~~~~~g~ai~~saltt~~gf~~l~~s~~~~~~  831 (862)
T TIGR03480       756 AMVLLGIPFNFANIIALPLLLGLGVDFGIYMVHRWRNGVDSGN--L--LQSSTARAVFFSALTTATAFGSLAVSSHPGTA  831 (862)
T ss_pred             HHHHHhccCcHHHHHHHHHHHhhhhhhHHHHHHHHHHhccchh--H--HHhhhHHHHHHHHHHHHHHHHHHHHhcCccHH
Confidence            9999999999999999999999999999999999976543211  1  11467999999999999999999999998877


Q ss_pred             HHH
Q psy8507         177 RIF  179 (197)
Q Consensus       177 ~~F  179 (197)
                      .+-
T Consensus       832 ~~G  834 (862)
T TIGR03480       832 SMG  834 (862)
T ss_pred             HHH
Confidence            643

The genomes containing members of this family share the machinery for the biosynthesis of hopanoid lipids. Furthermore, the genes of this family are usually located proximal to other components of this biological process. The proteins appear to be related to the RND family of export proteins, particularly the hydrophobe/amphiphile efflux-3 (HAE3) family represented by TIGR00921.

>PRK09579 multidrug efflux protein; Reviewed

Probab=98.45  E-value=6.3e-07  Score=91.09  Aligned_cols=99  Identities=11%  Similarity=0.055  Sum_probs=80.0

Q ss_pred             HHHHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc--cC-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccc
Q psy8507          95 LLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC--IG-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSE  171 (197)
Q Consensus        95 f~~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s--~~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~  171 (197)
                      |++|+++|.+||.+|++.+++++|+.||.+.|+.-.+.+.  .| ++.+-+.++..+++.|++.+.+||+++.+|++|.+
T Consensus       373 ~~~l~~~G~~ln~~sl~gli~~iGi~VddaIvv~e~i~~~~~~G~~~~~A~~~~~~~~~~pil~stlTti~~f~Pl~f~~  452 (1017)
T PRK09579        373 LFFMQMMGYSINLLTLLAMVLAIGLVVDDAIVVVENIHRHIEEGKSPFDAALEGAREIAMPVVSMTITLAAVYAPIGFLT  452 (1017)
T ss_pred             HHHHHHhCCCchHHHHHHHHHhhheeecCcEEeHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence            4499999999999999999999999999999998877653  23 44588999999999999999999999999999987


Q ss_pred             cchhHHHHHHHHHHHHHHHhhhhh
Q psy8507         172 FQFILRIFFYMLFGIVLVGLLYMV  195 (197)
Q Consensus       172 s~~~~~~FF~~~~~vi~~G~~hGL  195 (197)
                      ...- . ||+-+-.++++|++-++
T Consensus       453 g~~g-~-~~~~l~~~v~~~l~~S~  474 (1017)
T PRK09579        453 GLTG-A-LFKEFALTLAGAVIISG  474 (1017)
T ss_pred             Cchh-h-hHHHHHHHHHHHHHHHH
Confidence            4322 2 24555555666655443

>TIGR00966 3a0501s07 protein-export membrane protein SecF

Probab=98.41  E-value=1.1e-06  Score=75.98  Aligned_cols=95  Identities=19%  Similarity=0.136  Sum_probs=75.6

Q ss_pred             HHHHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc-----cCChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhc
Q psy8507          95 LLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC-----IGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAF  169 (197)
Q Consensus        95 f~~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s-----~~~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~f  169 (197)
                      +..|++.|+++|..++..+++.+|++||-+.++.-.+...     .++.++.+.++..+.+.|++.+.++|+++.+||++
T Consensus       139 ~~~l~~~g~~ln~~sl~gli~~iGi~Vdd~Ivv~d~i~e~~~~~~~~~~~~a~~~a~~~~~~~ii~ttltti~~flpl~~  218 (246)
T TIGR00966       139 VGVYSLFGIEVNLTTVAALLTIIGYSINDTVVVFDRIRENLRKYTRKTFTEVINLSINQTLSRTINTSLTTLLAVLALYV  218 (246)
T ss_pred             HHHHHHHCCcccHHHHHHHHHHHHHhccCeEEEehHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3399999999999999999999999999999987666532     22344778999999999999999999999999999


Q ss_pred             cccchhHHHHHHHHHHHHHHHhhhh
Q psy8507         170 SEFQFILRIFFYMLFGIVLVGLLYM  194 (197)
Q Consensus       170 s~s~~~~~~FF~~~~~vi~~G~~hG  194 (197)
                      ....+++-     +..++++|++-|
T Consensus       219 ~~g~~~~~-----~a~~~~~Gli~~  238 (246)
T TIGR00966       219 FGGGVIKD-----FSLALLVGVIVG  238 (246)
T ss_pred             hcchHHHH-----HHHHHHHHHHHH
Confidence            97754443     344444454433

This bacterial protein is always found with the homologous protein-export membrane protein SecD. In numerous lineages, this protein occurs as a SecDF fusion protein.

>PRK10614 multidrug efflux system subunit MdtC; Provisional

Probab=98.39  E-value=9.1e-07  Score=89.90  Aligned_cols=98  Identities=16%  Similarity=0.112  Sum_probs=77.9

Q ss_pred             HHHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc--cC-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccc
Q psy8507          96 LVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC--IG-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEF  172 (197)
Q Consensus        96 ~~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s--~~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s  172 (197)
                      .+|+++|++||.+|+.-+++++|+.||.+.|+.-.+.+.  .| ++.+-+.++.++++.|++.+.+||+++.+|++|.+.
T Consensus       375 ~~l~~~g~~ln~~sl~gl~~~iGi~Vd~aIvv~e~i~~~~~~g~~~~~A~~~~~~~~~~~i~~stltti~~f~Pl~~~~g  454 (1025)
T PRK10614        375 AAMYLCGFSLNNLSLMALTIATGFVVDDAIVVLENISRHLEAGMKPLQAALQGVREVGFTVLSMSLSLVAVFLPLLLMGG  454 (1025)
T ss_pred             HHHHHhCCChhHHHHHHHHHHhheeecCcEEEEeHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            399999999999999999999999999999998444332  23 445778899999999999999999999999999875


Q ss_pred             chhHHHHHHHHHHHHHHHhhhhh
Q psy8507         173 QFILRIFFYMLFGIVLVGLLYMV  195 (197)
Q Consensus       173 ~~~~~~FF~~~~~vi~~G~~hGL  195 (197)
                      ..- . ||+-+-+++++|++-++
T Consensus       455 ~~g-~-~~~~~~~~~~~~l~~S~  475 (1025)
T PRK10614        455 LPG-R-LFREFAVTLSVAIGISL  475 (1025)
T ss_pred             chh-h-hHHHHHHHHHHHHHHHH
Confidence            421 2 24556666666665443

>TIGR03480 HpnN hopanoid biosynthesis associated RND transporter like protein HpnN

Probab=98.35  E-value=1.8e-06  Score=85.95  Aligned_cols=81  Identities=19%  Similarity=0.181  Sum_probs=70.5

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc--cC-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC--IG-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQ  173 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s--~~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~  173 (197)
                      +|.+.|.++|.+|++..++.+|++|||+.|+..+|...  .| +.++-++++++++|.|++.+++||.+|.+.|.+++..
T Consensus       313 ~~~l~~~~ln~~s~~~~~lliGi~vD~~I~~~~r~~e~~~~g~~~~~A~~~a~~~~~~~i~~s~lTt~~gf~~l~~~~~~  392 (862)
T TIGR03480       313 FATLAVGHLNLISVAFAVLFIGLGVDFAIQFSLRYREERFRGGNHREALSVAARRMGAALLLAALATAAGFFAFLPTDYK  392 (862)
T ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccH
Confidence            88889999999999999999999999999999988764  23 3346679999999999999999999999999998866


Q ss_pred             hhHH
Q psy8507         174 FILR  177 (197)
Q Consensus       174 ~~~~  177 (197)
                      .++.
T Consensus       393 ~~~~  396 (862)
T TIGR03480       393 GVSE  396 (862)
T ss_pred             HHHH
Confidence            5443

The genomes containing members of this family share the machinery for the biosynthesis of hopanoid lipids. Furthermore, the genes of this family are usually located proximal to other components of this biological process. The proteins appear to be related to the RND family of export proteins, particularly the hydrophobe/amphiphile efflux-3 (HAE3) family represented by TIGR00921.

>PRK10555 aminoglycoside/multidrug efflux system; Provisional

Probab=98.32  E-value=1.6e-06  Score=88.29  Aligned_cols=98  Identities=13%  Similarity=0.197  Sum_probs=80.4

Q ss_pred             HHHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhccc---C-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccc
Q psy8507          96 LVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCI---G-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSE  171 (197)
Q Consensus        96 ~~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~---~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~  171 (197)
                      .+|+++|+++|.+|++.+++++|+.||.+.|+...+.+..   | ++.+-+.++.++++.|++.++++|+++.+|++|.+
T Consensus       381 ~~~~~~G~~ln~~sl~glii~iGi~Vd~aIvvve~i~~~~~~~G~~~~~Ai~~a~~~~~~~i~~stltti~~flPl~~~~  460 (1037)
T PRK10555        381 SVLYAFGYSINTLTMFAMVLAIGLLVDDAIVVVENVERIMSEEGLTPREATRKSMGQIQGALVGIAMVLSAVFVPMAFFG  460 (1037)
T ss_pred             HHHHHhCCChhHHHHHHHHHHhhheecCeEEeHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            3999999999999999999999999999999999987642   3 44588999999999999999999999999999987


Q ss_pred             cchhHHHHHHHHHHHHHHHhhhhh
Q psy8507         172 FQFILRIFFYMLFGIVLVGLLYMV  195 (197)
Q Consensus       172 s~~~~~~FF~~~~~vi~~G~~hGL  195 (197)
                      ... -.+ |+-+-+++++|++-++
T Consensus       461 G~~-g~~-~~~l~~~v~~~l~~S~  482 (1037)
T PRK10555        461 GTT-GAI-YRQFSITIVSAMVLSV  482 (1037)
T ss_pred             Cch-hHH-HHHHHHHHHHHHHHHH
Confidence            543 222 4555565666655443

>TIGR00915 2A0602 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family

Probab=98.30  E-value=1.6e-06  Score=88.30  Aligned_cols=97  Identities=10%  Similarity=0.125  Sum_probs=77.7

Q ss_pred             HHHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc---cC-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccc
Q psy8507          96 LVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC---IG-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSE  171 (197)
Q Consensus        96 ~~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s---~~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~  171 (197)
                      .+|+++|++||.+|++.+++++|+.||++.|+.-.+.+.   .| ++.+-+.++.++++.|++.+.++|+++.+|++|.+
T Consensus       381 ~~~~~~g~~ln~~sl~gli~~iGi~VD~aIvv~e~i~~~~~~~g~~~~~A~~~~~~~~~~~i~~ttltti~~flPl~~~~  460 (1044)
T TIGR00915       381 AVLAAFGFSINTLTMFAMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFFG  460 (1044)
T ss_pred             HHHHHhCCChhHHHHHHHHHHhhheecceEEEehHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            399999999999999999999999999999988877653   23 34477889999999999999999999999999987


Q ss_pred             cchhHHHHHHHHHHHHHHHhhhh
Q psy8507         172 FQFILRIFFYMLFGIVLVGLLYM  194 (197)
Q Consensus       172 s~~~~~~FF~~~~~vi~~G~~hG  194 (197)
                      ...- . ||+-+-.++++|++-+
T Consensus       461 G~~g-~-~~~~~~~~i~~~l~~S  481 (1044)
T TIGR00915       461 GSTG-A-IYRQFSITIVSAMALS  481 (1044)
T ss_pred             cchH-H-HHHHHHHHHHHHHHHH
Confidence            4332 2 2455555555555443

This family is one of several subfamilies within the scope of pfam model pfam00873.

>PRK15127 multidrug efflux system protein AcrB; Provisional

Probab=98.27  E-value=2.2e-06  Score=87.39  Aligned_cols=98  Identities=11%  Similarity=0.131  Sum_probs=78.4

Q ss_pred             HHHHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc---cC-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcc
Q psy8507          95 LLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC---IG-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFS  170 (197)
Q Consensus        95 f~~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s---~~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs  170 (197)
                      |.+|+++|++||.+|++.+++++|+.||.+.|+...+...   .| ++.+-+.++..+++.|++.+.++|+++.+||+|.
T Consensus       380 ~~~~~~~g~~ln~~sl~glil~iGi~VD~aIvvie~i~~~~~~~G~~~~~A~~~~~~~v~~~i~~~tltt~~~f~Pl~~~  459 (1049)
T PRK15127        380 FAVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFF  459 (1049)
T ss_pred             HHHHHHhCCCHhHHHHHHHHHHHHhhccceEEEeHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            4499999999999999999999999999999999998763   24 3447788999999999999999999999999997


Q ss_pred             ccchhHHHHHHHHHHHHHHHhhhh
Q psy8507         171 EFQFILRIFFYMLFGIVLVGLLYM  194 (197)
Q Consensus       171 ~s~~~~~~FF~~~~~vi~~G~~hG  194 (197)
                      +... -.+ |+-+-.++++|++-+
T Consensus       460 ~G~~-g~~-~~~~~~~~~~~l~~S  481 (1049)
T PRK15127        460 GGST-GAI-YRQFSITIVSAMALS  481 (1049)
T ss_pred             CCch-HHH-hHHHHHHHHHHHHHH
Confidence            6432 222 355555555555443

>PRK09577 multidrug efflux protein; Reviewed

Probab=98.24  E-value=2.9e-06  Score=86.33  Aligned_cols=97  Identities=12%  Similarity=0.096  Sum_probs=79.3

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc---cC-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC---IG-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEF  172 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s---~~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s  172 (197)
                      +|.++|++||.+|++-+++++|+.||++.|+...+.+.   .| ++.+-+.++..+++.|++.+.++|+++.+|++|.+.
T Consensus       381 ~m~~~g~~ln~~sl~gl~~~iGi~VD~aIvvie~i~~~~~~~G~~~~~A~~~a~~~~~~~i~~~tlt~~~~flPl~~~~g  460 (1032)
T PRK09577        381 VMLAAGFSINVLTMFGMVLAIGILVDDAIVVVENVERLMVEEGLSPYDATVKAMKQISGAIVGITVVLTSVFVPMAFFGG  460 (1032)
T ss_pred             HHHHhcccHHHHHHHHHHHheeeEecCcEEEehHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            99999999999999999999999999999999988764   23 344778999999999999999999999999999885


Q ss_pred             chhHHHHHHHHHHHHHHHhhhhh
Q psy8507         173 QFILRIFFYMLFGIVLVGLLYMV  195 (197)
Q Consensus       173 ~~~~~~FF~~~~~vi~~G~~hGL  195 (197)
                      ..-. + |+-+-.++++|++-++
T Consensus       461 ~~g~-~-~~~~~~~v~~~l~~S~  481 (1032)
T PRK09577        461 AVGN-I-YRQFALSLAVSIGFSA  481 (1032)
T ss_pred             cHHH-H-HHHHHHHHHHHHHHHH
Confidence            5433 2 4555555556655443

>TIGR00833 actII Transport protein

Probab=98.23  E-value=4.2e-06  Score=84.17  Aligned_cols=83  Identities=13%  Similarity=0.175  Sum_probs=68.5

Q ss_pred             HHHHhccc----cchhhHHHH-hhhhcceeeehHHHHhHhhccc---CChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhh
Q psy8507          97 VMYLMNIK----LNPISCVLI-VNSSGIYIHFISYICLSFLTCI---GNRDRRVRLSIEHMYSVVLHAGLILLVAISILA  168 (197)
Q Consensus        97 ~M~l~gi~----Ln~iS~v~L-i~sIG~sVDFtaHI~~~F~~s~---~~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~  168 (197)
                      +|++.|..    +|..+.+.+ ++.+|+++||+.|+...|....   +++++.+++++++.|.||+.++++|.+|.++|.
T Consensus       217 ~~~~lg~~~~~~l~~~~~~~l~~l~lGl~vDy~I~lv~r~~ee~~~g~~~~~Av~~a~~~~g~~I~~s~lT~~~gf~~l~  296 (910)
T TIGR00833       217 IVSLLGIPGLIGVNAQTTVLLTALVIGAGTDYAVFLTGRYHEERRKGESLEEAAAEALRGTGKAILGSALTVAVAFLALS  296 (910)
T ss_pred             HHHHHhhcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            78888875    455555544 7789999999999999997643   234578999999999999999999999999999


Q ss_pred             ccccchhHHHH
Q psy8507         169 FSEFQFILRIF  179 (197)
Q Consensus       169 fs~s~~~~~~F  179 (197)
                      +++..+++.+-
T Consensus       297 ~~~~~~~~~~G  307 (910)
T TIGR00833       297 LARLPSFKTLG  307 (910)
T ss_pred             HccChHHHHHH
Confidence            99988776653

Characterized members of the RND superfamily all probably catalyze substrate efflux via an H+ antiport mechanism. These proteins are found ubiquitously in bacteria, archaea and eukaryotes. This sub-family includes the S. coelicolor ActII3 protein, which may play a role in drug resistance, and the M. tuberculosis MmpL7 protein, which catalyzes export of an outer membrane lipid, phthiocerol dimycocerosate.

>TIGR01129 secD protein-export membrane protein SecD

Probab=98.16  E-value=5.5e-06  Score=76.63  Aligned_cols=96  Identities=14%  Similarity=0.129  Sum_probs=75.6

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhccc--C-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCI--G-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQ  173 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~--~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~  173 (197)
                      +|++.|..||..++.-+++++|++||.++++.-.+....  + +.++-+.++..+.++|++.+.+||+++.++|.+....
T Consensus       290 ~~~l~g~~l~l~siaglil~iG~~VD~~Ivi~erire~l~~g~~~~~Ai~~~~~~~~~~I~~s~lTtlia~l~L~~~g~g  369 (397)
T TIGR01129       290 ILSAFGATLTLPGIAGLILTIGMAVDANVLIYERIKEELRLGKSVRQAIEAGFERAFSTIFDANITTLIAALILYVFGTG  369 (397)
T ss_pred             HHHHHCCCccHHHHHHHHHHhheeeeceEEEeHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            899999999999999999999999999999988776432  2 3346788999999999999999999999999986655


Q ss_pred             hhHHHHHHHHHHHHHHHhhh
Q psy8507         174 FILRIFFYMLFGIVLVGLLY  193 (197)
Q Consensus       174 ~~~~~FF~~~~~vi~~G~~h  193 (197)
                      .++-| -.++.+-+++|++-
T Consensus       370 ~~~~f-A~tl~igii~s~~~  388 (397)
T TIGR01129       370 PVKGF-AVTLAIGIIASLFT  388 (397)
T ss_pred             chhHH-HHHHHHHHHHHHHH
Confidence            55443 33333334444443

SecD from Mycobacterium tuberculosis has a long Pro-rich insert.

>PRK10503 multidrug efflux system subunit MdtB; Provisional

Probab=98.14  E-value=4.7e-06  Score=84.95  Aligned_cols=99  Identities=13%  Similarity=0.150  Sum_probs=78.3

Q ss_pred             HHHHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhccc--C-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccc
Q psy8507          95 LLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCI--G-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSE  171 (197)
Q Consensus        95 f~~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~--~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~  171 (197)
                      |.+|+++|+++|.+|+..+++++|+.||.+.|+.-.+.+..  | ++.+.+.++..+++.|++.+.+||+++.+|++|++
T Consensus       383 ~~~l~~~g~~ln~~sl~gl~~~iG~~Vd~aIvv~e~i~~~~~~g~~~~~aa~~~~~~~~~~vl~~tltti~~f~Pl~~~~  462 (1040)
T PRK10503        383 FAVMVFLDFSINNLTLMALTIATGFVVDDAIVVIENISRYIEKGEKPLAAALKGAGEIGFTIISLTFSLIAVLIPLLFMG  462 (1040)
T ss_pred             HHHHHHhCCCHHHHHHHHHHHheeeeecCeEEEehhHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            34999999999999999999999999999999998887643  3 23477788889999999999999999999999987


Q ss_pred             cchhHHHHHHHHHHHHHHHhhhhh
Q psy8507         172 FQFILRIFFYMLFGIVLVGLLYMV  195 (197)
Q Consensus       172 s~~~~~~FF~~~~~vi~~G~~hGL  195 (197)
                      .-. -. ||+-+-.++.+|++-.+
T Consensus       463 g~~-G~-~~~~~~~~v~~~l~~S~  484 (1040)
T PRK10503        463 DIV-GR-LFREFAVTLAVAILISA  484 (1040)
T ss_pred             ccH-HH-HHHHHHHHHHHHHHHHH
Confidence            522 22 24555555566655443

>PRK13022 secF preprotein translocase subunit SecF; Reviewed

Probab=98.11  E-value=1e-05  Score=71.87  Aligned_cols=82  Identities=12%  Similarity=0.082  Sum_probs=71.6

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc-----cCChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC-----IGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSE  171 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s-----~~~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~  171 (197)
                      +|.+.|+++|..+++.+++.+|++||.+.|+.-.+...     .++.+|.+.+|..+.+.|++...+||++|++||.+..
T Consensus       170 ~~~l~g~~l~~~siaall~liG~sVnd~Ivv~drire~~~~~~~~~~~~av~~a~~~~~~~~l~TslTTl~~~l~L~~~g  249 (289)
T PRK13022        170 IFSLFQIEFDLTVIAALLTIIGYSLNDTVVVFDRIRENFRKIRRKTFAEIINLSINQTLSRTIITSLTTLLVVLALYLFG  249 (289)
T ss_pred             HHHHHCCcccHHHHHHHHHHHHHheeceEEEeeHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999999999999999998777532     2344588899999999999999999999999999998


Q ss_pred             cchhHHH
Q psy8507         172 FQFILRI  178 (197)
Q Consensus       172 s~~~~~~  178 (197)
                      ...++-+
T Consensus       250 ~~~i~~f  256 (289)
T PRK13022        250 GGTLHDF  256 (289)
T ss_pred             chhHHHH
Confidence            7665554

>PF00873 ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR001036 The Escherichia coli acrA and acrB genes encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors []

Probab=98.02  E-value=1.6e-05  Score=80.59  Aligned_cols=99  Identities=17%  Similarity=0.162  Sum_probs=80.2

Q ss_pred             HHHHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc----cCChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcc
Q psy8507          95 LLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC----IGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFS  170 (197)
Q Consensus        95 f~~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s----~~~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs  170 (197)
                      |.+|+++|++||.+|+.-|++|+|+-||=+.=+.-..++.    .+++.+-+.++..+++.|++-+.+||++..+|++|.
T Consensus       373 ~~~m~~~g~slN~~SL~gl~laiG~lVDdaIVV~Eni~r~~~~~g~~~~~Aa~~~~~ev~~~i~~stlTti~vF~Pl~f~  452 (1021)
T PF00873_consen  373 FIFMYLFGISLNIMSLAGLILAIGMLVDDAIVVVENIYRHLEEEGKSPLEAAIEGTKEVAPPILASTLTTIAVFLPLLFM  452 (1021)
T ss_dssp             HHHHHHTTTTBEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHHHHTCGGGGS
T ss_pred             HHHHHHcCCCchHHHHHhHHHhcccccccceehHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhc
Confidence            4499999999999999999999999999999888777543    233457789999999999999999999999999999


Q ss_pred             ccchhHHHHHHHHHHHHHHHhhhhh
Q psy8507         171 EFQFILRIFFYMLFGIVLVGLLYMV  195 (197)
Q Consensus       171 ~s~~~~~~FF~~~~~vi~~G~~hGL  195 (197)
                      +... -. ||+-+..+++++++-.|
T Consensus       453 ~G~~-g~-~~~~l~~~v~~al~~Sl  475 (1021)
T PF00873_consen  453 PGIA-GQ-FFRPLALTVIIALIASL  475 (1021)
T ss_dssp             BHHH-HH-HHHHHHHHHHHHHHHHH
T ss_pred             CCch-HH-HHHHHHHHHHHHHHHHH
Confidence            8544 33 34666666666655443

The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents. The structure of ligand-free AcrB shows that it is a homotrimer of 110kDa per subunit. Each subunit contains 12 transmembrane helices and two large periplasmic domains (each exceeding 300 residues) between helices 1 and 2, and helices 7 and 8. X-ray analysis of the overexpressed AcrB protein demonstrated that the three periplasmic domains form, in the centre, a funnel-like structure and a connected narrow (or closed) pore. The pore is opened to the periplasm through three vestibules located at subunit interfaces. These vestibules were proposed to allow direct access of drugs from the periplasm as well as the outer leaflet of the cytoplasmic membrane. The three transmembrane domains of AcrB protomers form a large, 30A-wide central cavity that spans the cytoplasmic membrane and extends to the cytoplasm X-ray crystallographic structures of the trimeric AcrB pump from E. coli with four structurally diverse ligands demonstrated that three molecules of ligand bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilising the binding. ; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2V50_B 1T9U_A 2HRT_B 3NOC_A 3NOG_A 4DX7_A 1OYD_A 3AOB_A 1T9V_A 4DX6_B ....

>PRK13023 bifunctional preprotein translocase subunit SecD/SecF; Reviewed

Probab=97.99  E-value=1.8e-05  Score=78.70  Aligned_cols=97  Identities=13%  Similarity=0.016  Sum_probs=77.9

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc---cCChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC---IGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQ  173 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s---~~~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~  173 (197)
                      +|+++|..||..++.-+++++|++||.++.+.-.+...   .++.++.+.++..+.++|++.+.+||+++.+||.+....
T Consensus       320 ~l~l~g~~Lnl~siaGlIL~IGm~VD~~Ivi~Erireel~~G~~~~~Av~~g~~~~~~~Il~s~lTTlia~lpL~~~g~g  399 (758)
T PRK13023        320 VLSLIGASISLASIAGLVLTIGLAVDAHILIYERVREDRRKGYSVVQAMESGFYRALSTIVDANLTTLIAALVLFLLGSG  399 (758)
T ss_pred             HHHHHCCCccHHHHHHHHHHHHHhccCcEEEeeHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhch
Confidence            99999999999999999999999999999998887532   234458899999999999999999999999999998776


Q ss_pred             hhHHHHHHHHHHHHHHHhhhh
Q psy8507         174 FILRIFFYMLFGIVLVGLLYM  194 (197)
Q Consensus       174 ~~~~~FF~~~~~vi~~G~~hG  194 (197)
                      .++-| ..++++-++.+++-.
T Consensus       400 ~ik~F-AitliiGi~~S~~~a  419 (758)
T PRK13023        400 TVHGF-ALTVAIGIGTTLFTT  419 (758)
T ss_pred             hHHHH-HHHHHHHHHHHHHHH
Confidence            65553 344444344444433

>PF12349 Sterol-sensing: Sterol-sensing domain of SREBP cleavage-activation

Probab=97.94  E-value=8.2e-05  Score=60.15  Aligned_cols=84  Identities=19%  Similarity=0.177  Sum_probs=72.8

Q ss_pred             HHHHHHhccccchhhH-HHHhhhhcceeeehHHHHhHhhcccCCh--hHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccc
Q psy8507          95 LLVMYLMNIKLNPISC-VLIVNSSGIYIHFISYICLSFLTCIGNR--DRRVRLSIEHMYSVVLHAGLILLVAISILAFSE  171 (197)
Q Consensus        95 f~~M~l~gi~Ln~iS~-v~Li~sIG~sVDFtaHI~~~F~~s~~~~--~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~  171 (197)
                      +++.++.|+++++++. +.-...+|+++|...++++++.++..+.  ++|+.+|+++.|++++...++++.+....++++
T Consensus        24 ~~i~~~~g~~~~~~~~e~~PFlvl~iG~dn~f~l~~~~~~~~~~~~~~~ri~~al~~~G~si~~t~l~~~~af~~~~~~~  103 (153)
T PF12349_consen   24 LGICSLFGVPFSLIPSEVLPFLVLGIGVDNMFVLARAVRRTPSSLPVPERIAEALSRVGPSILLTSLTEIVAFLIGAFSP  103 (153)
T ss_pred             HHHHHHHcCccchhhHHHHHHHHHHHhhhHHHHHHHHHHHhcccccHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHhh
Confidence            5578899999999986 5556778999999999999999876544  599999999999999999999999999888888


Q ss_pred             cchhHHH
Q psy8507         172 FQFILRI  178 (197)
Q Consensus       172 s~~~~~~  178 (197)
                      ..-++.|
T Consensus       104 ~~~l~~F  110 (153)
T PF12349_consen  104 VPALREF  110 (153)
T ss_pred             hHHHHHH
Confidence            7776654

>PRK08578 preprotein translocase subunit SecF; Reviewed

Probab=97.91  E-value=3.6e-05  Score=68.51  Aligned_cols=70  Identities=16%  Similarity=0.215  Sum_probs=58.1

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcccCChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFS  170 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~~~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs  170 (197)
                      +|+++|+++|..+++.+++.+|++||.+.++...+....++.+|.+.++++. +   +...+||++|++||.+.
T Consensus       178 ~~~l~g~~ln~~~i~gll~iiG~sVdd~IVv~dri~~~~~~~~eai~~a~~~-~---i~tslTTl~~~lpL~l~  247 (292)
T PRK08578        178 LMNLFGIELSLATVAALLMLIGYSVDSDILLTTRVLKRRGTFDESIKRAMRT-G---ITMTLTTIAAMAVLYIV  247 (292)
T ss_pred             HHHHHCccccHHHHHHHHHHHheeecCcEEEehHHHHccCCHHHHHHHHHHH-H---HHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999988877765545555778888743 3   34579999999999864

>PRK05812 secD preprotein translocase subunit SecD; Reviewed

Probab=97.87  E-value=5.7e-05  Score=71.92  Aligned_cols=95  Identities=16%  Similarity=0.084  Sum_probs=74.5

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc---cCChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC---IGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQ  173 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s---~~~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~  173 (197)
                      +|++.|+.||..+..-+++++|++||.++.+.-.+...   ..+.++-+..+..+.+.|++.+.+||+++.++|.+....
T Consensus       375 ~~~l~g~~l~l~siaGlil~iG~~VD~~IVI~ErIreel~~g~~~~~Ai~~~~~~~~~~Il~s~lTTlia~l~L~~~g~g  454 (498)
T PRK05812        375 VLSLLGATLTLPGIAGIVLTIGMAVDANVLIFERIREELREGRSLRSAIEAGFKRAFSTILDSNITTLIAAIILYALGTG  454 (498)
T ss_pred             HHHHHCCCchHHHHHHHHHhheeEEeceEEEeHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            89999999999999999999999999999888777542   223346788999999999999999999999999986655


Q ss_pred             hhHHHHHHHHHHHHHHHhh
Q psy8507         174 FILRIFFYMLFGIVLVGLL  192 (197)
Q Consensus       174 ~~~~~FF~~~~~vi~~G~~  192 (197)
                      .++-| -.++++-++.|++
T Consensus       455 ~i~~f-Aitl~iGii~s~~  472 (498)
T PRK05812        455 PVKGF-AVTLGIGILTSMF  472 (498)
T ss_pred             chhHH-HHHHHHHHHHHHH
Confidence            55543 3333333444443

>PRK13024 bifunctional preprotein translocase subunit SecD/SecF; Reviewed

Probab=97.83  E-value=5.3e-05  Score=75.29  Aligned_cols=82  Identities=13%  Similarity=0.137  Sum_probs=70.9

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhccc---CChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCI---GNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQ  173 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~---~~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~  173 (197)
                      +|++.|..+|..+.+.+++.+|++||.+.|+.-.+....   ++.++-+.++..+.+.|++.+.+||++|.++|.+....
T Consensus       308 ~l~l~g~~l~l~siaglil~iGi~Vd~~Ivi~eri~e~l~~g~~~~~Ai~~a~~~~~~~il~t~lTTii~~lpL~~~g~g  387 (755)
T PRK13024        308 ALSSLGAVLTLPGIAGLVLGIGMAVDANVLIFERIKEELRKGKSLKKAFKKGFKNAFSTILDSNITTLIAAAILFFFGTG  387 (755)
T ss_pred             HHHHHCCCccHHHHHHHHHHHHHHHhCcEEehHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            899999999999999999999999999999998886532   23457789999999999999999999999999986655


Q ss_pred             hhHHH
Q psy8507         174 FILRI  178 (197)
Q Consensus       174 ~~~~~  178 (197)
                      .++-|
T Consensus       388 ~~~~f  392 (755)
T PRK13024        388 PVKGF  392 (755)
T ss_pred             hhhhH
Confidence            55543

>TIGR00914 2A0601 heavy metal efflux pump (cobalt-zinc-cadmium)

Probab=97.68  E-value=8.7e-05  Score=75.77  Aligned_cols=98  Identities=14%  Similarity=0.044  Sum_probs=73.1

Q ss_pred             HHHHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc--c-----C------ChhHHHHHHHHHHhHHHHHHHHHHH
Q psy8507          95 LLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC--I-----G------NRDRRVRLSIEHMYSVVLHAGLILL  161 (197)
Q Consensus        95 f~~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s--~-----~------~~~~R~~~aL~~~G~pVl~ga~ST~  161 (197)
                      |.+|+++|++||.+|+.  .+++|+-||.+..+.-...+.  .     |      ++.+-+.++..+++.|++.+.+||+
T Consensus       383 ~~~m~~~g~sln~~sl~--~l~iGilVDdaIVvvE~i~r~~~~~~~~~g~~~~~~~~~~A~~~g~~~~~~pil~stlTti  460 (1051)
T TIGR00914       383 FIGMVFQGISANLMSLG--ALDFGLIVDGAVVIVENAHRRLAEAQHHHGRQLTLKERLHEVFAASREVRRPLIFGQLIIT  460 (1051)
T ss_pred             HHHHHHhCCcHHHHHHH--HHHHHhhhcCcEEeehHHHHHHHhcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34999999999999985  567899999999876553321  1     1      2225577899999999999999999


Q ss_pred             HHHHHhhccccchhHHHHHHHHHHHHHHHhhhhhc
Q psy8507         162 VAISILAFSEFQFILRIFFYMLFGIVLVGLLYMVL  196 (197)
Q Consensus       162 lgv~~L~fs~s~~~~~~FF~~~~~vi~~G~~hGLv  196 (197)
                      ++.+|++|.+... -. ||+-+-+++++|++-+++
T Consensus       461 ~~flPl~~~~g~~-g~-~~~~~~~~v~~~l~~Sll  493 (1051)
T TIGR00914       461 LVFLPIFTLTGVE-GK-MFHPMAFTVVLALAGAMI  493 (1051)
T ss_pred             HHHHHHHHccchH-HH-HhHHHHHHHHHHHHHHHH
Confidence            9999999877432 22 346666666777665543

This model represents a family of H+/heavy metal cation antiporters. This family is one of several subfamilies within the scope of pfam model pfam00873.

>TIGR00914 2A0601 heavy metal efflux pump (cobalt-zinc-cadmium)

Probab=97.67  E-value=3.6e-05  Score=78.53  Aligned_cols=76  Identities=17%  Similarity=0.115  Sum_probs=65.9

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhccc--C-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCI--G-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEF  172 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~--~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s  172 (197)
                      .|.++|.+||..|++-+++.+|+.||.+.|+.-.+....  | +.++-+.+|-.....||+.+++||++|.+||+++..
T Consensus       922 ~l~~~g~~l~~~s~~G~i~l~GivV~naIvlv~~~~~~~~~g~~~~~Ai~~a~~~r~rpIl~ttltti~g~lPl~~~~g 1000 (1051)
T TIGR00914       922 ALWLRGIPLSISAAVGFIALSGVAVLNGLVMISFIRKLLEEGPSLDEAVYEGALTRVRPVLMTALVASLGFVPMAIATG 1000 (1051)
T ss_pred             HHHHhCCCccHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHcCCCHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhcCC
Confidence            778899999999999999999999999999998776432  2 234667888888999999999999999999999863

This model represents a family of H+/heavy metal cation antiporters. This family is one of several subfamilies within the scope of pfam model pfam00873.

>PRK08343 secD preprotein translocase subunit SecD; Reviewed

Probab=97.64  E-value=0.00019  Score=66.94  Aligned_cols=82  Identities=16%  Similarity=0.093  Sum_probs=67.0

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcccC-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccchh
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIG-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQFI  175 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~~~  175 (197)
                      +|.++|..||-.+.+-+++++|++||-.+.+.....+... +.++-++...++..+|++.+.+||++|.+||++..+..+
T Consensus       305 ~l~l~g~tLtl~~IaGlIl~iGmaVD~~IvI~e~i~~~~~~~~~~ai~~g~~~a~~~Il~t~lTTiia~lpL~~~g~g~i  384 (417)
T PRK08343        305 FAALIGWQLDLASIAGIIAVIGTGVDDLIIITDEVLHEGKVPSRKVFLSRIKRAFFIIFAAAATTIAAMSPLAVMGLGDL  384 (417)
T ss_pred             HHHHHCCCccHHHHHHHHHHHHHeeeCcEEEhHHHHHhCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccc
Confidence            6789999999999999999999999999988854443322 334557888889999999999999999999998765554


Q ss_pred             HHH
Q psy8507         176 LRI  178 (197)
Q Consensus       176 ~~~  178 (197)
                      +-|
T Consensus       385 kgf  387 (417)
T PRK08343        385 KGF  387 (417)
T ss_pred             cch
Confidence            443

>PRK14726 bifunctional preprotein translocase subunit SecD/SecF; Provisional

Probab=97.64  E-value=0.00013  Score=73.47  Aligned_cols=97  Identities=16%  Similarity=0.114  Sum_probs=78.4

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhccc--C-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCI--G-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQ  173 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~--~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~  173 (197)
                      +|+++|..||..+..-++++||++||-++.|.-......  + +..+-+..+.++.+.|++.+.+||+++.++|.+-...
T Consensus       414 ~l~l~g~tLnl~~IaGiil~IGm~VD~~IVI~ErIreel~~G~s~~~Ai~~g~~~a~~~Il~s~lTTlia~lpL~~~g~~  493 (855)
T PRK14726        414 VLSLLGATLTLPGIAGIVLTIGMAVDSNVLIYERIREEEKTGHSLIQALDRGFSRALATIVDANVTILIAAVILFFLGSG  493 (855)
T ss_pred             HHHHhCcceeHHHHHHHHHHHHhhhCceEEeHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCc
Confidence            899999999999999999999999999999988776532  2 3336688999999999999999999999999999887


Q ss_pred             hhHHHHHHHHHHHHHHHhhhh
Q psy8507         174 FILRIFFYMLFGIVLVGLLYM  194 (197)
Q Consensus       174 ~~~~~FF~~~~~vi~~G~~hG  194 (197)
                      .++-| ..++.+-++.+++-.
T Consensus       494 ~ikgF-Avtl~igii~Sl~~A  513 (855)
T PRK14726        494 AVRGF-AVTLAVGILTTVFTA  513 (855)
T ss_pred             chHHH-HHHHHHHHHHHHHHH
Confidence            76654 344444445555443

>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]

Probab=97.59  E-value=0.00018  Score=73.71  Aligned_cols=93  Identities=15%  Similarity=0.183  Sum_probs=72.3

Q ss_pred             HHHHHHhccccchhhHHHHhhhhcceeeehHHHH----hHhhcccCChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcc
Q psy8507          95 LLVMYLMNIKLNPISCVLIVNSSGIYIHFISYIC----LSFLTCIGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFS  170 (197)
Q Consensus        95 f~~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~----~~F~~s~~~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs  170 (197)
                      |.+|+++|.+||-+|+..|++|||+-||=+.-+.    ++ +. ..+..+-+.++.++++.|++.+.++++...+|++|.
T Consensus       371 f~~m~~~GfslN~lTL~aLiLAiGllVDDAIVVvENI~R~-~~-G~~p~~Aa~~a~~ei~~~via~TlvliaVF~Pi~f~  448 (1009)
T COG0841         371 FAVMYAFGFSLNTLTLFALVLAIGLLVDDAIVVVENIERH-MR-GLPPREAAEKAMGEIGGAVIAITLVLIAVFLPMAFM  448 (1009)
T ss_pred             HHHHHHhCccchHhHHHHHHHhhheeEeccEEEEeeEEee-cC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            4499999999999999999999999999876433    32 33 334458899999999999999999999999999999


Q ss_pred             ccchhHHHHHHHHHHHHHHHh
Q psy8507         171 EFQFILRIFFYMLFGIVLVGL  191 (197)
Q Consensus       171 ~s~~~~~~FF~~~~~vi~~G~  191 (197)
                      +.-.- .| |+-+.+++.+++
T Consensus       449 ~G~~G-~~-f~~f~~tia~a~  467 (1009)
T COG0841         449 GGSTG-EL-FRQFAITIAVAM  467 (1009)
T ss_pred             CCcHH-HH-HHHHHHHHHHHH
Confidence            96432 22 344444444443

>PF02355 SecD_SecF: Protein export membrane protein; InterPro: IPR022813 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway

Probab=97.58  E-value=0.00033  Score=58.74  Aligned_cols=100  Identities=19%  Similarity=0.110  Sum_probs=75.2

Q ss_pred             HHHHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc-----cCChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhc
Q psy8507          95 LLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC-----IGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAF  169 (197)
Q Consensus        95 f~~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s-----~~~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~f  169 (197)
                      +.+|++.|+++|.-+...+++.+|.|||-+.=+.-.....     .++.++.+.+++.+.....+.+.++|++.+++|.+
T Consensus        72 l~~~~~~~~~l~l~~iaall~~iG~sVd~~IVifdRIre~~~~~~~~~~~~~~~~s~~~tl~r~i~t~~ttll~~~~L~~  151 (189)
T PF02355_consen   72 LGIFSLFGIELTLPSIAALLTIIGYSVDDNIVIFDRIREELRASRGKSLREAINISIKQTLSRTIDTSLTTLLAALILFF  151 (189)
T ss_dssp             HHHHHHHT-EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-STS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCcccHHHHHHHHHHHHHHHhcceeehHHHHHHhhhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3499999999999999999999999999998877666544     22334888999999999999999999999999988


Q ss_pred             cccchhHHHHHHHHHHHHHHHhhhhh
Q psy8507         170 SEFQFILRIFFYMLFGIVLVGLLYMV  195 (197)
Q Consensus       170 s~s~~~~~~FF~~~~~vi~~G~~hGL  195 (197)
                      -....++.|- .++++-++.|++..+
T Consensus       152 ~g~~~l~~Fa-~~l~iGvi~~~~ss~  176 (189)
T PF02355_consen  152 FGGGSLKGFA-LTLIIGVIIGTYSSL  176 (189)
T ss_dssp             C--CHHHHHH-HHHHHHHHHHHHHHH
T ss_pred             hccchHHHHH-HHHHHHHHHHHHHHH
Confidence            8877777654 444444555555443

Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. The chaperone protein SecB [] is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion []. Together with SecY and SecG, SecE forms a multimeric channel through which preproteins are translocated, using both proton motive forces and ATP-driven secretion. The latter is mediated by SecA. The structure of the Escherichia coli SecYEG assembly revealed a sandwich of two membranes interacting through the extensive cytoplasmic domains []. Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices. The SecD and SecF equivalents of the Gram-positive bacterium Bacillus subtilis are jointly present in one polypeptide, denoted SecDF, that is required to maintain a high capacity for protein secretion. Unlike the SecD subunit of the pre-protein translocase of E. coli, SecDF of B. subtilis was not required for the release of a mature secretory protein from the membrane, indicating that SecDF is involved in earlier translocation steps []. Comparison with SecD and SecF proteins from other organisms revealed the presence of 10 conserved regions in SecDF, some of which appear to be important for SecDF function. Interestingly, the SecDF protein of B. subtilis has 12 putative transmembrane domains. Thus, SecDF does not only show sequence similarity but also structural similarity to secondary solute transporters []. This entry represents bacterial SecD and SecF protein export membrane proteins and their archaeal homologues []. It is found in association with PF07549 from PFAM SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC []. SecD and SecF are required to maintain a proton motive force []. ; PDB: 3AQP_A 2RRN_A 3AQO_B.

>TIGR00917 2A060601 Niemann-Pick C type protein family

Probab=97.53  E-value=0.0004  Score=72.30  Aligned_cols=85  Identities=12%  Similarity=0.062  Sum_probs=67.7

Q ss_pred             HHHHHHHhccccchh-hHHHHhhhhcceeeehHHHHhHhhccc----C---------ChhHHHHHHHHHHhHHHHHHHHH
Q psy8507          94 LLLVMYLMNIKLNPI-SCVLIVNSSGIYIHFISYICLSFLTCI----G---------NRDRRVRLSIEHMYSVVLHAGLI  159 (197)
Q Consensus        94 ~f~~M~l~gi~Ln~i-S~v~Li~sIG~sVDFtaHI~~~F~~s~----~---------~~~~R~~~aL~~~G~pVl~ga~S  159 (197)
                      .+++|++.|++++++ +.+.=.+.+|++||..-.+.++|.+..    +         +.++|+.++|+++|.||+..++|
T Consensus       622 s~Gl~~~~Gi~~t~i~~~v~PFLvL~IGVD~ifilv~~~~r~~~~~~~~~~~~~~~~~~~~ri~~~l~~~G~sI~ltslt  701 (1204)
T TIGR00917       622 SVGVFSYIGLKATLIIMEVIPFLVLAVGVDNIFILVQTYQRLERFYREVGVDNEQELTLEQQLGRALGEVGPSITLASLS  701 (1204)
T ss_pred             HHHHHHHhCCcchHHHHHHHHHHHHHHHhhHHHHHHHHHHHhhhccccccccccccCCHHHHHHHHHHHhhHHHHHHHHH
Confidence            477999999999976 555545555666797666666665421    1         34599999999999999999999


Q ss_pred             HHHHHHHhhccccchhHHH
Q psy8507         160 LLVAISILAFSEFQFILRI  178 (197)
Q Consensus       160 T~lgv~~L~fs~s~~~~~~  178 (197)
                      +.+|.+..++++..-++.|
T Consensus       702 ~~~aF~~g~~s~~Pavr~F  720 (1204)
T TIGR00917       702 ESLAFFLGALSKMPAVRAF  720 (1204)
T ss_pred             HHHHHHHHhccCChHHHHH
Confidence            9999999999998887764

The model describes Niemann-Pick C type protein in eukaryotes. The defective protein has been associated with Niemann-Pick disease which is described in humans as autosomal recessive lipidosis. It is characterized by the lysosomal accumulation of unestrified cholesterol. It is an integral membrane protein, which indicates that this protein is most likely involved in cholesterol transport or acts as some component of cholesterol homeostasis.

>TIGR00833 actII Transport protein

Probab=97.47  E-value=0.00054  Score=69.20  Aligned_cols=80  Identities=13%  Similarity=0.103  Sum_probs=64.2

Q ss_pred             ccccch-hhHHHHhhhhcceeeehHHHHhHhhcccCC-hhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccchhHHHH
Q psy8507         102 NIKLNP-ISCVLIVNSSGIYIHFISYICLSFLTCIGN-RDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQFILRIF  179 (197)
Q Consensus       102 gi~Ln~-iS~v~Li~sIG~sVDFtaHI~~~F~~s~~~-~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~~~~~~F  179 (197)
                      |..++. ++.+..++-+|+++||++|+...|....+. .++.+..++.+.|.||+.+++++..+...|.+++...++.+-
T Consensus       798 g~~l~~~~~~~~~~il~glgvDY~I~l~sR~ree~~~g~~~av~~a~~~tg~~I~~a~~~~~~~f~~l~~s~~~~l~~~G  877 (910)
T TIGR00833       798 GAELHWSVLAGVFVLLVALGVDYNMLLVSRIKEESPAGNRTGIIRALGSTGGVITAAGLVFAGTMAALASAQLTAIAQFG  877 (910)
T ss_pred             CCCcchhHHHHHHHHHHHhhhchHHHHHHHHHHHHhcCccHHHHHHHHHhHHHHHHHHHHHHHHHHHHHhcchHHHHHHH
Confidence            344554 555656777999999999999999865422 346789999999999999999999999999999988777654


Q ss_pred             HH
Q psy8507         180 FY  181 (197)
Q Consensus       180 F~  181 (197)
                      +-
T Consensus       878 ~~  879 (910)
T TIGR00833       878 FT  879 (910)
T ss_pred             HH
Confidence            33

Characterized members of the RND superfamily all probably catalyze substrate efflux via an H+ antiport mechanism. These proteins are found ubiquitously in bacteria, archaea and eukaryotes. This sub-family includes the S. coelicolor ActII3 protein, which may play a role in drug resistance, and the M. tuberculosis MmpL7 protein, which catalyzes export of an outer membrane lipid, phthiocerol dimycocerosate.

>PRK15127 multidrug efflux system protein AcrB; Provisional

Probab=97.44  E-value=0.00019  Score=73.44  Aligned_cols=98  Identities=10%  Similarity=-0.029  Sum_probs=78.0

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc---cC-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC---IG-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEF  172 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s---~~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s  172 (197)
                      .|.++|.+||..|++-+++.+|+.||-+..+.-.....   .| +..+-+.+|-.....||+..++||++|++||+++..
T Consensus       915 ~l~~~g~~l~~~sl~Gli~l~GivV~naIvlvd~~~~~~~~~G~~~~~Ai~~a~~~R~rPIlmTtlTti~gllPl~l~~G  994 (1049)
T PRK15127        915 AATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLEAVRMRLRPILMTSLAFILGVMPLVISSG  994 (1049)
T ss_pred             HHHHhCCCccHHHHHHHHHHHHHHHcCeEEEeHHHHHHHHhcCCCHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhcCC
Confidence            88899999999999999999999999998887766532   23 344778999999999999999999999999999864


Q ss_pred             chhHHHHHHHHHHHHHHHhhhhhc
Q psy8507         173 QFILRIFFYMLFGIVLVGLLYMVL  196 (197)
Q Consensus       173 ~~~~~~FF~~~~~vi~~G~~hGLv  196 (197)
                      .-- . +++-+..+++.|++-+.+
T Consensus       995 ~g~-~-~~~plai~ii~GL~~St~ 1016 (1049)
T PRK15127        995 AGS-G-AQNAVGTGVMGGMVTATV 1016 (1049)
T ss_pred             CCH-H-HhcCchhhhhHHHHHHHH
Confidence            321 2 245566667777665543

>PF02460 Patched: Patched family; InterPro: IPR003392 The transmembrane protein, patched, is a receptor for the morphogene Sonic Hedgehog

Probab=97.42  E-value=0.00044  Score=68.55  Aligned_cols=85  Identities=14%  Similarity=0.149  Sum_probs=76.5

Q ss_pred             HHHHHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcccCCh--hHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccc
Q psy8507          94 LLLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGNR--DRRVRLSIEHMYSVVLHAGLILLVAISILAFSE  171 (197)
Q Consensus        94 ~f~~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~~~~--~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~  171 (197)
                      .|+++.+.|++.+++..+.--+.+|++||-.-.+.++|.+.....  +||+.+++++.|.++.-.++|..++..+-++++
T Consensus       266 ~~Gl~~~~G~~~~~i~~v~PFLvlgIGvDd~Fi~~~~~~~~~~~~~~~er~~~~l~~~g~SitiTslT~~~aF~ig~~t~  345 (798)
T PF02460_consen  266 SFGLLSLFGVPFNPIVLVIPFLVLGIGVDDMFIMIHAWRRTSPDLSVEERMAETLAEAGPSITITSLTNALAFAIGAITP  345 (798)
T ss_pred             HHHHHHHcCccchhhHHHHHHHHHHHHHhceEEeHHHHhhhchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            377999999999999999888899999999999999998776543  499999999999999999999999999999999


Q ss_pred             cchhHHH
Q psy8507         172 FQFILRI  178 (197)
Q Consensus       172 s~~~~~~  178 (197)
                      ...++.|
T Consensus       346 ~pav~~F  352 (798)
T PF02460_consen  346 IPAVRSF  352 (798)
T ss_pred             cHHHHHH
Confidence            9887764

In Drosophila melanogaster, this protein associates with the smoothened protein to transduce hedgehog signals, leading to the activation of wingless, decapentaplegic and patched itself. It participates in cell interactions that establish pattern within the segment and imaginal disks during development. The mouse homologue may play a role in epidermal development. The human Niemann-Pick C1 protein, defects in which cause Niemann-Pick type II disease, is also a member of this family. This protein is involved in the intracellular trafficking of cholesterol, and may play a role in vesicular trafficking in glia, a process that may be crucial for maintaining the structural functional integrity of nerve terminals.; GO: 0008158 hedgehog receptor activity, 0016020 membrane

>PRK12933 secD preprotein translocase subunit SecD; Reviewed

Probab=97.27  E-value=0.00094  Score=65.06  Aligned_cols=98  Identities=11%  Similarity=0.048  Sum_probs=75.8

Q ss_pred             HHHHh-ccccchhhHHHHhhhhcceeeehHHHHhHhh---cccCChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccc
Q psy8507          97 VMYLM-NIKLNPISCVLIVNSSGIYIHFISYICLSFL---TCIGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEF  172 (197)
Q Consensus        97 ~M~l~-gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~---~s~~~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s  172 (197)
                      +|+++ |..||-.+..-+++++|++||-.+=|.-.-.   ...++..+-+..+..+..+|++.+.+||+++.++|.+-..
T Consensus       482 vmsll~G~tLtLpgIAGiILtIGmaVDanIVI~ERIrEel~~G~s~~~Ai~~G~~~a~~~IldanlTTlia~lpL~~~Gg  561 (604)
T PRK12933        482 LLALIPGAVLTLPGIAGLVLTVGMAVDTNVLIFERIKDKLKEGRSFAQAIDTGFDSAFSTIFDANFTTMITAVVLYSIGN  561 (604)
T ss_pred             HHHHHhCCcccHHHHHHHHHHHHhhccCcEEEehHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            89998 9999999999999999999999986554442   2222344778899999999999999999999999988887


Q ss_pred             chhHHHHHHHHHHHHHHHhhhhh
Q psy8507         173 QFILRIFFYMLFGIVLVGLLYMV  195 (197)
Q Consensus       173 ~~~~~~FF~~~~~vi~~G~~hGL  195 (197)
                      -.++-| ..++.+-++.+++-++
T Consensus       562 g~ikgF-AvTL~iGIl~S~ftAi  583 (604)
T PRK12933        562 GPIQGF-ALTLGLGLLTSMFTGI  583 (604)
T ss_pred             ccchHH-HHHHHHHHHHHHHHHH
Confidence            666654 3444444555555443

>TIGR00918 2A060602 The Eukaryotic (Putative) Sterol Transporter (EST) Family

Probab=97.27  E-value=0.00085  Score=69.57  Aligned_cols=85  Identities=14%  Similarity=0.098  Sum_probs=74.2

Q ss_pred             HHHHHHHhccccchhh-HHHHhhhhcceeeehHHHHhHhhcccC--ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcc
Q psy8507          94 LLLVMYLMNIKLNPIS-CVLIVNSSGIYIHFISYICLSFLTCIG--NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFS  170 (197)
Q Consensus        94 ~f~~M~l~gi~Ln~iS-~v~Li~sIG~sVDFtaHI~~~F~~s~~--~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs  170 (197)
                      .++++++.|++.|++. .|.=-+.+|++||..-++.++|.+...  +-++|+.++|.++|.+|+..++|+.++..+.+++
T Consensus       444 s~Gl~~~~Gi~fn~i~~~ViPFLvLgIGVDn~Fllv~~~~~t~~~~~v~~r~~~~l~~~g~SI~~tslt~~~aF~~ga~t  523 (1145)
T TIGR00918       444 GLGLCALLGISFNAATTQVLPFLALGVGVDDVFLLAHAFSETGQNIPFEERTGECLKRTGASVVLTSISNVTAFFMAALI  523 (1145)
T ss_pred             HHHHHHHhCCchhHHHHhhhhHHHhhhhhcchhHHHHHHhhcCccCCHHHHHHHHHHHhcceeeHHHHHHHHHHHHHhcC
Confidence            4779999999999985 666677899999999999999976543  2349999999999999999999999999999999


Q ss_pred             ccchhHHH
Q psy8507         171 EFQFILRI  178 (197)
Q Consensus       171 ~s~~~~~~  178 (197)
                      +..-++.|
T Consensus       524 ~~Pavr~F  531 (1145)
T TIGR00918       524 PIPALRAF  531 (1145)
T ss_pred             CCHHHHHH
Confidence            98877764

>TIGR00915 2A0602 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family

Probab=97.24  E-value=0.00054  Score=70.14  Aligned_cols=98  Identities=12%  Similarity=-0.022  Sum_probs=77.2

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc--cC-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC--IG-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQ  173 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s--~~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~  173 (197)
                      .+.++|.+||..|++-+++.+|+.|+-+.++.-.+...  +| +.++-+.+|-..-..||+..++||++|++||+++...
T Consensus       914 ~l~~~g~~l~~~sl~G~i~l~GivVnnaIvlvd~~~~~~~~G~~~~~Ai~~a~~~RlRPIlmTtltti~gllPla~~~g~  993 (1044)
T TIGR00915       914 ATSLRGLSNDVYFQVGLLTTIGLSAKNAILIVEFAKELMAQGKSIVEAALEAARMRLRPILMTSLAFILGVVPLAISTGA  993 (1044)
T ss_pred             HHHHHCCCccHHHHHHHHHHHHHHHcceEeeHHHHHHHHHcCCCHHHHHHHHHHhhhchHHHHHHHHHHHHHHHHHhcCC
Confidence            67779999999999999999999999999988876533  23 3447788888999999999999999999999997532


Q ss_pred             hhHHHHHHHHHHHHHHHhhhhhc
Q psy8507         174 FILRIFFYMLFGIVLVGLLYMVL  196 (197)
Q Consensus       174 ~~~~~FF~~~~~vi~~G~~hGLv  196 (197)
                       --. +++-+-.+++.|++-+.+
T Consensus       994 -g~~-~~~plai~vigGL~~st~ 1014 (1044)
T TIGR00915       994 -GSG-SQHAIGTGVFGGMVTATV 1014 (1044)
T ss_pred             -ChH-HhCccHHHHHHHHHHHHH
Confidence             112 245566667777765543

This family is one of several subfamilies within the scope of pfam model pfam00873.

>PRK13024 bifunctional preprotein translocase subunit SecD/SecF; Reviewed

Probab=97.18  E-value=0.0015  Score=65.02  Aligned_cols=95  Identities=16%  Similarity=0.161  Sum_probs=77.8

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhccc-----CChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCI-----GNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSE  171 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~-----~~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~  171 (197)
                      +|++.|+++|...+..+++.+|+|||.++++--.+....     ++-++.+..++.+.+.+.+...+||++++++|.+..
T Consensus       620 ~~~l~~~~~~~~~iaall~iiGysvndtIvi~dRirE~~~~~~~~~~~~~v~~si~~tl~rti~ts~tt~~~~~~L~~~g  699 (755)
T PRK13024        620 FFSLFRLEVDLTFIAAILTIIGYSINDTVVVFDRIRENLRLYKKKDLREIVNKSINQTLSRTINTSLTTLLVLLALLIFG  699 (755)
T ss_pred             HHHHhcceEcHHHHHHHHHHHhheeeceEEEEhHHHHHhhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            999999999999999999999999999999988886532     223477889999999999999999999999999887


Q ss_pred             cchhHHHHHHHHHHHHHHHhh
Q psy8507         172 FQFILRIFFYMLFGIVLVGLL  192 (197)
Q Consensus       172 s~~~~~~FF~~~~~vi~~G~~  192 (197)
                      ...++-|-+.+++. ++.|..
T Consensus       700 ~~~i~~fa~~l~iG-ii~g~~  719 (755)
T PRK13024        700 GSSLRNFSLALLVG-LIVGTY  719 (755)
T ss_pred             CchHHHHHHHHHHH-HHHHHH
Confidence            77777754443333 445544

>PRK12911 bifunctional preprotein translocase subunit SecD/SecF; Reviewed

Probab=97.08  E-value=0.0011  Score=69.10  Aligned_cols=95  Identities=12%  Similarity=0.111  Sum_probs=72.0

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc---cCChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC---IGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQ  173 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s---~~~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~  173 (197)
                      +|.++|+.||..++.-++++||++||-++-|.-.....   .++..+-+..+..+..+|++.+.+||+++.++|.+....
T Consensus       951 ~LsLlGitLTLpgIAGIILlIGmAVDdnIVIfERIREELr~Gksl~eAI~~G~~~afs~ILdTnLTTLIA~lPLf~fGtG 1030 (1403)
T PRK12911        951 ALQYLDAPLTLSGLAGIVLAMGMAVDANVLVFERIREEYLLSRSLSESVEAGYKKAFSAIFDSNLTTILASALLLMLDTG 1030 (1403)
T ss_pred             HHHHHCCCchHHHHHHHHHHHHHhhcCCEEEehHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            88999999999999999999999999998777554332   223347788999999999999999999999999665554


Q ss_pred             hhHHHHHHHHHHHHHHHhh
Q psy8507         174 FILRIFFYMLFGIVLVGLL  192 (197)
Q Consensus       174 ~~~~~FF~~~~~vi~~G~~  192 (197)
                      .++-| ..++++-++.|++
T Consensus      1031 ~vkgF-AvTLiIGII~Smf 1048 (1403)
T PRK12911       1031 PIKGF-ALTLIIGIFSSMF 1048 (1403)
T ss_pred             ccccH-HHHHHHHHHHHHH
Confidence            44543 2333333344443

>PRK10503 multidrug efflux system subunit MdtB; Provisional

Probab=97.08  E-value=0.0017  Score=66.57  Aligned_cols=98  Identities=15%  Similarity=0.033  Sum_probs=72.0

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhh---cccC-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFL---TCIG-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEF  172 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~---~s~~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s  172 (197)
                      .|.+.|.+||..|++-+++.+|+.||-+.=+.-...   +..| +.+|-+.+|-+....||+..++||++|.+||+++..
T Consensus       908 ~l~l~g~~l~~~sliGli~l~GivV~naIvlvd~~~~~~~~~G~~~~eAi~~a~~~R~rPIlmTtltti~gllPlal~~G  987 (1040)
T PRK10503        908 ALMIAGSELDVIAIIGIILLIGIVKKNAIMMIDFALAAEREQGMSPRDAIYQACLLRFRPILMTTLAALLGALPLMLSTG  987 (1040)
T ss_pred             HHHHhCCCccHHHHHHHHHHHHHHHcCeEEEehHHhHHHHHcCCCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcC
Confidence            788899999999999999999996655443332111   1234 345788999999999999999999999999999863


Q ss_pred             chhHHHHHHHHHHHHHHHhhhhhc
Q psy8507         173 QFILRIFFYMLFGIVLVGLLYMVL  196 (197)
Q Consensus       173 ~~~~~~FF~~~~~vi~~G~~hGLv  196 (197)
                      .- -- +++-+..+++.|++-+.+
T Consensus       988 ~g-~e-~~~pla~~ii~GL~~St~ 1009 (1040)
T PRK10503        988 VG-AE-LRRPLGICMVGGLIVSQV 1009 (1040)
T ss_pred             CC-hH-HhCcchHHHHHHHHHHHH
Confidence            31 12 246666667777665543

>PRK10555 aminoglycoside/multidrug efflux system; Provisional

Probab=96.91  E-value=0.0022  Score=65.72  Aligned_cols=98  Identities=10%  Similarity=-0.030  Sum_probs=75.2

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhc--ccC-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLT--CIG-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQ  173 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~--s~~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~  173 (197)
                      .|.+.|.+||..+++-+++.+|+.|+-+.=+.-....  ..| +.++-+.+|-.....||+..++||++|++||+++...
T Consensus       913 ~L~i~g~~l~~~sl~Gli~l~GivV~naIvlvd~i~~~~~~G~~~~~Ai~~A~~~RlRPIlmTtltti~gllPlal~~g~  992 (1037)
T PRK10555        913 ATWMRGLENDVYFQVGLLTVIGLSAKNAILIVEFANEMNQKGHDLFEATLHASRQRLRPILMTSLAFIFGVLPMATSTGA  992 (1037)
T ss_pred             HHHHhCCCccHHHHHHHHHHHHHHHcCeEEeHHHHHHHHHcCCCHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHhcCC
Confidence            7888999999999999999999999987655443332  222 3457788899999999999999999999999998643


Q ss_pred             hhHHHHHHHHHHHHHHHhhhhhc
Q psy8507         174 FILRIFFYMLFGIVLVGLLYMVL  196 (197)
Q Consensus       174 ~~~~~FF~~~~~vi~~G~~hGLv  196 (197)
                      -- . +++-+-.+++.|++-+.+
T Consensus       993 g~-~-~~~pla~~ii~GL~~St~ 1013 (1037)
T PRK10555        993 GS-G-SQHAVGTGVMGGMISATI 1013 (1037)
T ss_pred             Ch-H-HhcccHHHHHHHHHHHHH
Confidence            21 2 246666667777766543

>PRK13021 secF preprotein translocase subunit SecF; Reviewed

Probab=96.63  E-value=0.0084  Score=53.81  Aligned_cols=93  Identities=11%  Similarity=0.023  Sum_probs=71.6

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhccc----C-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCI----G-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSE  171 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~----~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~  171 (197)
                      ++.+.|.++|.-+.+-+++-+|.||+-+.=+--.+....    + +.+|-+.+|....-.|++..++||++|++||++.-
T Consensus       169 ~l~l~g~~l~~~~iaglLtliG~svnd~IVi~drire~~~~~~~~~~~e~i~~ai~~~lrr~l~TslTt~l~llpL~l~G  248 (297)
T PRK13021        169 FFALTQMEFNLTVLAAVLAILGYSLNDSIIIADRIRELLIAKPKLAIQEINNQAIVATFSRTMVTSGTTLMTVGALWIMG  248 (297)
T ss_pred             HHHHHCCCccHHHHHHHHHHHHHeeeCCEEEeeHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            788899999999999999999999998876655554221    1 33477889999999999999999999999999876


Q ss_pred             cchhHHHHHHHHHHHHHHHhhhh
Q psy8507         172 FQFILRIFFYMLFGIVLVGLLYM  194 (197)
Q Consensus       172 s~~~~~~FF~~~~~vi~~G~~hG  194 (197)
                      ....+-|     ...++.|++-|
T Consensus       249 ~~~~~~f-----A~~li~Gli~g  266 (297)
T PRK13021        249 GGPLEGF-----SIAMFIGILTG  266 (297)
T ss_pred             hhhHHHH-----HHHHHHHHHHH
Confidence            5555543     33344554443

>PRK09577 multidrug efflux protein; Reviewed

Probab=96.37  E-value=0.0052  Score=63.03  Aligned_cols=96  Identities=13%  Similarity=-0.056  Sum_probs=72.1

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc--cC-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC--IG-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQ  173 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s--~~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~  173 (197)
                      .+.+.|.+||..+++-+++.+|+.|+-+.++.-.....  +| +.++-+.+|-..-..||+..++||++|++||+++.-.
T Consensus       909 ~l~l~g~~l~~~s~~G~i~L~GivVnnaIllvd~~~~~~~~G~~~~~Ai~~a~~~R~RPIlmTtltti~gllPla~~~g~  988 (1032)
T PRK09577        909 GVTLRGMPNDIYFKVGLIATIGLSAKNAILIVEVAKDLVAQRMSLADAALEAARLRLRPIVMTSLAFGVGVLPLAFASGA  988 (1032)
T ss_pred             HHHHhCCCccHHHHHHHHHHHHHHHcCcEEEeHHHHHHHHcCCCHHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHccCC
Confidence            45556999999999999999999999988877655432  22 3447788888999999999999999999999998532


Q ss_pred             hhHHHHHHHHHHHHHHHhhhh
Q psy8507         174 FILRIFFYMLFGIVLVGLLYM  194 (197)
Q Consensus       174 ~~~~~FF~~~~~vi~~G~~hG  194 (197)
                      =-.  +.+-+-.+++.|++-+
T Consensus       989 g~~--~~~pla~~iigGL~~s 1007 (1032)
T PRK09577        989 ASG--AQIAIGTGVLGGVITA 1007 (1032)
T ss_pred             ChH--HhcCchhhhhhhHHHH
Confidence            111  1344555556665544

>PRK14726 bifunctional preprotein translocase subunit SecD/SecF; Provisional

Probab=96.25  E-value=0.018  Score=58.43  Aligned_cols=82  Identities=16%  Similarity=0.088  Sum_probs=67.0

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhccc----C-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCI----G-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSE  171 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~----~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~  171 (197)
                      +|++.|+++|..+.+.+++-+|+||+.+..+.-.+....    + +-.+....++.....-++..++||++|+++|++..
T Consensus       715 ~~~l~g~~ls~~~iaglLtliGysvndtIVi~DRIrE~~~~~~~~~~~~~~~~si~~tl~Rii~TslTTll~llpL~l~G  794 (855)
T PRK14726        715 LFVLTGIEFNLTSIAAILTIVGYSLNDTVVVYDRVRENLRRYKKMPLPILIDASINQTLSRTVLTSATTLLALLALYLFG  794 (855)
T ss_pred             HHHHHCCCccHHHHHHHHHHHHHeeeCcEEEehHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            899999999999999999999999999999988875322    2 11256667777777779999999999999999986


Q ss_pred             cchhHHH
Q psy8507         172 FQFILRI  178 (197)
Q Consensus       172 s~~~~~~  178 (197)
                      ....+.|
T Consensus       795 ~~~i~~f  801 (855)
T PRK14726        795 GEVIRSF  801 (855)
T ss_pred             chhHHHH
Confidence            6655554

>PRK09579 multidrug efflux protein; Reviewed

Probab=96.07  E-value=0.0076  Score=61.76  Aligned_cols=75  Identities=15%  Similarity=0.076  Sum_probs=61.4

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhh---cccC-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFL---TCIG-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSE  171 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~---~s~~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~  171 (197)
                      .+.+.|.+||..+++-+++.+|+.|+-+.-+...+.   ...| +.++-+.+|-.....||+..++||++|++||++..
T Consensus       888 ~L~i~~~~l~~~s~~G~i~L~GivVnnaIllvd~~~~~r~~~G~~~~~Ai~~a~~~R~RPIlmTtlTti~gllPla~~~  966 (1017)
T PRK09579        888 PLFLGVSSMNIYTQVGLVTLIGLISKHGILIVEFANQLRHEQGLSRREAIEEAAAIRLRPVLMTTAAMVFGMVPLILAT  966 (1017)
T ss_pred             HHHHhCCCccHHHHHHHHHHHHHHHcCcEEehHHHHHHHHhcCCCHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhc
Confidence            556778899999999999999999999985544332   2233 34577888999999999999999999999999974

>PF00873 ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR001036 The Escherichia coli acrA and acrB genes encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors []

Probab=95.86  E-value=0.023  Score=57.92  Aligned_cols=97  Identities=15%  Similarity=0.138  Sum_probs=74.8

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc---cCC-hhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC---IGN-RDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEF  172 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s---~~~-~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s  172 (197)
                      .+.+.|.+||..|++-+++-+|+.|.-+.=+.-.+...   .|. ..|-+.+|-..-..||+..++||++|++||+++..
T Consensus       906 ~l~i~g~~l~~~s~iG~i~L~GIvVnNaIllvd~~~~~~~~~g~~~~eAi~~a~~~RlRPIlmTtlTti~G~lPla~~~g  985 (1021)
T PF00873_consen  906 GLFITGQPLSFMSLIGIIALIGIVVNNAILLVDFINELRKREGMPLEEAIIEAARSRLRPILMTTLTTILGMLPLALGIG  985 (1021)
T ss_dssp             HHHHTTBEBSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-S
T ss_pred             HHhhccccccccceehHHHHHHHHHhhhHHHHHHHHHHhhhccccHHHHHHHHHHHHHHHHHHHHhhhhccccccccccC
Confidence            77888999999999999999999998887666555432   233 33777888888889999999999999999999875


Q ss_pred             chhHHHHHHHHHHHHHHHhhhhh
Q psy8507         173 QFILRIFFYMLFGIVLVGLLYMV  195 (197)
Q Consensus       173 ~~~~~~FF~~~~~vi~~G~~hGL  195 (197)
                      .=-.  +.+-+..+++.|++-+.
T Consensus       986 ~g~~--~~~pla~~iigGL~~st 1006 (1021)
T PF00873_consen  986 EGAE--FWQPLAIVIIGGLLFST 1006 (1021)
T ss_dssp             TTHH--HHHHHHHHHHHHHHHHH
T ss_pred             CCcc--ccCchhhHHHHHHHHHH
Confidence            3211  34667777788876654

The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents. The structure of ligand-free AcrB shows that it is a homotrimer of 110kDa per subunit. Each subunit contains 12 transmembrane helices and two large periplasmic domains (each exceeding 300 residues) between helices 1 and 2, and helices 7 and 8. X-ray analysis of the overexpressed AcrB protein demonstrated that the three periplasmic domains form, in the centre, a funnel-like structure and a connected narrow (or closed) pore. The pore is opened to the periplasm through three vestibules located at subunit interfaces. These vestibules were proposed to allow direct access of drugs from the periplasm as well as the outer leaflet of the cytoplasmic membrane. The three transmembrane domains of AcrB protomers form a large, 30A-wide central cavity that spans the cytoplasmic membrane and extends to the cytoplasm X-ray crystallographic structures of the trimeric AcrB pump from E. coli with four structurally diverse ligands demonstrated that three molecules of ligand bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilising the binding. ; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2V50_B 1T9U_A 2HRT_B 3NOC_A 3NOG_A 4DX7_A 1OYD_A 3AOB_A 1T9V_A 4DX6_B ....

>PRK10614 multidrug efflux system subunit MdtC; Provisional

Probab=95.55  E-value=0.021  Score=58.56  Aligned_cols=96  Identities=15%  Similarity=0.016  Sum_probs=70.0

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhc--cc-C-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLT--CI-G-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEF  172 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~--s~-~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s  172 (197)
                      .+.++|.+||-.|++-+++.+|+.|+-+.=+.-.+..  .. | +.++-+.+|-..-..||+..++||++|++||+++..
T Consensus       894 ~L~l~g~~l~~~s~iG~i~L~GIvvnNaIllvd~~~~~~~~~g~~~~~Aii~A~~~RlRPIlmTtlTti~GllPlal~~g  973 (1025)
T PRK10614        894 ALELFNAPFSLIALIGIMLLIGIVKKNAIMMVDFALEAQRNGNLTAQEAIFQACLLRFRPIMMTTLAALFGALPLVLSGG  973 (1025)
T ss_pred             HHHHHCCCccHHHHHHHHHHHHHHHcCeEEehHHHHHHHHhcCCCHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhcC
Confidence            7778899999999999999999999877665433221  12 2 334667778888889999999999999999999753


Q ss_pred             chhHHHHHHHHHHHHHHHhhhh
Q psy8507         173 QFILRIFFYMLFGIVLVGLLYM  194 (197)
Q Consensus       173 ~~~~~~FF~~~~~vi~~G~~hG  194 (197)
                      .=- . +++-+-.+++.|++-+
T Consensus       974 ~g~-~-~~~pmAi~iigGL~~s  993 (1025)
T PRK10614        974 DGA-E-LRQPLGITIVGGLVMS  993 (1025)
T ss_pred             CCH-H-HhCCchhhhhhHHHHH
Confidence            211 1 2355555666666554

>COG0342 SecD Preprotein translocase subunit SecD [Intracellular trafficking and secretion]

Probab=94.35  E-value=0.096  Score=50.33  Aligned_cols=95  Identities=15%  Similarity=0.112  Sum_probs=71.6

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcccC---ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIG---NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQ  173 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~~---~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~  173 (197)
                      .|++.|..|+-=+..-+|.+||++||--+=|.-.-....+   +....+....++-.+.|+.+.+||+++.++|..--+-
T Consensus       385 vls~lgatLtLpgIAGiILtIGmaVDaNVlI~ERIrEElr~G~s~~~ai~~G~~rAf~tI~DsN~TTlia~~~L~~~GtG  464 (506)
T COG0342         385 VLSLLGATLTLPGIAGIILTIGMAVDANVLIFERIREELRNGKSVLSAIDAGFKRAFSTILDSNATTLIAAAILFALGTG  464 (506)
T ss_pred             HHHHhcccccchhhhHHHHhhhhcccccEEeeHHHHHHHhcCccHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHhccC
Confidence            8899999999999999999999999987766655443222   2235566678899999999999999999999877777


Q ss_pred             hhHHHHHHHHHHHHHHHhh
Q psy8507         174 FILRIFFYMLFGIVLVGLL  192 (197)
Q Consensus       174 ~~~~~FF~~~~~vi~~G~~  192 (197)
                      -++=| -.++.+=++.+++
T Consensus       465 ~vKGF-A~Tl~lGi~~smf  482 (506)
T COG0342         465 PVKGF-AVTLILGILTSMF  482 (506)
T ss_pred             CchHH-HHHHHHHHHHHhh
Confidence            66664 3444443444544

>KOG1934|consensus

Probab=94.32  E-value=0.096  Score=53.33  Aligned_cols=84  Identities=12%  Similarity=0.145  Sum_probs=74.3

Q ss_pred             HHHHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcccCCh--hHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccc
Q psy8507          95 LLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGNR--DRRVRLSIEHMYSVVLHAGLILLVAISILAFSEF  172 (197)
Q Consensus        95 f~~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~~~~--~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s  172 (197)
                      |+++.+.|...|+|-++.=-..+|++||=+-=+.++..+..+..  ++|+.++|.+.|.++.-.++|-+++..+=++++.
T Consensus       301 ~G~l~~~G~~f~sI~~v~PFLvl~IGVDD~Flml~aW~rt~~~~~~~~Rm~~~laeag~SItITSlTn~lsFgiG~~T~~  380 (868)
T KOG1934|consen  301 FGLLFWCGFPFNSIVCVMPFLVLGIGVDDAFLMLAAWRRTSKKLSVEERMAETLAEAGPSITITSLTNVLSFGIGAITPT  380 (868)
T ss_pred             HHHHHHcCCCCcceeeecchheeeecccHHHHHHHHHHhcCccCCHHHHHHHHHHHhcCeeeHHHHHHHHHHHhccCCCc
Confidence            78999999999999999988899999999999999999876654  4999999999999999998888888888888888


Q ss_pred             chhHHH
Q psy8507         173 QFILRI  178 (197)
Q Consensus       173 ~~~~~~  178 (197)
                      .-++.|
T Consensus       381 p~v~~F  386 (868)
T KOG1934|consen  381 PAVQIF  386 (868)
T ss_pred             HHHHHH
Confidence            776653

>KOG1935|consensus

Probab=93.61  E-value=0.16  Score=51.68  Aligned_cols=83  Identities=12%  Similarity=0.120  Sum_probs=71.8

Q ss_pred             HHHHHHhccccchhhH-HHHhhhhcceeeehHHHHhHhhcccCChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccc
Q psy8507          95 LLVMYLMNIKLNPISC-VLIVNSSGIYIHFISYICLSFLTCIGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQ  173 (197)
Q Consensus        95 f~~M~l~gi~Ln~iS~-v~Li~sIG~sVDFtaHI~~~F~~s~~~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~  173 (197)
                      .++-++.||.+|+-+. |.=-.+.|++||..--.+|+|....+. .+|+...|++.|.+|+-.+++++++.++-++.+-.
T Consensus       459 LGl~t~lGI~FNAAtTQVvPFLaLGlGVDd~FlL~hay~e~~~~-~~~~~~~lk~tG~Svl~tsinni~aF~~aallPIP  537 (1143)
T KOG1935|consen  459 LGLATLLGIEFNAATTQVVPFLALGLGVDDMFLLLHAYREVVKL-HEEMGELLKETGMSVLLTSINNILAFLMAALLPIP  537 (1143)
T ss_pred             hhHHHHhceeeccccceeehhhhhccChhHHHHHHHHHHHHhhh-HHHHHHHHHHhCcchhHHHhhhHHHHHHHhhcCcH
Confidence            5589999999998765 445679999999999999999776544 79999999999999999999999999999988877


Q ss_pred             hhHHH
Q psy8507         174 FILRI  178 (197)
Q Consensus       174 ~~~~~  178 (197)
                      -.+.|
T Consensus       538 ALrsF  542 (1143)
T KOG1935|consen  538 ALRSF  542 (1143)
T ss_pred             HHHHH
Confidence            76654

>COG0341 SecF Preprotein translocase subunit SecF [Intracellular trafficking and secretion]

Probab=90.96  E-value=1.7  Score=39.40  Aligned_cols=82  Identities=10%  Similarity=0.083  Sum_probs=58.0

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhH----hhcccC-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLS----FLTCIG-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSE  171 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~----F~~s~~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~  171 (197)
                      +|++.|+++|.-+...|.+-||.||+=+.=+--.    ....++ +..|-+..++...-.-.+.-.++|++.+++|.+=.
T Consensus       177 ~~slfgiE~~l~~IAAlLtiIGYSvNDtIVvfDRIREn~r~~~~~~~~~iin~si~qTlsRti~Ts~ttll~~~~l~~fg  256 (305)
T COG0341         177 FFSLFGIEFNLATIAALLTIIGYSVNDTIVVFDRIRENLRKYRRETLREIINTSINQTLTRTINTSVTTLLVVVALLLFG  256 (305)
T ss_pred             HHHHhheeecHHHHHHHHHHeeeccCCeEEEEhHHHHHHhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            9999999999999999999999999988644322    211111 12255666777777777777888999888776544


Q ss_pred             cchhHHH
Q psy8507         172 FQFILRI  178 (197)
Q Consensus       172 s~~~~~~  178 (197)
                      -..++.|
T Consensus       257 g~~l~~f  263 (305)
T COG0341         257 GGSLKDF  263 (305)
T ss_pred             chHHHHH
Confidence            3445543

>COG4258 Predicted exporter [General function prediction only]

Probab=88.04  E-value=1.3  Score=43.96  Aligned_cols=74  Identities=19%  Similarity=0.221  Sum_probs=58.2

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcccCChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccchhH
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQFIL  176 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~~~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~~~~  176 (197)
                      ...+.|+.||-.+.+.++...|++.+|+.-..++-    .++.|-..     .--.+.-+.++|+++.-+|++|...++.
T Consensus       689 ~~a~aGvplnLfhllal~LvlgvG~nYalFfs~~~----~~~ae~lt-----tl~alala~ltTlltfgLLa~Sa~pvLs  759 (788)
T COG4258         689 VLAMAGVPLNLFHLLALVLVLGVGINYALFFSNAG----DPRAEPLT-----TLLALALAMLTTLLTFGLLAFSATPVLS  759 (788)
T ss_pred             HHHHcCCchhHHHHHHHHHHHHcccchhhhhhccc----CCCCchHH-----HHHHHHHHHHHHHHHHHHHHhcccHHHH
Confidence            66788999999999999999999999998776643    22223222     2334567789999999999999999988


Q ss_pred             HHH
Q psy8507         177 RIF  179 (197)
Q Consensus       177 ~~F  179 (197)
                      .|-
T Consensus       760 sfG  762 (788)
T COG4258         760 SFG  762 (788)
T ss_pred             Hhh
Confidence            764

>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]

Probab=87.84  E-value=1.2  Score=46.15  Aligned_cols=73  Identities=12%  Similarity=0.116  Sum_probs=59.8

Q ss_pred             HHHHhccccchhhHHHHhhhhcce-------eeehHHHHhHhhcccCChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIY-------IHFISYICLSFLTCIGNRDRRVRLSIEHMYSVVLHAGLILLVAISILAF  169 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~s-------VDFtaHI~~~F~~s~~~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~f  169 (197)
                      -+.+.|.++|..+++-+++-+|+.       |||.-|.-+    .-.+++|-+.+|=..-..||+..++++++|++||++
T Consensus       893 ~L~l~g~~~~i~a~IGli~LiGiv~KNaIllVefa~~~~~----~G~~~~eAiieA~~~RlRPIlMTtla~ilG~iPLal  968 (1009)
T COG0841         893 ALLLTGLPLDVYAQIGLITLIGLVAKNAILIVEFANELRA----EGLSLREAILEAARLRLRPILMTSLAAILGVLPLAL  968 (1009)
T ss_pred             HHHHhCCCCcHHHHHHHHHHHHHHhcCcEEEEhHHHHHHH----cCCCHHHHHHHHhhhhhhhHHHHHHHHHHhhhhhhh
Confidence            667889999999999999999987       566655443    122345778888888899999999999999999998


Q ss_pred             cccc
Q psy8507         170 SEFQ  173 (197)
Q Consensus       170 s~s~  173 (197)
                      +...
T Consensus       969 ~~g~  972 (1009)
T COG0841         969 STGA  972 (1009)
T ss_pred             cccc
Confidence            8754

>PRK13023 bifunctional preprotein translocase subunit SecD/SecF; Reviewed

Probab=83.60  E-value=6.4  Score=39.86  Aligned_cols=94  Identities=15%  Similarity=0.075  Sum_probs=69.4

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc---cC--ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC---IG--NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSE  171 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s---~~--~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~  171 (197)
                      ++++.|+++|.-....+++-+|.|++=++=+--.-...   .+  +-++-+-.++.+.-.=.+...+||++.+++|.+--
T Consensus       621 ~fsl~~~e~~l~~IAAlLTiiGYSiNDTIVVfDRIREn~~~~~~~~~~eivn~SInqTl~RTI~TS~TTll~~l~L~ifG  700 (758)
T PRK13023        621 MFIVFRMEFNLWSVAAILTIIGYSLNDTVVIYDRVRENLRRYKSAPLPAIIDASINQTLSRTLLTSFVTFLAHVPLYAFG  700 (758)
T ss_pred             HHHHhCceecHHHHHHHHHHHhhcccCeEEEeHHHHHHHhhcCCCCHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHhc
Confidence            88999999999999999999999999987554333221   11  22366778888888888888999999999997766


Q ss_pred             cchhHHHHHHHHHHHHHHHh
Q psy8507         172 FQFILRIFFYMLFGIVLVGL  191 (197)
Q Consensus       172 s~~~~~~FF~~~~~vi~~G~  191 (197)
                      ...++.|=+.+++. ++.|.
T Consensus       701 g~~i~~Fal~lliG-iv~Gt  719 (758)
T PRK13023        701 GSEIRMFALALSVG-IIVAS  719 (758)
T ss_pred             CccHHHHHHHHHHH-HHHHH
Confidence            66677765555444 34443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	197
3aqp_A	741	Probable secdf protein-export membrane protein; tr	98.86
3aqp_A	741	Probable secdf protein-export membrane protein; tr	98.82
2v50_A	1052	Multidrug resistance protein MEXB; DDM, RND, membr	98.77
4dx5_A	1057	Acriflavine resistance protein B; multidrug efflux	98.63
2v50_A	1052	Multidrug resistance protein MEXB; DDM, RND, membr	98.53
3ne5_A	1054	Cation efflux system protein CUSA; transmembrane h	98.41
4dx5_A	1057	Acriflavine resistance protein B; multidrug efflux	98.23
3ne5_A	1054	Cation efflux system protein CUSA; transmembrane h	98.06

>3aqp_A Probable secdf protein-export membrane protein; translocon, cell membrane, MEM protein transport, translocation, transmembrane, transport; 3.30A {Thermus thermophilus} PDB: 2rrn_A

Probab=98.86  E-value=3.4e-09  Score=102.62  Aligned_cols=99  Identities=15%  Similarity=0.106  Sum_probs=85.0

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhccc-----CChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCI-----GNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSE  171 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~-----~~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~  171 (197)
                      +|+++|+++|..+++.+++.+|++||+++|+...|....     .+.+|.+.+|+.+.+.|++..++||++|+++|+++.
T Consensus       611 ~l~l~g~~l~~~~i~~~l~liGisvd~~I~l~~r~re~~~~~~g~~~~eav~~a~~~~~~~il~Tsltt~~g~~~L~~~g  690 (741)
T 3aqp_A          611 MYSLLGLEFSIPTIAALLTIVGYSINDSIVVSDRIRENQKLLRHLPYAELVNRSINQTLSRTVMTSLTTLLPILALLFLG  690 (741)
T ss_dssp             HHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHhcCccHHHHHHHHHHHHHhhcceEEehHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            899999999999999999999999999999999997542     244588999999999999999999999999999999


Q ss_pred             cchhHHHHHHHHHHHHHHHhhhhhc
Q psy8507         172 FQFILRIFFYMLFGIVLVGLLYMVL  196 (197)
Q Consensus       172 s~~~~~~FF~~~~~vi~~G~~hGLv  196 (197)
                      ...++.+- ..+..-+++|+++.|+
T Consensus       691 ~~~~~~~g-~~~~~Gl~~~~~~sl~  714 (741)
T 3aqp_A          691 GSVLRDFA-LAIFVGIFVGTYSSIY  714 (741)
T ss_dssp             CHHHHHHH-HHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHH-HHHHHHHHHHHHHHHH
Confidence            98887764 4444445677777664

>3aqp_A Probable secdf protein-export membrane protein; translocon, cell membrane, MEM protein transport, translocation, transmembrane, transport; 3.30A {Thermus thermophilus} PDB: 2rrn_A

Probab=98.82  E-value=9.2e-09  Score=99.62  Aligned_cols=99  Identities=9%  Similarity=-0.012  Sum_probs=84.1

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhccc---CChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCI---GNRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEFQ  173 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~---~~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s~  173 (197)
                      +|+++|.+||..+++.+++++|++||+++|+...|....   ++.++.+.+++++.+.|++.+.+||++|.++|++++..
T Consensus       315 ~l~l~g~~l~l~~i~glil~iGi~VD~~I~i~eri~e~~~~g~~~~~Ai~~~~~~~~~~Il~s~lTt~i~f~~L~~~~~~  394 (741)
T 3aqp_A          315 LLSGLGATLTLPGIAGLVLTLGAAVDGNVLSFERIKEELRAGKKLRQAIPEGFRHSTLTIMDVNIAHLLAAAALYQYATG  394 (741)
T ss_dssp             HHHHHCCBCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCT
T ss_pred             HHHHHCCCccHHHHHHHHHHHHHHHhchhhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Confidence            899999999999999999999999999999999997653   24458899999999999999999999999999999988


Q ss_pred             hhHHHHHHHHHHHHHHHhhhhhc
Q psy8507         174 FILRIFFYMLFGIVLVGLLYMVL  196 (197)
Q Consensus       174 ~~~~~FF~~~~~vi~~G~~hGLv  196 (197)
                      .++-| -.++.+-++++++..++
T Consensus       395 ~~~~f-a~~~~~gi~~s~~~al~  416 (741)
T 3aqp_A          395 PVRGF-AVILAIGVVASVFSNLV  416 (741)
T ss_dssp             HHHHH-HHHHHHHHHHHHHHHHH
T ss_pred             ccchH-HHHHHHHHHHHHHHHHH
Confidence            77665 34444556666666553

>2v50_A Multidrug resistance protein MEXB; DDM, RND, membrane, detergent, transport, cell membrane, transmembrane, membrane protein; HET: LMT; 3.00A {Pseudomonas aeruginosa PA01}

Probab=98.77  E-value=5.4e-09  Score=103.96  Aligned_cols=98  Identities=10%  Similarity=0.156  Sum_probs=79.1

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc---cC-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC---IG-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEF  172 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s---~~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s  172 (197)
                      +|+++|+++|.+|++.+++++|++||++.|+...|...   .| ++++.+.+|..+.+.||+.+++||++|.+||+|++.
T Consensus       382 ~l~~~g~~ln~~s~~gl~~~iGi~vd~aI~~~~~~~~~~~~~g~~~~~A~~~a~~~~~~pil~t~ltt~~~f~pl~~~~~  461 (1052)
T 2v50_A          382 VLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLSPREAARKSMGQIQGALVGIAMVLSAVFLPMAFFGG  461 (1052)
T ss_dssp             HHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHTTSSTTHHHHHHHHHTTHHHHTCCH
T ss_pred             HHHHhCCCHHHHHHHHHHHHHHhhccceEEEehHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            99999999999999999999999999999999999653   34 455889999999999999999999999999999986


Q ss_pred             c---hhHHHHHHHHHHHHHHHhhhhh
Q psy8507         173 Q---FILRIFFYMLFGIVLVGLLYMV  195 (197)
Q Consensus       173 ~---~~~~~FF~~~~~vi~~G~~hGL  195 (197)
                      .   +++.+ ..++..-++++++..|
T Consensus       462 ~~g~~~~~~-~~~~~~gl~~s~~~~l  486 (1052)
T 2v50_A          462 STGVIYRQF-SITIVSAMALSVIVAL  486 (1052)
T ss_dssp             HHHHHHHHH-HHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHH-HHHHHHHHHHHHHHHH
Confidence            3   44433 2333333444444444

>4dx5_A Acriflavine resistance protein B; multidrug efflux protein, membrane protein, transpor; HET: LMT OCT D10 HEX D12 MIY C14 LMU DD9 UND GOL; 1.90A {Escherichia coli} PDB: 2hrt_A* 2gif_A* 4dx7_A* 4dx6_A* 3noc_A* 1oy6_A* 1oy9_A* 1oyd_A* 1oy8_A* 1oye_A 2rdd_A* 2w1b_A* 3d9b_A 2i6w_A* 3nog_A* 1t9x_A* 1t9t_A* 1t9v_A* 1t9w_A* 1t9u_A* ...

Probab=98.63  E-value=5.5e-08  Score=96.60  Aligned_cols=75  Identities=13%  Similarity=0.198  Sum_probs=69.2

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc--c-C-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC--I-G-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSE  171 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s--~-~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~  171 (197)
                      +|+++|..+|.+|++.+++++|++||++.|+...|...  . | ++++.+.+|..+.+.||+.+++||++|.+||+|++
T Consensus       382 ~l~~~g~~ln~~sl~gl~~~iGi~vd~aIv~~~~~~~~~~~~g~~~~~A~~~a~~~~~~pi~~t~ltt~~~f~pl~~~~  460 (1057)
T 4dx5_A          382 VLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFFG  460 (1057)
T ss_dssp             HHHHTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSGGGGCC
T ss_pred             HHHHhCCcHHHHHHHHHHHHeeccccceEEeHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            89999999999999999999999999999999988753  1 3 44588999999999999999999999999999998

>2v50_A Multidrug resistance protein MEXB; DDM, RND, membrane, detergent, transport, cell membrane, transmembrane, membrane protein; HET: LMT; 3.00A {Pseudomonas aeruginosa PA01}

Probab=98.53  E-value=1.5e-07  Score=93.57  Aligned_cols=76  Identities=11%  Similarity=0.008  Sum_probs=69.4

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhccc--C-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccc
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCI--G-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSEF  172 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~--~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~s  172 (197)
                      .|.++|.++|..+++.+++.+|++||++.|+...|....  | +.++.+.+|..+.+.||+..++||++|++||+|+..
T Consensus       914 ~~~~~g~~l~~~~~~g~~~l~Gi~vd~~I~lv~~~~~~~~~g~~~~~Ai~~a~~~~~rpil~t~~tt~~g~~pl~~~~~  992 (1052)
T 2v50_A          914 ATSMRGLSNDVFFQVGLLTTIGLSAKNAILIVEFAKELHEQGKGIVEAAIEACRMRLRPIVMTSLAFILGVVPLAISTG  992 (1052)
T ss_dssp             HHHHTTCCBSHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCHHHHHHHHHHHHHHHHHHHHHHHHTTSHHHHTCCS
T ss_pred             HHHHHCCCccHHHHHHHHHHHHHHHcCeEEEeehHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHhcCC
Confidence            789999999999999999999999999999999887543  2 345889999999999999999999999999999986

>3ne5_A Cation efflux system protein CUSA; transmembrane helix, metal transport; 2.90A {Escherichia coli} PDB: 3k07_A 3k0i_A 3kso_A 3kss_A 3t53_A 3t51_A 3t56_A 4dop_A 4dnt_A

Probab=98.41  E-value=2.6e-07  Score=91.75  Aligned_cols=77  Identities=13%  Similarity=0.055  Sum_probs=67.9

Q ss_pred             HHHHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcccC-------------C-hhHHHHHHHHHHhHHHHHHHHHH
Q psy8507          95 LLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIG-------------N-RDRRVRLSIEHMYSVVLHAGLIL  160 (197)
Q Consensus        95 f~~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~~-------------~-~~~R~~~aL~~~G~pVl~ga~ST  160 (197)
                      |.+|+++|.++|.+|++.+++++|++||++.|+...+.....             . +.+-+.+|..+++.|++.++++|
T Consensus       385 ~~~l~~~g~~ln~~sl~gl~l~iGi~vd~aIvvve~~~~~~~~~~~~~~~~~~~g~~~~~a~~~a~~~~~~~i~~s~ltt  464 (1054)
T 3ne5_A          385 FIVMHFQGLNANIMSLGGIAIAVGAMVDAAIVMIENAHKRLEEWQHQHPDATLDNKTRWQVITDASVEVGPALFISLLII  464 (1054)
T ss_dssp             HHHHHHHTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHSCSSCCCTTHHHHHHHTTTTTHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHhhheecCcEEEeeHHHHHHhhccccccccccccCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            338999999999999999999999999999999988765332             2 23678889999999999999999


Q ss_pred             HHHHHHhhccc
Q psy8507         161 LVAISILAFSE  171 (197)
Q Consensus       161 ~lgv~~L~fs~  171 (197)
                      ++|++||+|++
T Consensus       465 ~~~f~pl~~~~  475 (1054)
T 3ne5_A          465 TLSFIPIFTLE  475 (1054)
T ss_dssp             HHTTGGGGGCC
T ss_pred             HHHHHHHHHhc
Confidence            99999999987

>4dx5_A Acriflavine resistance protein B; multidrug efflux protein, membrane protein, transpor; HET: LMT OCT D10 HEX D12 MIY C14 LMU DD9 UND GOL; 1.90A {Escherichia coli} PDB: 2hrt_A* 2gif_A* 4dx7_A* 4dx6_A* 3noc_A* 1oy6_A* 1oy9_A* 1oyd_A* 1oy8_A* 1oye_A 2rdd_A* 2w1b_A* 3d9b_A 2i6w_A* 3nog_A* 1t9x_A* 1t9t_A* 1t9v_A* 1t9w_A* 1t9u_A* ...

Probab=98.23  E-value=3.3e-06  Score=83.95  Aligned_cols=93  Identities=11%  Similarity=-0.005  Sum_probs=75.6

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc---cC-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccc-
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC---IG-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFSE-  171 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s---~~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs~-  171 (197)
                      .|.+.|..+|..+++.+++.+|++||++.|+...|...   .| +.++-+.+|..+.+.||+..++||++|+++|+++. 
T Consensus       915 ~l~~~g~~l~~~~~~g~i~l~Gi~vd~~I~lv~~~~~~~~~~g~~~~~Ai~~a~~~~~rpil~t~ltt~~g~~pl~~~~g  994 (1057)
T 4dx5_A          915 AATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMPLVISTG  994 (1057)
T ss_dssp             HHHHHTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTCCS
T ss_pred             HHHHHCCCccHHHHHHHHHHHHHHHcCeEEEehHHhHHHHHcCCCHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHhcC
Confidence            78899999999999999999999999999999888544   33 34588999999999999999999999999999996 


Q ss_pred             --cchhHHHHHHHHHHHHHHHhhhh
Q psy8507         172 --FQFILRIFFYMLFGIVLVGLLYM  194 (197)
Q Consensus       172 --s~~~~~~FF~~~~~vi~~G~~hG  194 (197)
                        ..++     +-+-.++++|++-+
T Consensus       995 ~g~~~~-----~~~g~~~~~Gl~~s 1014 (1057)
T 4dx5_A          995 AGSGAQ-----NAVGTGVMGGMVTA 1014 (1057)
T ss_dssp             TTHHHH-----HHHHHHHHHHHHHH
T ss_pred             Cchhhh-----cccHHHHHHHHHHH
Confidence              3333     33444445554443

>3ne5_A Cation efflux system protein CUSA; transmembrane helix, metal transport; 2.90A {Escherichia coli} PDB: 3k07_A 3k0i_A 3kso_A 3kss_A 3t53_A 3t51_A 3t56_A 4dop_A 4dnt_A

Probab=98.06  E-value=4.9e-06  Score=82.63  Aligned_cols=75  Identities=8%  Similarity=0.109  Sum_probs=64.0

Q ss_pred             HHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcccC--------------ChhHHHHHHHHHHhHHHHHHHHHHHH
Q psy8507          97 VMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTCIG--------------NRDRRVRLSIEHMYSVVLHAGLILLV  162 (197)
Q Consensus        97 ~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s~~--------------~~~~R~~~aL~~~G~pVl~ga~ST~l  162 (197)
                      .|.+.|..+|..+++.+++.+|++||++.|+...+.....              +..+-+.+|....+.||+..++||++
T Consensus       921 ~l~l~g~~l~~~~~~g~i~l~Gi~vd~~I~lv~~~~~~~~~~~~~~~~~~~~g~~~~~Ai~~a~~~~~rpil~t~ltti~ 1000 (1054)
T 3ne5_A          921 LLWWMGFHLSVATGTGFIALAGVAAEFGVVMLMYLRHAIEAVPSLNNPQTFSEQKLDEALYHGAVLRVRPKAMTVAVIIA 1000 (1054)
T ss_dssp             HHHHHTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTHHHHTTTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCccHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhhhhhhcccccCCCCHHHHHHHHHHHhHhHHHHHHHHHHH
Confidence            7889999999999999999999999999999744432211              12366788899999999999999999


Q ss_pred             HHHHhhccc
Q psy8507         163 AISILAFSE  171 (197)
Q Consensus       163 gv~~L~fs~  171 (197)
                      |++||+++.
T Consensus      1001 g~~pl~~~~ 1009 (1054)
T 3ne5_A         1001 GLLPILWGT 1009 (1054)
T ss_dssp             HHHHHHSCC
T ss_pred             HHHHHHhhc
Confidence            999999996

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	197
d1iwga7	199	Multidrug efflux transporter AcrB transmembrane do	99.16
d1iwga8	222	Multidrug efflux transporter AcrB transmembrane do	98.56

>d1iwga7 f.35.1.1 (A:7-37,A:331-498) Multidrug efflux transporter AcrB transmembrane domain {Escherichia coli [TaxId: 562]}

class: Membrane and cell surface proteins and peptides
fold: Multidrug efflux transporter AcrB transmembrane domain
superfamily: Multidrug efflux transporter AcrB transmembrane domain
family: Multidrug efflux transporter AcrB transmembrane domain
domain: Multidrug efflux transporter AcrB transmembrane domain
species: Escherichia coli [TaxId: 562]

Probab=99.16  E-value=1.7e-11  Score=99.23  Aligned_cols=101  Identities=11%  Similarity=0.157  Sum_probs=81.5

Q ss_pred             HHHHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc---cC-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcc
Q psy8507          95 LLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC---IG-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFS  170 (197)
Q Consensus        95 f~~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s---~~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs  170 (197)
                      +.+|+++|+++|.++++.+++++|++||++.|+.++|.+.   +| +++|++.++.+++|.|++.+++||..|.++|+++
T Consensus        81 ~~~m~~~g~~l~~~s~~~~~i~igi~vd~~i~i~~~~~~~~~~~g~~~~eAi~~a~~~~g~~i~~s~lTt~~~f~~l~~~  160 (199)
T d1iwga7          81 FAVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFF  160 (199)
T ss_dssp             HHHHHTTTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSCCSHHHHHHGGGTHHHHHHHHHHHHHHHHTTTTCC
T ss_pred             HHHhhcCCCchHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhcCCCHHHHHHHHHhHhhhHHHHHHHHHHHHHHHHhcC
Confidence            3499999999999999999999999999999999988543   33 4569999999999999999999999999999998


Q ss_pred             ccch---hHHHHHHHHHHHHHHHhhhhhc
Q psy8507         171 EFQF---ILRIFFYMLFGIVLVGLLYMVL  196 (197)
Q Consensus       171 ~s~~---~~~~FF~~~~~vi~~G~~hGLv  196 (197)
                      +..-   ++.+- ......+.+++++.+.
T Consensus       161 ~~~~~~~~~~~g-~~i~~gv~~s~i~al~  188 (199)
T d1iwga7         161 GGSTGAIYRQFS-ITIVSAMALSVLVALI  188 (199)
T ss_dssp             CTTSHHHHHHHH-HHHHHHHHHHHHHTTT
T ss_pred             CCcHHHHHHHHH-HHHHHHHHHHHHHHHH
Confidence            8653   44432 3333444556666553

>d1iwga8 f.35.1.1 (A:513-566,A:869-1036) Multidrug efflux transporter AcrB transmembrane domain {Escherichia coli [TaxId: 562]}

class: Membrane and cell surface proteins and peptides
fold: Multidrug efflux transporter AcrB transmembrane domain
superfamily: Multidrug efflux transporter AcrB transmembrane domain
family: Multidrug efflux transporter AcrB transmembrane domain
domain: Multidrug efflux transporter AcrB transmembrane domain
species: Escherichia coli [TaxId: 562]

Probab=98.56  E-value=1.4e-07  Score=76.82  Aligned_cols=99  Identities=12%  Similarity=-0.024  Sum_probs=80.5

Q ss_pred             HHHHHHhccccchhhHHHHhhhhcceeeehHHHHhHhhcc---cC-ChhHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcc
Q psy8507          95 LLVMYLMNIKLNPISCVLIVNSSGIYIHFISYICLSFLTC---IG-NRDRRVRLSIEHMYSVVLHAGLILLVAISILAFS  170 (197)
Q Consensus        95 f~~M~l~gi~Ln~iS~v~Li~sIG~sVDFtaHI~~~F~~s---~~-~~~~R~~~aL~~~G~pVl~ga~ST~lgv~~L~fs  170 (197)
                      +..|.+.|.++|..+.+.+++.+|++||++.|+...|...   +| +.+|.+.+|..+.+.|++.+++||++|.+||+++
T Consensus        99 ~~~l~~~g~~~~~~~~~g~i~l~Gi~v~~~i~~~~~~~~~~~~~g~~~~~Ai~~a~~~~~~~i~~t~ltti~gf~pl~~~  178 (222)
T d1iwga8          99 LLAATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMPLVIS  178 (222)
T ss_dssp             HHHHHHTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSCCCTTHHHHHHHHTTHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHcCCchhhhhcccccchhhhhhhHHHHHHHHhccccccccCCHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHhc
Confidence            5589999999999999999999999999999999988642   22 4458899999999999999999999999999998


Q ss_pred             ccchhHHHHHHHHHHHHHHHhhhhh
Q psy8507         171 EFQFILRIFFYMLFGIVLVGLLYMV  195 (197)
Q Consensus       171 ~s~~~~~~FF~~~~~vi~~G~~hGL  195 (197)
                      +..-..  +++-+-.+++.|++-+.
T Consensus       179 ~~~g~~--~~~~la~~v~~Gll~s~  201 (222)
T d1iwga8         179 TGAGSG--AQNAVGTGVMGGMVTAT  201 (222)
T ss_dssp             CSSSCH--HHHHHHHHHHHHHHHHH
T ss_pred             cccHHH--HHHHHHHHHHHHHHHHH
Confidence            754322  23445555666665544