Psyllid ID: psy16375

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------9
Protein Sequence
MAMLTQFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFPVIQI
Secondary Structure (PSIPRED)
cccccccccccccccEEEEEEEcEEEEEEEcccEEEEHHHHHcccccccHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
ccEEHEcccccccccEEEEEEEcEEEEEEEEccEEEEEccEEcccccccHEHHHHHHccHccHHHHHHHHHHHHHHHHHHHHcccHccc
Coil and Loop (DISEMBL)
mamltqfrkpngvlpyFIIIVLPYFIIIVGLENILVLTKSIisipshldSKIRIAQGlskegwsiTKNFFLELTVLTAglltffpviqi
Flexible Loop (DISEMBL)
mamltqfrkpngvLPYFIIIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAglltffpviqi
Low Complexity Region (SEG)
MAMLTQFRKPNGVLpyfiiivlpyfiiivGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFPVIQI
Disordered region (IsUnstruct)
********KPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFPVI**
Disordered Region (DISOPRED)
********KPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFPVIQI
Disordered Region (DISEMBL)
MAMLTQFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFPVIQI
Disordered Region (DISPRO)
*AMLTQFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFPVIQI
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHii
Transmembrane Helix (HMMTOP)
oooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAMLTQFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFPVIQI
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	89	2.2.26 [Sep-21-2011]
Q5MNU5	1279	Sterol regulatory element	yes	N/A	0.764	0.053	0.529	3e-16
Q12770	1279	Sterol regulatory element	yes	N/A	0.764	0.053	0.529	3e-16
P97260	1276	Sterol regulatory element	yes	N/A	0.764	0.053	0.529	4e-16
A2RRU4	1276	Sterol regulatory element	yes	N/A	0.764	0.053	0.529	4e-16
A6QM06	1278	Sterol regulatory element	yes	N/A	0.764	0.053	0.529	5e-16
Q6GQT6	1276	Sterol regulatory element	yes	N/A	0.764	0.053	0.529	6e-16
A0JPH4	1311	Sterol regulatory element	N/A	N/A	0.764	0.051	0.5	4e-15

>sp|Q5MNU5|SCAP_PIG Sterol regulatory element-binding protein cleavage-activating protein OS=Sus scrofa GN=SCAP PE=2 SV=2

 Score = 83.6 bits (205), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 36/68 (52%), Positives = 48/68 (70%)

Query: 21  VLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGL 80
           + PY ++++GLEN+LVLTKS++S P  L+ K+RIAQGLS E WSI KN   EL ++  G 
Sbjct: 348 IFPYLVVVIGLENVLVLTKSVVSTPVDLEVKLRIAQGLSSESWSIMKNMATELGIILIGY 407

Query: 81  LTFFPVIQ 88
            T  P IQ
Sbjct: 408 FTLVPAIQ 415

Escort protein required for cholesterol as well as lipid homeostasis. Regulates export of the SCAP/SREBF complex from the ER upon low cholesterol. Formation of a ternary complex with INSIG at high sterol concentrations leads to masking of an ER-export signal in SCAP and retention of the complex in the ER. Low sterol concentrations trigger release of INSIG, a conformational change in the SSC domain of SCAP, unmasking of the ER export signal, recruitment into COPII-coated vesicles, transport to the Golgi complex, proteolytic cleavage of SREBF in the Golgi, release of the transcription factor fragment of SREBF from the membrane, its import into the nucleus and up-regulation of LDLR, INSIG1 and the mevalonate pathway.
Sus scrofa (taxid: 9823)

>sp|Q12770|SCAP_HUMAN Sterol regulatory element-binding protein cleavage-activating protein OS=Homo sapiens GN=SCAP PE=1 SV=4

 Score = 83.6 bits (205), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 36/68 (52%), Positives = 48/68 (70%)

Query: 21  VLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGL 80
           + PY ++++GLEN+LVLTKS++S P  L+ K+RIAQGLS E WSI KN   EL ++  G 
Sbjct: 348 IFPYLVVVIGLENVLVLTKSVVSTPVDLEVKLRIAQGLSSESWSIMKNMATELGIILIGY 407

Query: 81  LTFFPVIQ 88
            T  P IQ
Sbjct: 408 FTLVPAIQ 415

Escort protein required for cholesterol as well as lipid homeostasis. Regulates export of the SCAP/SREBF complex from the ER upon low cholesterol. Formation of a ternary complex with INSIG at high sterol concentrations leads to masking of an ER-export signal in SCAP and retention of the complex in the ER. Low sterol concentrations trigger release of INSIG, a conformational change in the SSC domain of SCAP, unmasking of the ER export signal, recruitment into COPII-coated vesicles, transport to the Golgi complex, proteolytic cleavage of SREBF in the Golgi, release of the transcription factor fragment of SREBF from the membrane, its import into the nucleus and up-regulation of LDLR, INSIG1 and the mevalonate pathway.

Homo sapiens (taxid: 9606)

>sp|P97260|SCAP_CRIGR Sterol regulatory element-binding protein cleavage-activating protein OS=Cricetulus griseus GN=SCAP PE=1 SV=1

 Score = 83.2 bits (204), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 36/68 (52%), Positives = 48/68 (70%)

Query: 21  VLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGL 80
           + PY ++++GLEN+LVLTKS++S P  L+ K+RIAQGLS E WSI KN   EL ++  G 
Sbjct: 348 IFPYLVVVIGLENVLVLTKSVVSTPVDLEVKLRIAQGLSSESWSIMKNVATELGIILIGY 407

Query: 81  LTFFPVIQ 88
            T  P IQ
Sbjct: 408 FTLVPAIQ 415

Escort protein required for cholesterol as well as lipid homeostasis. Regulates export of the SCAP/SREBF complex from the ER upon low cholesterol. Formation of a ternary complex with INSIG at high sterol concentrations leads to masking of an ER-export signal in SCAP and retention of the complex in the ER. Low sterol concentrations trigger release of INSIG, a conformational change in the SSC domain of SCAP, unmasking of the ER export signal, recruitment into COPII-coated vesicles, transport to the Golgi complex, proteolytic cleavage of SREBF in the Golgi, release of the transcription factor fragment of SREBF from the membrane, its import into the nucleus and up-regulation of LDLR, INSIG1 and the mevalonate pathway.

Cricetulus griseus (taxid: 10029)

>sp|A2RRU4|SCAP_RAT Sterol regulatory element-binding protein cleavage-activating protein OS=Rattus norvegicus GN=Scap PE=2 SV=1

 Score = 83.2 bits (204), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 36/68 (52%), Positives = 48/68 (70%)

Query: 21  VLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGL 80
           + PY ++++GLEN+LVLTKS++S P  L+ K+RIAQGLS E WSI KN   EL ++  G 
Sbjct: 348 IFPYLVVVIGLENVLVLTKSVVSTPVDLEVKLRIAQGLSSESWSIMKNVATELGIILIGY 407

Query: 81  LTFFPVIQ 88
            T  P IQ
Sbjct: 408 FTLVPAIQ 415

Escort protein required for cholesterol as well as lipid homeostasis. Regulates export of the SCAP/SREBF complex from the ER upon low cholesterol. Formation of a ternary complex with INSIG at high sterol concentrations leads to masking of an ER-export signal in SCAP and retention of the complex in the ER. Low sterol concentrations trigger release of INSIG, a conformational change in the SSC domain of SCAP, unmasking of the ER export signal, recruitment into COPII-coated vesicles, transport to the Golgi complex, proteolytic cleavage of SREBF in the Golgi, release of the transcription factor fragment of SREBF from the membrane, its import into the nucleus and up-regulation of LDLR, INSIG1 and the mevalonate pathway.

Rattus norvegicus (taxid: 10116)

>sp|A6QM06|SCAP_BOVIN Sterol regulatory element-binding protein cleavage-activating protein OS=Bos taurus GN=SCAP PE=2 SV=1

 Score = 82.8 bits (203), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 36/68 (52%), Positives = 48/68 (70%)

Query: 21  VLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGL 80
           + PY ++++GLEN+LVLTKS++S P  L+ K+RIAQGLS E WSI KN   EL ++  G 
Sbjct: 348 IFPYLVVVIGLENVLVLTKSVVSTPVDLEVKLRIAQGLSSESWSIMKNMATELGIVLIGY 407

Query: 81  LTFFPVIQ 88
            T  P IQ
Sbjct: 408 FTLVPAIQ 415

Escort protein required for cholesterol as well as lipid homeostasis. Regulates export of the SCAP/SREBF complex from the ER upon low cholesterol. Formation of a ternary complex with INSIG at high sterol concentrations leads to masking of an ER-export signal in SCAP and retention of the complex in the ER. Low sterol concentrations trigger release of INSIG, a conformational change in the SSC domain of SCAP, unmasking of the ER export signal, recruitment into COPII-coated vesicles, transport to the Golgi complex, proteolytic cleavage of SREBF in the Golgi, release of the transcription factor fragment of SREBF from the membrane, its import into the nucleus and up-regulation of LDLR, INSIG1 and the mevalonate pathway.

Bos taurus (taxid: 9913)

>sp|Q6GQT6|SCAP_MOUSE Sterol regulatory element-binding protein cleavage-activating protein OS=Mus musculus GN=Scap PE=1 SV=1

 Score = 82.8 bits (203), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 36/68 (52%), Positives = 48/68 (70%)

Query: 21  VLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGL 80
           + PY ++++GLEN+LVLTKS++S P  L+ K+RIAQGLS E WSI KN   EL ++  G 
Sbjct: 348 IFPYLVVVIGLENVLVLTKSVVSTPVDLEVKLRIAQGLSSESWSIMKNAATELGIILIGY 407

Query: 81  LTFFPVIQ 88
            T  P IQ
Sbjct: 408 FTLVPAIQ 415

Escort protein required for cholesterol as well as lipid homeostasis. Regulates export of the SCAP/SREBF complex from the ER upon low cholesterol. Formation of a ternary complex with INSIG at high sterol concentrations leads to masking of an ER-export signal in SCAP and retention of the complex in the ER. Low sterol concentrations trigger release of INSIG, a conformational change in the SSC domain of SCAP, unmasking of the ER export signal, recruitment into COPII-coated vesicles, transport to the Golgi complex, proteolytic cleavage of SREBF in the Golgi, release of the transcription factor fragment of SREBF from the membrane, its import into the nucleus and up-regulation of LDLR, INSIG1 and the mevalonate pathway.

Mus musculus (taxid: 10090)

>sp|A0JPH4|SCAP_XENLA Sterol regulatory element-binding protein cleavage-activating protein OS=Xenopus laevis GN=scap PE=2 SV=1

 Score = 80.1 bits (196), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 34/68 (50%), Positives = 46/68 (67%)

Query: 21  VLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGL 80
           + PY ++++GLEN+LVLTKS++S P  L+ K+RIAQGL  E W I KN   EL ++  G 
Sbjct: 346 IFPYLVVVIGLENVLVLTKSVVSTPVDLEVKLRIAQGLRNESWFIMKNMATELGIILIGY 405

Query: 81  LTFFPVIQ 88
            T  P IQ
Sbjct: 406 FTLVPAIQ 413

Escort protein required for cholesterol as well as lipid homeostasis. Regulates export of the scap/srebf complex from the ER upon low cholesterol. Low sterol concentrations trigger a conformational change in the SSC domain of scap, unmasking of the ER export signal, recruitment into COPII-coated vesicles, transport to the Golgi complex, proteolytic cleavage of srebf in the Golgi, release of the transcription factor fragment of srebf from the membrane, its import into the nucleus and up-regulation of ldlr, and the mevalonate pathway.

Xenopus laevis (taxid: 8355)

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	89
345484020	1335	PREDICTED: sterol regulatory element-bin	0.764	0.050	0.735	1e-21
383854002	1322	PREDICTED: sterol regulatory element-bin	0.764	0.051	0.705	5e-21
66555130	1329	PREDICTED: sterol regulatory element-bin	0.775	0.051	0.681	7e-21
380020480	1328	PREDICTED: LOW QUALITY PROTEIN: sterol r	0.764	0.051	0.705	8e-21
350411518	1328	PREDICTED: sterol regulatory element-bin	0.764	0.051	0.705	9e-21
340729793	1328	PREDICTED: sterol regulatory element-bin	0.764	0.051	0.705	9e-21
260811942	1454	hypothetical protein BRAFLDRAFT_118545 [	0.764	0.046	0.676	3e-20
170055672	1260	sterol regulatory element-binding protei	0.764	0.053	0.661	4e-20
321478572	1235	hypothetical protein DAPPUDRAFT_190908 [	0.764	0.055	0.632	5e-20
332016798	1437	Sterol regulatory element-binding protei	0.764	0.047	0.676	6e-20

>gi|345484020|ref|XP_003424927.1| PREDICTED: sterol regulatory element-binding protein cleavage-activating protein-like [Nasonia vitripennis]

 Score =  107 bits (266), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 50/68 (73%), Positives = 57/68 (83%)

Query: 21  VLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGL 80
           V PY +IIVGLEN+LVLTKSI+S P+HLD KIR+AQGLSKEGWSITKN   E+T+LT GL
Sbjct: 325 VFPYLVIIVGLENVLVLTKSIVSTPAHLDVKIRVAQGLSKEGWSITKNLLTEVTILTIGL 384

Query: 81  LTFFPVIQ 88
            TF P IQ
Sbjct: 385 FTFVPAIQ 392

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383854002|ref|XP_003702511.1| PREDICTED: sterol regulatory element-binding protein cleavage-activating protein-like [Megachile rotundata]

 Score =  104 bits (260), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 48/68 (70%), Positives = 56/68 (82%)

Query: 21  VLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGL 80
           V PY +IIVGLEN+L+LTKS++S PSHLD KIR+AQ LSKEGWSITKN   E+T+LT GL
Sbjct: 332 VFPYLVIIVGLENVLILTKSVVSTPSHLDVKIRVAQALSKEGWSITKNLLTEVTILTIGL 391

Query: 81  LTFFPVIQ 88
            TF P IQ
Sbjct: 392 FTFVPAIQ 399

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66555130|ref|XP_394934.2| PREDICTED: sterol regulatory element-binding protein cleavage-activating protein-like [Apis mellifera]

 Score =  104 bits (259), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 47/69 (68%), Positives = 57/69 (82%)

Query: 20  IVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAG 79
           ++ PY +IIVGLEN+LVLTKS++S P+HLD KIR+AQ LSKEGWSITKN   E+T+LT G
Sbjct: 334 VIFPYLVIIVGLENVLVLTKSVVSTPAHLDVKIRVAQALSKEGWSITKNLLTEVTILTIG 393

Query: 80  LLTFFPVIQ 88
           L TF P IQ
Sbjct: 394 LFTFVPAIQ 402

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380020480|ref|XP_003694111.1| PREDICTED: LOW QUALITY PROTEIN: sterol regulatory element-binding protein cleavage-activating protein-like [Apis florea]

 Score =  104 bits (259), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 48/68 (70%), Positives = 56/68 (82%)

Query: 21  VLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGL 80
           V PY +IIVGLEN+LVLTKS++S P+HLD KIR+AQ LSKEGWSITKN   E+T+LT GL
Sbjct: 334 VFPYLVIIVGLENVLVLTKSVVSTPAHLDVKIRVAQALSKEGWSITKNLLTEVTILTIGL 393

Query: 81  LTFFPVIQ 88
            TF P IQ
Sbjct: 394 FTFVPAIQ 401

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350411518|ref|XP_003489375.1| PREDICTED: sterol regulatory element-binding protein cleavage-activating protein-like [Bombus impatiens]

 Score =  104 bits (259), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 48/68 (70%), Positives = 56/68 (82%)

Query: 21  VLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGL 80
           V PY +IIVGLEN+LVLTKS++S P+HLD KIR+AQ LSKEGWSITKN   E+T+LT GL
Sbjct: 334 VFPYLVIIVGLENVLVLTKSVVSTPAHLDVKIRVAQALSKEGWSITKNLLTEVTILTIGL 393

Query: 81  LTFFPVIQ 88
            TF P IQ
Sbjct: 394 FTFVPAIQ 401

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340729793|ref|XP_003403180.1| PREDICTED: sterol regulatory element-binding protein cleavage-activating protein-like [Bombus terrestris]

 Score =  103 bits (258), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 48/68 (70%), Positives = 56/68 (82%)

Query: 21  VLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGL 80
           V PY +IIVGLEN+LVLTKS++S P+HLD KIR+AQ LSKEGWSITKN   E+T+LT GL
Sbjct: 334 VFPYLVIIVGLENVLVLTKSVVSTPAHLDVKIRVAQALSKEGWSITKNLLTEVTILTIGL 393

Query: 81  LTFFPVIQ 88
            TF P IQ
Sbjct: 394 FTFVPAIQ 401

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|260811942|ref|XP_002600680.1| hypothetical protein BRAFLDRAFT_118545 [Branchiostoma floridae] gi|229285969|gb|EEN56692.1| hypothetical protein BRAFLDRAFT_118545 [Branchiostoma floridae]

 Score =  102 bits (255), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 46/68 (67%), Positives = 52/68 (76%)

Query: 21  VLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGL 80
           + PY ++IVGLENILVLTKS++S P HLD  IRIAQGLSKEGWSITKN   EL +  AG 
Sbjct: 368 IFPYLVVIVGLENILVLTKSVVSTPVHLDVNIRIAQGLSKEGWSITKNLLTELAIACAGY 427

Query: 81  LTFFPVIQ 88
            TF P IQ
Sbjct: 428 FTFVPAIQ 435

Source: Branchiostoma floridae

Species: Branchiostoma floridae

Genus: Branchiostoma

Family: Branchiostomidae

Phylum: Chordata

Superkingdom: Eukaryota

>gi|170055672|ref|XP_001863686.1| sterol regulatory element-binding protein cleavage-activating protein [Culex quinquefasciatus] gi|167875561|gb|EDS38944.1| sterol regulatory element-binding protein cleavage-activating protein [Culex quinquefasciatus]

 Score =  102 bits (253), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 45/68 (66%), Positives = 58/68 (85%)

Query: 21  VLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGL 80
           V PY +I+VGLEN+LV+TKS+++  ++LD KIR+AQGLS+EGWSITKN  LE+T+LT GL
Sbjct: 359 VYPYLVILVGLENVLVITKSVLTTDNNLDVKIRVAQGLSREGWSITKNLLLEITILTIGL 418

Query: 81  LTFFPVIQ 88
            TF PVIQ
Sbjct: 419 CTFVPVIQ 426

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321478572|gb|EFX89529.1| hypothetical protein DAPPUDRAFT_190908 [Daphnia pulex]

 Score =  101 bits (252), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 43/68 (63%), Positives = 56/68 (82%)

Query: 21  VLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGL 80
           + PY ++IVGLENILVLT+S++S P++LD KIR+AQGLS+EGW+ITKN   E+T+LT G 
Sbjct: 381 IFPYLVVIVGLENILVLTRSVVSTPANLDVKIRVAQGLSREGWNITKNLLTEVTILTVGF 440

Query: 81  LTFFPVIQ 88
            TF P IQ
Sbjct: 441 FTFVPAIQ 448

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332016798|gb|EGI57619.1| Sterol regulatory element-binding protein cleavage-activating protein [Acromyrmex echinatior]

 Score =  101 bits (251), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 46/68 (67%), Positives = 53/68 (77%)

Query: 21  VLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGL 80
           V PY +II GLENI VLTKS++S P+ LD KIR+AQ LSKEGWSITKN   E+T+LT GL
Sbjct: 443 VFPYLVIIFGLENIQVLTKSVVSTPAQLDVKIRVAQALSKEGWSITKNLLTEVTILTIGL 502

Query: 81  LTFFPVIQ 88
            TF P IQ
Sbjct: 503 FTFVPAIQ 510

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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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	89
FB|FBgn0033052	1276	SCAP "SCAP" [Drosophila melano	0.662	0.046	0.610	4.4e-13
ZFIN|ZDB-GENE-040107-41	1252	scap "SREBF chaperone" [Danio	0.662	0.047	0.593	2.4e-12
UNIPROTKB|F8W921	1023	SCAP "Sterol regulatory elemen	0.662	0.057	0.576	1e-11
UNIPROTKB|F1PI33	1278	SCAP "Uncharacterized protein"	0.662	0.046	0.576	1.4e-11
UNIPROTKB|Q12770	1279	SCAP "Sterol regulatory elemen	0.662	0.046	0.576	1.4e-11
UNIPROTKB|Q5MNU5	1279	SCAP "Sterol regulatory elemen	0.662	0.046	0.576	1.4e-11
UNIPROTKB|F1SNT3	1280	SCAP "Sterol regulatory elemen	0.662	0.046	0.576	1.4e-11
UNIPROTKB|P97260	1276	SCAP "Sterol regulatory elemen	0.662	0.046	0.576	1.8e-11
RGD|1309378	1276	Scap "SREBF chaperone" [Rattus	0.662	0.046	0.576	1.8e-11
UNIPROTKB|A6QM06	1278	SCAP "Sterol regulatory elemen	0.662	0.046	0.576	1.8e-11

FB|FBgn0033052 SCAP "SCAP" [Drosophila melanogaster (taxid:7227)]

 Score = 186 (70.5 bits), Expect = 4.4e-13, P = 4.4e-13
 Identities = 36/59 (61%), Positives = 44/59 (74%)

Query:    30 GLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFPVIQ 88
             GLEN LV+TKS++S+    D KIR+AQ LSKEGW I+K    E+T+LT GL TF PVIQ
Sbjct:   439 GLENSLVITKSVVSMDETFDVKIRVAQALSKEGWHISKTLLTEITILTIGLATFVPVIQ 497

GO:0000042 "protein targeting to Golgi" evidence=NAS

GO:0035103 "sterol regulatory element binding protein cleavage" evidence=NAS

GO:0016485 "protein processing" evidence=NAS

GO:0016021 "integral to membrane" evidence=IEA

ZFIN|ZDB-GENE-040107-41 scap "SREBF chaperone" [Danio rerio (taxid:7955)]

 Score = 179 (68.1 bits), Expect = 2.4e-12, P = 2.4e-12
 Identities = 35/59 (59%), Positives = 42/59 (71%)

Query:    30 GLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFPVIQ 88
             GLEN+LVLTKS++S P  L+ K+RIAQGLS E WSI KN   EL ++  G  TF P IQ
Sbjct:   354 GLENVLVLTKSVVSTPVDLEVKLRIAQGLSNESWSIMKNMATELCIILIGYFTFVPAIQ 412

GO:0016021 "integral to membrane" evidence=IEA

GO:0006629 "lipid metabolic process" evidence=IMP

GO:0019915 "lipid storage" evidence=IMP

UNIPROTKB|F8W921 SCAP "Sterol regulatory element-binding protein cleavage-activating protein" [Homo sapiens (taxid:9606)]

 Score = 172 (65.6 bits), Expect = 1.0e-11, P = 1.0e-11
 Identities = 34/59 (57%), Positives = 41/59 (69%)

Query:    30 GLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFPVIQ 88
             GLEN+LVLTKS++S P  L+ K+RIAQGLS E WSI KN   EL ++  G  T  P IQ
Sbjct:   102 GLENVLVLTKSVVSTPVDLEVKLRIAQGLSSESWSIMKNMATELGIILIGYFTLVPAIQ 160

GO:0016021 "integral to membrane" evidence=IEA

UNIPROTKB|F1PI33 SCAP "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 172 (65.6 bits), Expect = 1.4e-11, P = 1.4e-11
 Identities = 34/59 (57%), Positives = 41/59 (69%)

Query:    30 GLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFPVIQ 88
             GLEN+LVLTKS++S P  L+ K+RIAQGLS E WSI KN   EL ++  G  T  P IQ
Sbjct:   357 GLENVLVLTKSVVSTPVDLEVKLRIAQGLSSESWSIMKNMATELGIILIGYFTLVPAIQ 415

GO:0016021 "integral to membrane" evidence=IEA

UNIPROTKB|Q12770 SCAP "Sterol regulatory element-binding protein cleavage-activating protein" [Homo sapiens (taxid:9606)]

 Score = 172 (65.6 bits), Expect = 1.4e-11, P = 1.4e-11
 Identities = 34/59 (57%), Positives = 41/59 (69%)

Query:    30 GLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFPVIQ 88
             GLEN+LVLTKS++S P  L+ K+RIAQGLS E WSI KN   EL ++  G  T  P IQ
Sbjct:   357 GLENVLVLTKSVVSTPVDLEVKLRIAQGLSSESWSIMKNMATELGIILIGYFTLVPAIQ 415

GO:0001666 "response to hypoxia" evidence=IEA

GO:0007568 "aging" evidence=IEA

GO:0008203 "cholesterol metabolic process" evidence=IEA

GO:0032403 "protein complex binding" evidence=IEA

GO:0032868 "response to insulin stimulus" evidence=IEA

GO:0042304 "regulation of fatty acid biosynthetic process" evidence=IEA

GO:0043234 "protein complex" evidence=IEA

GO:0000139 "Golgi membrane" evidence=IEA

GO:0005789 "endoplasmic reticulum membrane" evidence=IEA

GO:0012507 "ER to Golgi transport vesicle membrane" evidence=IEA

GO:0045541 "negative regulation of cholesterol biosynthetic process" evidence=NAS

GO:0005794 "Golgi apparatus" evidence=NAS

GO:0051082 "unfolded protein binding" evidence=NAS

GO:0005783 "endoplasmic reticulum" evidence=NAS

GO:0032933 "SREBP signaling pathway" evidence=IMP

GO:0016021 "integral to membrane" evidence=NAS

GO:0045716 "positive regulation of low-density lipoprotein particle receptor biosynthetic process" evidence=NAS

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|Q5MNU5 SCAP "Sterol regulatory element-binding protein cleavage-activating protein" [Sus scrofa (taxid:9823)]

 Score = 172 (65.6 bits), Expect = 1.4e-11, P = 1.4e-11
 Identities = 34/59 (57%), Positives = 41/59 (69%)

Query:    30 GLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFPVIQ 88
             GLEN+LVLTKS++S P  L+ K+RIAQGLS E WSI KN   EL ++  G  T  P IQ
Sbjct:   357 GLENVLVLTKSVVSTPVDLEVKLRIAQGLSSESWSIMKNMATELGIILIGYFTLVPAIQ 415

GO:0012507 "ER to Golgi transport vesicle membrane" evidence=IEA

GO:0005789 "endoplasmic reticulum membrane" evidence=IEA

GO:0000139 "Golgi membrane" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0008203 "cholesterol metabolic process" evidence=IEA

UNIPROTKB|F1SNT3 SCAP "Sterol regulatory element-binding protein cleavage-activating protein" [Sus scrofa (taxid:9823)]

 Score = 172 (65.6 bits), Expect = 1.4e-11, P = 1.4e-11
 Identities = 34/59 (57%), Positives = 41/59 (69%)

Query:    30 GLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFPVIQ 88
             GLEN+LVLTKS++S P  L+ K+RIAQGLS E WSI KN   EL ++  G  T  P IQ
Sbjct:   357 GLENVLVLTKSVVSTPVDLEVKLRIAQGLSSESWSIMKNMATELGIILIGYFTLVPAIQ 415

GO:0045540 "regulation of cholesterol biosynthetic process" evidence=IEA

GO:0042304 "regulation of fatty acid biosynthetic process" evidence=IEA

GO:0032933 "SREBP signaling pathway" evidence=IEA

GO:0032868 "response to insulin stimulus" evidence=IEA

GO:0008203 "cholesterol metabolic process" evidence=IEA

GO:0005789 "endoplasmic reticulum membrane" evidence=IEA

GO:0001666 "response to hypoxia" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

UNIPROTKB|P97260 SCAP "Sterol regulatory element-binding protein cleavage-activating protein" [Cricetulus griseus (taxid:10029)]

 Score = 171 (65.3 bits), Expect = 1.8e-11, P = 1.8e-11
 Identities = 34/59 (57%), Positives = 41/59 (69%)

Query:    30 GLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFPVIQ 88
             GLEN+LVLTKS++S P  L+ K+RIAQGLS E WSI KN   EL ++  G  T  P IQ
Sbjct:   357 GLENVLVLTKSVVSTPVDLEVKLRIAQGLSSESWSIMKNVATELGIILIGYFTLVPAIQ 415

GO:0005515 "protein binding" evidence=IPI

GO:0005783 "endoplasmic reticulum" evidence=IDA

GO:0008022 "protein C-terminus binding" evidence=IPI

GO:0016020 "membrane" evidence=IDA

GO:0032933 "SREBP signaling pathway" evidence=ISS

GO:0035105 "sterol regulatory element binding protein import into nucleus" evidence=IMP

GO:0072600 "establishment of protein localization to Golgi" evidence=IMP

GO:0090110 "cargo loading into COPII-coated vesicle" evidence=IDA

GO:0030127 "COPII vesicle coat" evidence=IDA

RGD|1309378 Scap "SREBF chaperone" [Rattus norvegicus (taxid:10116)]

 Score = 171 (65.3 bits), Expect = 1.8e-11, P = 1.8e-11
 Identities = 34/59 (57%), Positives = 41/59 (69%)

Query:    30 GLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFPVIQ 88
             GLEN+LVLTKS++S P  L+ K+RIAQGLS E WSI KN   EL ++  G  T  P IQ
Sbjct:   357 GLENVLVLTKSVVSTPVDLEVKLRIAQGLSSESWSIMKNVATELGIILIGYFTLVPAIQ 415

GO:0000139 "Golgi membrane" evidence=IEA

GO:0001666 "response to hypoxia" evidence=IEA;ISO

GO:0005789 "endoplasmic reticulum membrane" evidence=IEA;ISO

GO:0007568 "aging" evidence=IEP

GO:0008203 "cholesterol metabolic process" evidence=IEA;ISO

GO:0012507 "ER to Golgi transport vesicle membrane" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0019217 "regulation of fatty acid metabolic process" evidence=ISO

GO:0032403 "protein complex binding" evidence=IPI

GO:0032868 "response to insulin stimulus" evidence=IEA;ISO

GO:0032933 "SREBP signaling pathway" evidence=IEA;ISO

GO:0042304 "regulation of fatty acid biosynthetic process" evidence=IEA;ISO

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

GO:0043234 "protein complex" evidence=IDA

GO:0045540 "regulation of cholesterol biosynthetic process" evidence=IEA;ISO

UNIPROTKB|A6QM06 SCAP "Sterol regulatory element-binding protein cleavage-activating protein" [Bos taurus (taxid:9913)]

 Score = 171 (65.3 bits), Expect = 1.8e-11, P = 1.8e-11
 Identities = 34/59 (57%), Positives = 41/59 (69%)

Query:    30 GLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFPVIQ 88
             GLEN+LVLTKS++S P  L+ K+RIAQGLS E WSI KN   EL ++  G  T  P IQ
Sbjct:   357 GLENVLVLTKSVVSTPVDLEVKLRIAQGLSSESWSIMKNMATELGIVLIGYFTLVPAIQ 415

GO:0012507 "ER to Golgi transport vesicle membrane" evidence=IEA

GO:0005789 "endoplasmic reticulum membrane" evidence=IEA

GO:0000139 "Golgi membrane" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0008203 "cholesterol metabolic process" evidence=IEA

---

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)
A2RRU4	SCAP_RAT	No assigned EC number	0.5294	0.7640	0.0532	yes	N/A
P97260	SCAP_CRIGR	No assigned EC number	0.5294	0.7640	0.0532	yes	N/A
Q12770	SCAP_HUMAN	No assigned EC number	0.5294	0.7640	0.0531	yes	N/A
Q5MNU5	SCAP_PIG	No assigned EC number	0.5294	0.7640	0.0531	yes	N/A
Q6GQT6	SCAP_MOUSE	No assigned EC number	0.5294	0.7640	0.0532	yes	N/A
A6QM06	SCAP_BOVIN	No assigned EC number	0.5294	0.7640	0.0532	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	89
pfam12349	153	pfam12349, Sterol-sensing, Sterol-sensing domain o	1e-14

>gnl|CDD|192997 pfam12349, Sterol-sensing, Sterol-sensing domain of SREBP cleavage-activation

 Score = 64.1 bits (157), Expect = 1e-14
 Identities = 24/72 (33%), Positives = 38/72 (52%)

Query: 18  IIIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLT 77
              V+P+ ++ VG++N+ +L  ++   P  LD + RIA+ L + G SIT     EL    
Sbjct: 38  PGEVIPFLVLAVGVDNMFLLVHAVQRTPRSLDVEERIAEALGEVGPSITLTSLTELLAFL 97

Query: 78  AGLLTFFPVIQI 89
            G LT  P +Q 
Sbjct: 98  IGALTPMPAVQE 109

Sterol regulatory element-binding proteins (SREBPs) are membrane-bound transcription factors that promote lipid synthesis in animal cells. They are embedded in the membranes of the endoplasmic reticulum (ER) in a helical hairpin orientation and are released from the ER by a two-step proteolytic process. Proteolysis begins when the SREBPs are cleaved at Site-1, which is located at a leucine residue in the middle of the hydrophobic loop in the lumen of the ER. Upon proteolytic processing SREBP can activate the expression of genes involved in cholesterol biosynthesis and uptake. SCAP stimulates cleavage of SREBPs via fusion of the their two C-termini. This domain is the transmembrane region that traverses the membrane eight times and is the sterol-sensing domain of the cleavage protein. WD40 domains are found towards the C-terminus. Length = 153

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	89
TIGR00920	886	2A060605 3-hydroxy-3-methylglutaryl-coenzyme A red	99.89
PF12349	153	Sterol-sensing: Sterol-sensing domain of SREBP cle	99.88
KOG1934|consensus	868		99.87
PF02460	798	Patched: Patched family; InterPro: IPR003392 The t	99.87
TIGR00918	1145	2A060602 The Eukaryotic (Putative) Sterol Transpor	99.87
TIGR00917	1204	2A060601 Niemann-Pick C type protein family. The m	99.77
KOG1933|consensus	1201		99.66
KOG1935|consensus	1143		99.31
TIGR00921	719	2A067 The (Largely Archaeal Putative) Hydrophobe/A	98.07
TIGR00921	719	2A067 The (Largely Archaeal Putative) Hydrophobe/A	97.68
COG1033	727	Predicted exporters of the RND superfamily [Genera	96.83
PF03176	333	MMPL: MMPL family; InterPro: IPR004869 Proteins of	96.55
TIGR03480	862	HpnN hopanoid biosynthesis associated RND transpor	96.5
PF02460	798	Patched: Patched family; InterPro: IPR003392 The t	95.68
TIGR00833	910	actII Transport protein. Characterized members of	95.57
TIGR00916	192	2A0604s01 protein-export membrane protein, SecD/Se	95.39
TIGR03480	862	HpnN hopanoid biosynthesis associated RND transpor	95.02
TIGR00918	1145	2A060602 The Eukaryotic (Putative) Sterol Transpor	94.72
COG1033	727	Predicted exporters of the RND superfamily [Genera	93.64
PRK13022	289	secF preprotein translocase subunit SecF; Reviewed	90.35
KOG1934|consensus	868		88.66
PF02355	189	SecD_SecF: Protein export membrane protein; InterP	88.53
PRK09579	1017	multidrug efflux protein; Reviewed	87.78
PRK10614	1025	multidrug efflux system subunit MdtC; Provisional	87.75
PRK10555	1037	aminoglycoside/multidrug efflux system; Provisiona	87.32
PRK09577	1032	multidrug efflux protein; Reviewed	86.89
TIGR00966	246	3a0501s07 protein-export membrane protein SecF. Th	86.74
TIGR00833	910	actII Transport protein. Characterized members of	86.61
PRK13024	755	bifunctional preprotein translocase subunit SecD/S	86.37
PRK13023	758	bifunctional preprotein translocase subunit SecD/S	84.91
TIGR01129	397	secD protein-export membrane protein SecD. SecD fr	82.47
TIGR00915	1044	2A0602 The (Largely Gram-negative Bacterial) Hydro	82.02
TIGR00917	1204	2A060601 Niemann-Pick C type protein family. The m	81.88
PRK08343	417	secD preprotein translocase subunit SecD; Reviewed	81.27

>TIGR00920 2A060605 3-hydroxy-3-methylglutaryl-coenzyme A reductase

Probab=99.89  E-value=3.4e-24  Score=183.50  Aligned_cols=86  Identities=22%  Similarity=0.254  Sum_probs=80.9

Q ss_pred             hhhhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhccCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhcc
Q psy16375          4 LTQFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTF   83 (89)
Q Consensus         4 ~~~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t~   83 (89)
                      -+|+|+++|+++|+|.|++|||+|+||+||+|+|++.-.++++++++++||+++|++.||||++++++|+++|++|+++.
T Consensus       107 S~Gl~s~lG~~~t~I~eViPFLvLaIGVDnifiLa~~~~~t~~~~~v~eRIa~~l~~vGpSItltslte~l~F~vGtls~  186 (886)
T TIGR00920       107 STAVIHFLGSELTGLNEALPFFLLLIDLSKASALAKFALSSNSQDEVRDNIARGMAILGPTITLDTVVETLVIGVGTMSG  186 (886)
T ss_pred             HHHHHHHhCCcHHHHHHHHhHHHhhhchhhHHHHHhhhhccCCCCCHHHHHHHHHHHhccceeHHHHHHHHHHHHhccCC
Confidence            36899999999999999999999999999999997663388899999999999999999999999999999999999999


Q ss_pred             CCcccC
Q psy16375         84 FPVIQI   89 (89)
Q Consensus        84 ~Pavq~   89 (89)
                      |||||.
T Consensus       187 mPAV~~  192 (886)
T TIGR00920       187 VRRLEV  192 (886)
T ss_pred             CHHHHH
Confidence            999983

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

Probab=99.88  E-value=1.1e-23  Score=148.17  Aligned_cols=84  Identities=27%  Similarity=0.402  Sum_probs=80.8

Q ss_pred             hhhhhhcccchhh-hhhccceeeEeeecchhhhHhhhhhccCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhcc
Q psy16375          5 TQFRKPNGVLPYF-IIIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTF   83 (89)
Q Consensus         5 ~~~~s~~gv~~tl-i~eViPFLVl~IGvDniflit~av~~t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t~   83 (89)
                      -++++++|++.++ ..|++|||+++||+||+|.++|+|.+++.+.++++|++++++++|||+++++++|+.+|.+|++++
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            3778999999999 679999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCccc
Q psy16375         84 FPVIQ   88 (89)
Q Consensus        84 ~Pavq   88 (89)
                      +|++|
T Consensus       104 ~~~l~  108 (153)
T PF12349_consen  104 VPALR  108 (153)
T ss_pred             hHHHH
Confidence            99986

>KOG1934|consensus

Probab=99.87  E-value=4.2e-23  Score=177.06  Aligned_cols=84  Identities=21%  Similarity=0.315  Sum_probs=81.2

Q ss_pred             hhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhccCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhccCC
Q psy16375          6 QFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFP   85 (89)
Q Consensus         6 ~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t~~P   85 (89)
                      |+..+.|++..-|.-|+||||++||+||+|+|.+||++|++++++||||+++++++||||++|++|++++|++|++|+.|
T Consensus       302 G~l~~~G~~f~sI~~v~PFLvl~IGVDD~Flml~aW~rt~~~~~~~~Rm~~~laeag~SItITSlTn~lsFgiG~~T~~p  381 (868)
T KOG1934|consen  302 GLLFWCGFPFNSIVCVMPFLVLGIGVDDAFLMLAAWRRTSKKLSVEERMAETLAEAGPSITITSLTNVLSFGIGAITPTP  381 (868)
T ss_pred             HHHHHcCCCCcceeeecchheeeecccHHHHHHHHHHhcCccCCHHHHHHHHHHHhcCeeeHHHHHHHHHHHhccCCCcH
Confidence            67788899888899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccC
Q psy16375         86 VIQI   89 (89)
Q Consensus        86 avq~   89 (89)
                      |||+
T Consensus       382 ~v~~  385 (868)
T KOG1934|consen  382 AVQI  385 (868)
T ss_pred             HHHH
Confidence            9984

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

Probab=99.87  E-value=2.6e-23  Score=173.88  Aligned_cols=84  Identities=20%  Similarity=0.368  Sum_probs=81.7

Q ss_pred             hhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhccCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhccCC
Q psy16375          6 QFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFP   85 (89)
Q Consensus         6 ~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t~~P   85 (89)
                      |+++++|++.+.+.+++|||+++||+||+|+++++|++++++.+++||++++++++||||++|++|++++|++|+++++|
T Consensus       268 Gl~~~~G~~~~~i~~v~PFLvlgIGvDd~Fi~~~~~~~~~~~~~~~er~~~~l~~~g~SitiTslT~~~aF~ig~~t~~p  347 (798)
T PF02460_consen  268 GLLSLFGVPFNPIVLVIPFLVLGIGVDDMFIMIHAWRRTSPDLSVEERMAETLAEAGPSITITSLTNALAFAIGAITPIP  347 (798)
T ss_pred             HHHHHcCccchhhHHHHHHHHHHHHHhceEEeHHHHhhhchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcH
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccC
Q psy16375         86 VIQI   89 (89)
Q Consensus        86 avq~   89 (89)
                      |||.
T Consensus       348 av~~  351 (798)
T PF02460_consen  348 AVRS  351 (798)
T ss_pred             HHHH
Confidence            9983

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

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

Probab=99.87  E-value=4.9e-23  Score=180.33  Aligned_cols=85  Identities=16%  Similarity=0.252  Sum_probs=82.1

Q ss_pred             hhhhhhcccchhhh-hhccceeeEeeecchhhhHhhhhhccCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhcc
Q psy16375          5 TQFRKPNGVLPYFI-IIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTF   83 (89)
Q Consensus         5 ~~~~s~~gv~~tli-~eViPFLVl~IGvDniflit~av~~t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t~   83 (89)
                      .|+++++|++.|++ .+|+|||+|+||+||+|+|+|+|++++++.++++|+++++++.||||++|++||+++|++|++++
T Consensus       445 ~Gl~~~~Gi~fn~i~~~ViPFLvLgIGVDn~Fllv~~~~~t~~~~~v~~r~~~~l~~~g~SI~~tslt~~~aF~~ga~t~  524 (1145)
T TIGR00918       445 LGLCALLGISFNAATTQVLPFLALGVGVDDVFLLAHAFSETGQNIPFEERTGECLKRTGASVVLTSISNVTAFFMAALIP  524 (1145)
T ss_pred             HHHHHHhCCchhHHHHhhhhHHHhhhhhcchhHHHHHHhhcCccCCHHHHHHHHHHHhcceeeHHHHHHHHHHHHHhcCC
Confidence            58999999999995 79999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcccC
Q psy16375         84 FPVIQI   89 (89)
Q Consensus        84 ~Pavq~   89 (89)
                      |||||.
T Consensus       525 ~Pavr~  530 (1145)
T TIGR00918       525 IPALRA  530 (1145)
T ss_pred             CHHHHH
Confidence            999973

>TIGR00917 2A060601 Niemann-Pick C type protein family

Probab=99.77  E-value=1.3e-19  Score=159.14  Aligned_cols=84  Identities=23%  Similarity=0.389  Sum_probs=77.8

Q ss_pred             hhhhhhcccchhh-hhhccceeeEeeecchhhhHhhhhhccCC-----------CCCHHHHHHHHHhhhchHHHHHHHHH
Q psy16375          5 TQFRKPNGVLPYF-IIIVLPYFIIIVGLENILVLTKSIISIPS-----------HLDSKIRIAQGLSKEGWSITKNFFLE   72 (89)
Q Consensus         5 ~~~~s~~gv~~tl-i~eViPFLVl~IGvDniflit~av~~t~~-----------~~~v~~RIa~~ls~~G~SIt~t~lte   72 (89)
                      .|+++++|++.|+ +.|++||||++||+||+|+++++|.+...           +.++++||+++++++||||++|++|+
T Consensus       623 ~Gl~~~~Gi~~t~i~~~v~PFLvL~IGVD~ifilv~~~~r~~~~~~~~~~~~~~~~~~~~ri~~~l~~~G~sI~ltslt~  702 (1204)
T TIGR00917       623 VGVFSYIGLKATLIIMEVIPFLVLAVGVDNIFILVQTYQRLERFYREVGVDNEQELTLEQQLGRALGEVGPSITLASLSE  702 (1204)
T ss_pred             HHHHHHhCCcchHHHHHHHHHHHHHHHhhHHHHHHHHHHHhhhccccccccccccCCHHHHHHHHHHHhhHHHHHHHHHH
Confidence            4889999999998 69999999999999999999999976432           23899999999999999999999999


Q ss_pred             HHHHHHhhhccCCccc
Q psy16375         73 LTVLTAGLLTFFPVIQ   88 (89)
Q Consensus        73 i~~f~iG~~t~~Pavq   88 (89)
                      +++|++|+++++||||
T Consensus       703 ~~aF~~g~~s~~Pavr  718 (1204)
T TIGR00917       703 SLAFFLGALSKMPAVR  718 (1204)
T ss_pred             HHHHHHHhccCChHHH
Confidence            9999999999999997

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=99.66  E-value=2e-17  Score=145.65  Aligned_cols=83  Identities=24%  Similarity=0.329  Sum_probs=79.1

Q ss_pred             hhhhhcccchhh-hhhccceeeEeeecchhhhHhhhhhccCCC--CCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhc
Q psy16375          6 QFRKPNGVLPYF-IIIVLPYFIIIVGLENILVLTKSIISIPSH--LDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLT   82 (89)
Q Consensus         6 ~~~s~~gv~~tl-i~eViPFLVl~IGvDniflit~av~~t~~~--~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t   82 (89)
                      |+||++|+++|+ +.||+||||+++|+||+|+++++..+....  .+.|+||..++.|.||||+.+++.|..+|.+|+++
T Consensus       601 g~FS~~gi~~t~i~i~VipflVlavgvdnifilv~~~qr~~~~~~~~~~~~I~~~l~~~~Psil~~slse~~~ff~g~~~  680 (1201)
T KOG1933|consen  601 GFFSYLGITSTLIIIEVIPFLVLAVGVDNIFILVHTYQRDGRSKSEPLEQRIGSVLGEVGPSILLSSLSENFCFFLGAFV  680 (1201)
T ss_pred             hHHHhhcchhhheeeeeeeeEEEEEeeccEEEEEeeecccccccCCCcccccchhhhccCcHHHHhHHHhhhHHhhhhcc
Confidence            699999999999 899999999999999999999999866555  88999999999999999999999999999999999


Q ss_pred             cCCccc
Q psy16375         83 FFPVIQ   88 (89)
Q Consensus        83 ~~Pavq   88 (89)
                      .||||.
T Consensus       681 ~mPav~  686 (1201)
T KOG1933|consen  681 DMPAVR  686 (1201)
T ss_pred             cCccee
Confidence            999986

>KOG1935|consensus

Probab=99.31  E-value=1e-12  Score=113.89  Aligned_cols=80  Identities=13%  Similarity=0.218  Sum_probs=75.0

Q ss_pred             hhhhhcccchhh-hhhccceeeEeeecchhhhHhhhhhccCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhccC
Q psy16375          6 QFRKPNGVLPYF-IIIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFF   84 (89)
Q Consensus         6 ~~~s~~gv~~tl-i~eViPFLVl~IGvDniflit~av~~t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t~~   84 (89)
                      |+++++|+...- -..|.|||-|++|+||||+++|+..+..+.   ++|+++-|+|.|+||..|++-++++|..|++.++
T Consensus       460 Gl~t~lGI~FNAAtTQVvPFLaLGlGVDd~FlL~hay~e~~~~---~~~~~~~lk~tG~Svl~tsinni~aF~~aallPI  536 (1143)
T KOG1935|consen  460 GLATLLGIEFNAATTQVVPFLALGLGVDDMFLLLHAYREVVKL---HEEMGELLKETGMSVLLTSINNILAFLMAALLPI  536 (1143)
T ss_pred             hHHHHhceeeccccceeehhhhhccChhHHHHHHHHHHHHhhh---HHHHHHHHHHhCcchhHHHhhhHHHHHHHhhcCc
Confidence            788999998877 688999999999999999999999988764   9999999999999999999999999999999999


Q ss_pred             Cccc
Q psy16375         85 PVIQ   88 (89)
Q Consensus        85 Pavq   88 (89)
                      ||.+
T Consensus       537 PALr  540 (1143)
T KOG1935|consen  537 PALR  540 (1143)
T ss_pred             HHHH
Confidence            9975

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

Probab=98.07  E-value=3.9e-06  Score=69.28  Aligned_cols=85  Identities=13%  Similarity=0.107  Sum_probs=74.6

Q ss_pred             hhhhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhc-cCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhc
Q psy16375          4 LTQFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIIS-IPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLT   82 (89)
Q Consensus         4 ~~~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~-t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t   82 (89)
                      ..|+..++|...+.+.-.+|.+++++|+|+-+.+.+.+++ .....+.++++.+++++.|++|+.+.+|-++.|+.-.++
T Consensus       234 ~~g~~~~~g~~l~~~~~~~~~l~lgi~vd~~ihl~~r~~~~~~~g~~~~~ai~~a~~~~g~~i~~t~~t~~~gf~~l~~s  313 (719)
T TIGR00921       234 VLGIMGWLGIPLYATTLLAVPMLIGVGIDYGIQTLNRYEEERDIGRAKGEAIVTAVRRTGRAVLIALLTTSAGFAALALS  313 (719)
T ss_pred             HHHHHHHhCCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHcCCCHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHhc
Confidence            3577888999888888889999999999999888877653 456778999999999999999999999999999999999


Q ss_pred             cCCccc
Q psy16375         83 FFPVIQ   88 (89)
Q Consensus        83 ~~Pavq   88 (89)
                      ++|.+|
T Consensus       314 ~~~~~~  319 (719)
T TIGR00921       314 EFPMVS  319 (719)
T ss_pred             cChHHH
Confidence            998775

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=97.68  E-value=3.9e-05  Score=63.43  Aligned_cols=85  Identities=14%  Similarity=0.204  Sum_probs=71.9

Q ss_pred             hhhhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhccCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhcc
Q psy16375          4 LTQFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTF   83 (89)
Q Consensus         4 ~~~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t~   83 (89)
                      ..|+..++|++.+...-+..-+.+++|+|+-+.+.+.+++...+.+.++++.+++++.|++++.+.++-++.|+.-+++.
T Consensus       608 ~~g~~~~~gi~l~~~~~~~~~i~lGigvDy~i~~~~r~~~~~~~~~~~~ai~~a~~~~g~ai~~s~lt~~~gf~~l~~s~  687 (719)
T TIGR00921       608 AIGLMGLRGIPSFLAMATTISIILGLGMDYSIHLAERYFEERKEHGPKEAITHTMERTGPGILFSGLTTAGGFLSLLLSH  687 (719)
T ss_pred             HHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhcc
Confidence            35677888998877666677799999999998888887765444678999999999999999999999999999989988


Q ss_pred             CCccc
Q psy16375         84 FPVIQ   88 (89)
Q Consensus        84 ~Pavq   88 (89)
                      .|.+|
T Consensus       688 ~~~~~  692 (719)
T TIGR00921       688 FPIMR  692 (719)
T ss_pred             CHHHH
Confidence            88765

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=96.83  E-value=0.0013  Score=56.87  Aligned_cols=83  Identities=10%  Similarity=0.071  Sum_probs=72.0

Q ss_pred             hhhhhcccchhhhhhccceeeEeeecchhhhHhhhhh-ccCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhccC
Q psy16375          6 QFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSII-SIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFF   84 (89)
Q Consensus         6 ~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~-~t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t~~   84 (89)
                      |+.-++|...|-.+-..|.+.+++|.|+-.-+.+... +.+...+.+|++.+++++.|+.+..+.+|...=|.-=+++.+
T Consensus       239 G~m~llG~plt~~s~~~~~llIgiGidy~vh~~nr~~ee~~~~~~~~eAv~~ai~~~g~avl~a~lTT~~GF~Sl~~s~i  318 (727)
T COG1033         239 GAMGLLGIPLTITTSAVPPLLIGIGIDYGVHFHNRYEEERRKGRTVEEAVVEAIKHTGPAVLIAALTTAAGFLSLLTSSI  318 (727)
T ss_pred             HHHHHhCCCchhHHHHHHHHHhhhhhhHHHHHHHHHHHHHhcCCCHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHccc
Confidence            5677889888888889999999999999988888765 455558899999999999999999999999999976678888


Q ss_pred             Cccc
Q psy16375         85 PVIQ   88 (89)
Q Consensus        85 Pavq   88 (89)
                      |+++
T Consensus       319 ~~i~  322 (727)
T COG1033         319 PAIK  322 (727)
T ss_pred             HHHH
Confidence            8764

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

Probab=96.55  E-value=0.0024  Score=48.39  Aligned_cols=65  Identities=15%  Similarity=0.236  Sum_probs=50.6

Q ss_pred             eeeEeeecchhhhHhhhhh-ccCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhccCCccc
Q psy16375         24 YFIIIVGLENILVLTKSII-SIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFPVIQ   88 (89)
Q Consensus        24 FLVl~IGvDniflit~av~-~t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t~~Pavq   88 (89)
                      .+.+++|+|.-..+.+-++ +-....+.++.+.+++++.|..|+.+.+|-+..|+.=.++..|.+|
T Consensus       209 ~l~lgvgidy~i~l~~r~ree~~~g~~~~~ai~~a~~~~g~~i~~s~ltt~~gf~~L~~s~~~~~~  274 (333)
T PF03176_consen  209 VLLLGVGIDYSIHLINRYREELRRGMSRKEAIRRAVRSTGRAILLSALTTAIGFGSLLFSPFPPLR  274 (333)
T ss_pred             hhHHHhhhhhHHHHHHHHHHHHHhccchHHHHHHHHhccCchhHHHHHHHHHHHHHHHHhhhhHHH
Confidence            3668899996666555554 3444567889999999999999999999999998876777776654

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=96.50  E-value=0.0021  Score=55.26  Aligned_cols=81  Identities=10%  Similarity=-0.005  Sum_probs=60.8

Q ss_pred             hhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhc-cCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhccC
Q psy16375          6 QFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIIS-IPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFF   84 (89)
Q Consensus         6 ~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~-t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t~~   84 (89)
                      ++..++|...+.++-+.|.+++++|+||-+.+.+...+ .....+.++.+.+++++.|++++.+.+|.+..|+.=.++.+
T Consensus       312 ~~~~l~~~~ln~~s~~~~~lliGi~vD~~I~~~~r~~e~~~~g~~~~~A~~~a~~~~~~~i~~s~lTt~~gf~~l~~~~~  391 (862)
T TIGR03480       312 AFATLAVGHLNLISVAFAVLFIGLGVDFAIQFSLRYREERFRGGNHREALSVAARRMGAALLLAALATAAGFFAFLPTDY  391 (862)
T ss_pred             HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Confidence            34455666666688889999999999997766655443 23345678899999999999999999999999864344444


Q ss_pred             Cc
Q psy16375         85 PV   86 (89)
Q Consensus        85 Pa   86 (89)
                      |.
T Consensus       392 ~~  393 (862)
T TIGR03480       392 KG  393 (862)
T ss_pred             HH
Confidence            43

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.

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

Probab=95.68  E-value=0.012  Score=50.24  Aligned_cols=78  Identities=14%  Similarity=0.137  Sum_probs=63.1

Q ss_pred             hhhhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhccCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhc
Q psy16375          4 LTQFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLT   82 (89)
Q Consensus         4 ~~~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t   82 (89)
                      +-|+.+++|++..-++-+.=-+.++..+|=.--++++..++..+ +.++|+.++|++.|++++...++-+++...=+++
T Consensus       686 v~G~m~~~g~~l~~vs~v~l~~~iG~sVd~~~Hi~~~f~~~~~~-~~~~r~~~al~~~g~pv~~~~~st~l~~~~l~f~  763 (798)
T PF02460_consen  686 VIGFMSLWGVDLDPVSMVNLIMSIGFSVDFSAHIAYAFVHSQGS-TRDERVAEALSSMGWPVLQGALSTFLGVLPLAFS  763 (798)
T ss_pred             HHHhhhccccCcchHHHHHHHHHhchhhHHHHHHHHHheecccc-hHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHh
Confidence            34788999999888766665666777789999999999888765 8999999999999999999988887665443333

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

>TIGR00833 actII Transport protein

Probab=95.57  E-value=0.0098  Score=51.81  Aligned_cols=67  Identities=18%  Similarity=0.118  Sum_probs=53.4

Q ss_pred             cceeeEeeecchhhhHhhhhhc-cCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhccCCccc
Q psy16375         22 LPYFIIIVGLENILVLTKSIIS-IPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFPVIQ   88 (89)
Q Consensus        22 iPFLVl~IGvDniflit~av~~-t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t~~Pavq   88 (89)
                      ++-+++++|+|+-+.+.+.+++ .....+.++.+.+++++.|+.|+.+.+|-+..|+--.++..|.++
T Consensus       237 l~~l~lGl~vDy~I~lv~r~~ee~~~g~~~~~Av~~a~~~~g~~I~~s~lT~~~gf~~l~~~~~~~~~  304 (910)
T TIGR00833       237 LTALVIGAGTDYAVFLTGRYHEERRKGESLEEAAAEALRGTGKAILGSALTVAVAFLALSLARLPSFK  304 (910)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccChHHH
Confidence            3467789999986666665543 344567889999999999999999999999999888888777554

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.

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

Probab=95.39  E-value=0.012  Score=42.78  Aligned_cols=76  Identities=14%  Similarity=-0.019  Sum_probs=62.3

Q ss_pred             hhhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhcc-C--CCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhh
Q psy16375          5 TQFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISI-P--SHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGL   80 (89)
Q Consensus         5 ~~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t-~--~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~   80 (89)
                      -+++.++|...+..+-.-+-+++++++||-+++....++. .  ...+.++.+.++.++.++++..+.+|-+..|.-=.
T Consensus        88 ~g~m~l~G~~ln~~s~~glil~iGi~Vd~aIvv~e~~~~~~~~~~g~~~~~Av~~a~~~~~~~il~ttlTtii~f~pl~  166 (192)
T TIGR00916        88 LGVLSLFGATLTLPGIAGLLTIIGYSVDDTVVIFDRIREELRKYKGRTFREAINLGINQTLSRIIDTNVTTLLAVLALY  166 (192)
T ss_pred             HHHHHHHCCcccHHHHHHHHHHHHHhhcCeEEehHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3567788888888777788888999999999888776542 2  45688999999999999999999999988876433

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.

>TIGR03480 HpnN hopanoid biosynthesis associated RND transporter like protein HpnN

Probab=95.02  E-value=0.023  Score=49.00  Aligned_cols=79  Identities=9%  Similarity=-0.014  Sum_probs=60.7

Q ss_pred             hhhhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhccCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhcc
Q psy16375          4 LTQFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTF   83 (89)
Q Consensus         4 ~~~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t~   83 (89)
                      ..++..++|++.++..-+.--++++||+|+-+.+.+.+++...+..    ..  -++.|.+|+.+.+|-++.|+.=+++.
T Consensus       753 ~~g~m~~~gi~l~~~~~~~~~l~lGigVDy~I~~~~r~~~~~~~~~----~~--~~~~g~ai~~saltt~~gf~~l~~s~  826 (862)
T TIGR03480       753 TVAAMVLLGIPFNFANIIALPLLLGLGVDFGIYMVHRWRNGVDSGN----LL--QSSTARAVFFSALTTATAFGSLAVSS  826 (862)
T ss_pred             HHHHHHHHhccCcHHHHHHHHHHHhhhhhhHHHHHHHHHHhccchh----HH--HhhhHHHHHHHHHHHHHHHHHHHHhc
Confidence            3567788899998855555557799999999999998876532111    11  14679999999999999999999999


Q ss_pred             CCccc
Q psy16375         84 FPVIQ   88 (89)
Q Consensus        84 ~Pavq   88 (89)
                      .|..+
T Consensus       827 ~~~~~  831 (862)
T TIGR03480       827 HPGTA  831 (862)
T ss_pred             CccHH
Confidence            99864

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.

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

Probab=94.72  E-value=0.049  Score=49.43  Aligned_cols=72  Identities=14%  Similarity=0.063  Sum_probs=60.1

Q ss_pred             hhhhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhccCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHH
Q psy16375          4 LTQFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLT   77 (89)
Q Consensus         4 ~~~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~   77 (89)
                      +-|+.+++|++.+.++-+.=-+-+++|||-..-++++..+...  +.++|+.++|++.|++++...+|-++.+.
T Consensus      1006 v~G~M~lwgI~LnaVS~vnLimsIGisVefsaHI~~~F~~~~~--~r~eR~~~AL~~~G~pVl~g~lTT~lGvl 1077 (1145)
T TIGR00918      1006 LFGMMGLLGIKLSAIPVVILIASVGIGVEFTVHIALGFLTAIG--DRNRRAVLALEHMFAPVLDGALSTLLGVL 1077 (1145)
T ss_pred             HHHHHHHHcCCccHHHHHHHHHHHhhhhhhhHHHHHHHHhcCC--CHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence            4588899999999877777667799999999999999886543  46999999999999999999987755543

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

Probab=93.64  E-value=0.096  Score=45.61  Aligned_cols=82  Identities=16%  Similarity=0.136  Sum_probs=67.8

Q ss_pred             hhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhccCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhccCC
Q psy16375          6 QFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFP   85 (89)
Q Consensus         6 ~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t~~P   85 (89)
                      ++--++|++.++....+==+++++|+|--+.+++...+.-.+...+|.+-+++++.|+.++-+.+|-..=|+.=.+++.|
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            34557889999977778889999999999999998775443333889999999999999999999988888777777777


Q ss_pred             cc
Q psy16375         86 VI   87 (89)
Q Consensus        86 av   87 (89)
                      .+
T Consensus       691 i~  692 (727)
T COG1033         691 II  692 (727)
T ss_pred             HH
Confidence            64

>PRK13022 secF preprotein translocase subunit SecF; Reviewed

Probab=90.35  E-value=0.15  Score=39.29  Aligned_cols=74  Identities=14%  Similarity=-0.041  Sum_probs=59.5

Q ss_pred             hhhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhcc---CCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHH
Q psy16375          5 TQFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISI---PSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTA   78 (89)
Q Consensus         5 ~~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t---~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~i   78 (89)
                      -++++++|...++.+-.-.-.++++.+||-+++...+++.   .++.+.++.+.++.++....+..+++|-+..|.-
T Consensus       168 lg~~~l~g~~l~~~siaall~liG~sVnd~Ivv~drire~~~~~~~~~~~~av~~a~~~~~~~~l~TslTTl~~~l~  244 (289)
T PRK13022        168 LGIFSLFQIEFDLTVIAALLTIIGYSLNDTVVVFDRIRENFRKIRRKTFAEIINLSINQTLSRTIITSLTTLLVVLA  244 (289)
T ss_pred             HHHHHHHCCcccHHHHHHHHHHHHHheeceEEEeeHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4678889999888555566677899999999998776542   2357899999999999999999999998877653

>KOG1934|consensus

Probab=88.66  E-value=0.39  Score=42.69  Aligned_cols=82  Identities=15%  Similarity=0.137  Sum_probs=59.5

Q ss_pred             hhhhhhhcccchhhhhhccceeeEeee--cchhhhHhhhhhccCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhh
Q psy16375          4 LTQFRKPNGVLPYFIIIVLPYFIIIVG--LENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLL   81 (89)
Q Consensus         4 ~~~~~s~~gv~~tli~eViPFLVl~IG--vDniflit~av~~t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~   81 (89)
                      ..|++|++||....|+-+-  ++.+||  ||..--++-.......+.+.++|+..+|+..||.+..+.+.-+++...=++
T Consensus       718 V~G~lslW~V~LDpISmi~--iiMsIGFSVD~~AHi~yhy~~~~~~~t~~~Rv~~aL~~vgwPv~Qa~lSTiL~v~pL~~  795 (868)
T KOG1934|consen  718 VFGFLSLWGVDLDPISMIT--IIMSIGFSVDFSAHVAYHYYQSRKSSTPRERLRSALSAVGWPVLQAGLSTILGVLPLLF  795 (868)
T ss_pred             HhhhhHHhcCCccHHHHHH--HHHhCCceeeehhheeeeeEecCCCCCHHHHHHHHHHhhhhHHHhhhhHHHHHHHHHHh
Confidence            3588999999988754333  344555  566666666655555556899999999999999999999998888765555


Q ss_pred             ccCCcc
Q psy16375         82 TFFPVI   87 (89)
Q Consensus        82 t~~Pav   87 (89)
                      ++-..+
T Consensus       796 V~sYmv  801 (868)
T KOG1934|consen  796 VPSYMV  801 (868)
T ss_pred             chHHHH
Confidence            544433

>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=88.53  E-value=0.67  Score=33.76  Aligned_cols=70  Identities=11%  Similarity=0.012  Sum_probs=52.0

Q ss_pred             hhhhhhhcccchhh--hhhccceeeEeeecchhhhHhhhhhcc---CCCCCHHHHHHHHHhhhchHHHHHHHHHHHH
Q psy16375          4 LTQFRKPNGVLPYF--IIIVLPYFIIIVGLENILVLTKSIISI---PSHLDSKIRIAQGLSKEGWSITKNFFLELTV   75 (89)
Q Consensus         4 ~~~~~s~~gv~~tl--i~eViPFLVl~IGvDniflit~av~~t---~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~   75 (89)
                      .-++++++|.+.++  ++..  .++++-++||-.++...+++.   +.+.+.++++.++.++.-..+..+.+|-+.+
T Consensus        71 ~l~~~~~~~~~l~l~~iaal--l~~iG~sVd~~IVifdRIre~~~~~~~~~~~~~~~~s~~~tl~r~i~t~~ttll~  145 (189)
T PF02355_consen   71 TLGIFSLFGIELTLPSIAAL--LTIIGYSVDDNIVIFDRIREELRASRGKSLREAINISIKQTLSRTIDTSLTTLLA  145 (189)
T ss_dssp             HHHHHHHHT-EE-HHHHHHH--HHHHHHHHHHHHHHHHHHHHHHCC-STS-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCcccHHHHHHH--HHHHHHHHhcceeehHHHHHHhhhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45788899998888  4444  467788899999999988754   5678899999999999988777787775443

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.

>PRK09579 multidrug efflux protein; Reviewed

Probab=87.78  E-value=0.67  Score=41.22  Aligned_cols=71  Identities=11%  Similarity=0.088  Sum_probs=53.4

Q ss_pred             hhhhcccchhhhhhccceeeEeeecchhhhHhhhhhc-cCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHH
Q psy16375          7 FRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIIS-IPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLT   77 (89)
Q Consensus         7 ~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~-t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~   77 (89)
                      ++.++|.....++-.-.-+.+++.+||-+++.....+ -....+..+.+.++.++.+++++.+.+|-++.|.
T Consensus       375 ~l~~~G~~ln~~sl~gli~~iGi~VddaIvv~e~i~~~~~~G~~~~~A~~~~~~~~~~pil~stlTti~~f~  446 (1017)
T PRK09579        375 FMQMMGYSINLLTLLAMVLAIGLVVDDAIVVVENIHRHIEEGKSPFDAALEGAREIAMPVVSMTITLAAVYA  446 (1017)
T ss_pred             HHHHhCCCchHHHHHHHHHhhheeecCcEEeHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4456677666655555555677779998887776543 3345678899999999999999999999886653

>PRK10614 multidrug efflux system subunit MdtC; Provisional

Probab=87.75  E-value=0.47  Score=42.09  Aligned_cols=72  Identities=10%  Similarity=0.083  Sum_probs=54.4

Q ss_pred             hhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhc-cCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHH
Q psy16375          6 QFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIIS-IPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLT   77 (89)
Q Consensus         6 ~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~-t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~   77 (89)
                      .++.++|...+.++-.-.-+.+++++||-+++.....+ -....+..+.+.++.++.+++++.+.+|-++.|.
T Consensus       375 ~~l~~~g~~ln~~sl~gl~~~iGi~Vd~aIvv~e~i~~~~~~g~~~~~A~~~~~~~~~~~i~~stltti~~f~  447 (1025)
T PRK10614        375 AAMYLCGFSLNNLSLMALTIATGFVVDDAIVVLENISRHLEAGMKPLQAALQGVREVGFTVLSMSLSLVAVFL  447 (1025)
T ss_pred             HHHHHhCCChhHHHHHHHHHHhheeecCcEEEEeHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45567788777755555556778889999998865443 2334567899999999999999999999887764

>PRK10555 aminoglycoside/multidrug efflux system; Provisional

Probab=87.32  E-value=0.65  Score=41.35  Aligned_cols=71  Identities=8%  Similarity=0.053  Sum_probs=57.7

Q ss_pred             hhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhcc--CCCCCHHHHHHHHHhhhchHHHHHHHHHHHHH
Q psy16375          6 QFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISI--PSHLDSKIRIAQGLSKEGWSITKNFFLELTVL   76 (89)
Q Consensus         6 ~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t--~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f   76 (89)
                      +++.++|.....++-.-+-+.+++.+||-+++.....+.  ....+.++.+.++.++.+.+++.+.+|-++.|
T Consensus       381 ~~~~~~G~~ln~~sl~glii~iGi~Vd~aIvvve~i~~~~~~~G~~~~~Ai~~a~~~~~~~i~~stltti~~f  453 (1037)
T PRK10555        381 SVLYAFGYSINTLTMFAMVLAIGLLVDDAIVVVENVERIMSEEGLTPREATRKSMGQIQGALVGIAMVLSAVF  453 (1037)
T ss_pred             HHHHHhCCChhHHHHHHHHHHhhheecCeEEeHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356677877777777777778888899999999987654  34568899999999999999999999877655

>PRK09577 multidrug efflux protein; Reviewed

Probab=86.89  E-value=0.92  Score=40.37  Aligned_cols=71  Identities=8%  Similarity=0.060  Sum_probs=56.8

Q ss_pred             hhhhcccchhhhhhccceeeEeeecchhhhHhhhhhcc--CCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHH
Q psy16375          7 FRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISI--PSHLDSKIRIAQGLSKEGWSITKNFFLELTVLT   77 (89)
Q Consensus         7 ~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t--~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~   77 (89)
                      +..++|...+.++-.-.-+.+++.+||-+++.....+.  ....+..+.+.++.++.+++++-+.+|-+..|.
T Consensus       381 ~m~~~g~~ln~~sl~gl~~~iGi~VD~aIvvie~i~~~~~~~G~~~~~A~~~a~~~~~~~i~~~tlt~~~~fl  453 (1032)
T PRK09577        381 VMLAAGFSINVLTMFGMVLAIGILVDDAIVVVENVERLMVEEGLSPYDATVKAMKQISGAIVGITVVLTSVFV  453 (1032)
T ss_pred             HHHHhcccHHHHHHHHHHHheeeEecCcEEEehHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44557777777777777788899999999999987654  345677899999999999999998888877764

>TIGR00966 3a0501s07 protein-export membrane protein SecF

Probab=86.74  E-value=0.54  Score=35.17  Aligned_cols=74  Identities=11%  Similarity=-0.022  Sum_probs=56.4

Q ss_pred             hhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhcc---CCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHh
Q psy16375          6 QFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISI---PSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAG   79 (89)
Q Consensus         6 ~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t---~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG   79 (89)
                      +++.++|...++.+-.---+++++.+||-+++....++.   .+..+.++.+.++.++....+..+.+|-+..|.-=
T Consensus       140 ~~l~~~g~~ln~~sl~gli~~iGi~Vdd~Ivv~d~i~e~~~~~~~~~~~~a~~~a~~~~~~~ii~ttltti~~flpl  216 (246)
T TIGR00966       140 GVYSLFGIEVNLTTVAALLTIIGYSINDTVVVFDRIRENLRKYTRKTFTEVINLSINQTLSRTINTSLTTLLAVLAL  216 (246)
T ss_pred             HHHHHHCCcccHHHHHHHHHHHHHhccCeEEEehHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445667777777555555567788999999988665532   23568889999999999999999999998887643

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.

>TIGR00833 actII Transport protein

Probab=86.61  E-value=0.56  Score=41.13  Aligned_cols=67  Identities=15%  Similarity=0.154  Sum_probs=50.2

Q ss_pred             ccceeeEeeecchhhhHhhhhhccCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhccCCccc
Q psy16375         21 VLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTFFPVIQ   88 (89)
Q Consensus        21 ViPFLVl~IGvDniflit~av~~t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t~~Pavq   88 (89)
                      .++-+.+++|+|.-..+.+-+++... ...++.+.+++++.|..|+.+.++-+..|+.-.+++.|.++
T Consensus       808 ~~~~il~glgvDY~I~l~sR~ree~~-~g~~~av~~a~~~tg~~I~~a~~~~~~~f~~l~~s~~~~l~  874 (910)
T TIGR00833       808 GVFVLLVALGVDYNMLLVSRIKEESP-AGNRTGIIRALGSTGGVITAAGLVFAGTMAALASAQLTAIA  874 (910)
T ss_pred             HHHHHHHHhhhchHHHHHHHHHHHHh-cCccHHHHHHHHHhHHHHHHHHHHHHHHHHHHHhcchHHHH
Confidence            34566688999966555555444322 22468899999999999999999999988888888877654

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.

>PRK13024 bifunctional preprotein translocase subunit SecD/SecF; Reviewed

Probab=86.37  E-value=0.55  Score=40.80  Aligned_cols=81  Identities=10%  Similarity=-0.050  Sum_probs=62.2

Q ss_pred             hhhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhc-cCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhcc
Q psy16375          5 TQFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIIS-IPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTF   83 (89)
Q Consensus         5 ~~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~-t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t~   83 (89)
                      -+++.++|...++..-.-..+++++++||-.++....++ .....+.++.+.++.++...++..+.+|-+..|..=++..
T Consensus       306 l~~l~l~g~~l~l~siaglil~iGi~Vd~~Ivi~eri~e~l~~g~~~~~Ai~~a~~~~~~~il~t~lTTii~~lpL~~~g  385 (755)
T PRK13024        306 LGALSSLGAVLTLPGIAGLVLGIGMAVDANVLIFERIKEELRKGKSLKKAFKKGFKNAFSTILDSNITTLIAAAILFFFG  385 (755)
T ss_pred             HHHHHHHCCCccHHHHHHHHHHHHHHHhCcEEehHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            366788899888865556677889999998888776543 2345578899999999999999999999988776544434


Q ss_pred             CC
Q psy16375         84 FP   85 (89)
Q Consensus        84 ~P   85 (89)
                      .+
T Consensus       386 ~g  387 (755)
T PRK13024        386 TG  387 (755)
T ss_pred             cc
Confidence            33

>PRK13023 bifunctional preprotein translocase subunit SecD/SecF; Reviewed

Probab=84.91  E-value=0.6  Score=40.95  Aligned_cols=76  Identities=11%  Similarity=0.038  Sum_probs=59.5

Q ss_pred             hhhhhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhcc-CCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHH
Q psy16375          3 MLTQFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISI-PSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTA   78 (89)
Q Consensus         3 ~~~~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t-~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~i   78 (89)
                      +.-++++++|...|+.+-.-=.+.+++++||-.++...+++. ....+.++.+.++.++..++|..+.+|-+..|..
T Consensus       316 ~tl~~l~l~g~~Lnl~siaGlIL~IGm~VD~~Ivi~Erireel~~G~~~~~Av~~g~~~~~~~Il~s~lTTlia~lp  392 (758)
T PRK13023        316 ILTAVLSLIGASISLASIAGLVLTIGLAVDAHILIYERVREDRRKGYSVVQAMESGFYRALSTIVDANLTTLIAALV  392 (758)
T ss_pred             HHHHHHHHHCCCccHHHHHHHHHHHHHhccCcEEEeeHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345678888988888333333467789999999998877632 3346789999999999999999999999888765

>TIGR01129 secD protein-export membrane protein SecD

Probab=82.47  E-value=2  Score=34.74  Aligned_cols=74  Identities=11%  Similarity=0.029  Sum_probs=56.0

Q ss_pred             hhhhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhc-cCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHH
Q psy16375          4 LTQFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIIS-IPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLT   77 (89)
Q Consensus         4 ~~~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~-t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~   77 (89)
                      .-++++++|...++.+-.==.+.+++.+||-.++..-+++ .....+.++.+.++.++..++|.-+.+|-+.+|.
T Consensus       287 ~l~~~~l~g~~l~l~siaglil~iG~~VD~~Ivi~erire~l~~g~~~~~Ai~~~~~~~~~~I~~s~lTtlia~l  361 (397)
T TIGR01129       287 ILAILSAFGATLTLPGIAGLILTIGMAVDANVLIYERIKEELRLGKSVRQAIEAGFERAFSTIFDANITTLIAAL  361 (397)
T ss_pred             HHHHHHHHCCCccHHHHHHHHHHhheeeeceEEEeHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3467888888888833333346778899999998886553 2334578899999999999999999998887654

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

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

Probab=82.02  E-value=1.5  Score=39.07  Aligned_cols=70  Identities=9%  Similarity=0.061  Sum_probs=50.5

Q ss_pred             hhhcccchhhhhhccceeeEeeecchhhhHhhhhhcc--CCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHH
Q psy16375          8 RKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISI--PSHLDSKIRIAQGLSKEGWSITKNFFLELTVLT   77 (89)
Q Consensus         8 ~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t--~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~   77 (89)
                      +.++|.....++-.-.-+.+++.+||-+++....++.  ....+..+.+.++.++.+++++.+.+|-++.|.
T Consensus       383 ~~~~g~~ln~~sl~gli~~iGi~VD~aIvv~e~i~~~~~~~g~~~~~A~~~~~~~~~~~i~~ttltti~~fl  454 (1044)
T TIGR00915       383 LAAFGFSINTLTMFAMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFV  454 (1044)
T ss_pred             HHHhCCChhHHHHHHHHHHhhheecceEEEehHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445655555444444455566699999988876643  345678899999999999999999988876654

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

>TIGR00917 2A060601 Niemann-Pick C type protein family

Probab=81.88  E-value=2.8  Score=38.43  Aligned_cols=77  Identities=10%  Similarity=0.026  Sum_probs=52.3

Q ss_pred             hhhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhccCCCCCHHHHHHHHHhhhchHHHHH-HHHHHHHHHHhhhc
Q psy16375          5 TQFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKN-FFLELTVLTAGLLT   82 (89)
Q Consensus         5 ~~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t~~~~~v~~RIa~~ls~~G~SIt~t-~ltei~~f~iG~~t   82 (89)
                      -|+..++|++...++-+-=-+.+++++|=.--+.|+.... ...+.++|+.+++++.|++++-. .+|-++.|..=+++
T Consensus      1091 ~g~M~~~gisLN~vSlv~Li~avGisV~f~~hI~~~f~~~-~~~~~~~ra~~al~~vg~~v~~g~tlT~~~g~~~L~f~ 1168 (1204)
T TIGR00917      1091 VGIMHLWNISLNAVSVVNLVMAKGISIEFCSHINAQFSTS-KHFSRNHRAKEALGGMGSSVFSGITLTKLVGVVVLGFS 1168 (1204)
T ss_pred             HHHHHHhCCCHhHHHHHHHHHHhhhHHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            4677888988877655554444455556555666665544 23467899999999999999988 56666665444433

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.

>PRK08343 secD preprotein translocase subunit SecD; Reviewed

Probab=81.27  E-value=2  Score=35.09  Aligned_cols=71  Identities=11%  Similarity=0.178  Sum_probs=52.9

Q ss_pred             hhhhhhhcccchhh--hhhccceeeEeeecchhhhHhhhhhccCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHH
Q psy16375          4 LTQFRKPNGVLPYF--IIIVLPYFIIIVGLENILVLTKSIISIPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLT   77 (89)
Q Consensus         4 ~~~~~s~~gv~~tl--i~eViPFLVl~IGvDniflit~av~~t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~   77 (89)
                      +-++++++|...|+  ++-.  .+.+++++||-.++.....+.-. .+.++.+.++.+++..+|.-+.+|-+.++.
T Consensus       302 ~lg~l~l~g~tLtl~~IaGl--Il~iGmaVD~~IvI~e~i~~~~~-~~~~~ai~~g~~~a~~~Il~t~lTTiia~l  374 (417)
T PRK08343        302 ILGFAALIGWQLDLASIAGI--IAVIGTGVDDLIIITDEVLHEGK-VPSRKVFLSRIKRAFFIIFAAAATTIAAMS  374 (417)
T ss_pred             HHHHHHHHCCCccHHHHHHH--HHHHHHeeeCcEEEhHHHHHhCC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34556778888887  4333  36678899999999977654422 256777888899999999999999887765

---

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	89
3aqp_A	741	Probable secdf protein-export membrane protein; tr	97.03
2v50_A	1052	Multidrug resistance protein MEXB; DDM, RND, membr	92.55
3aqp_A	741	Probable secdf protein-export membrane protein; tr	92.21
4dx5_A	1057	Acriflavine resistance protein B; multidrug efflux	89.91
4dx5_A	1057	Acriflavine resistance protein B; multidrug efflux	86.27
2v50_A	1052	Multidrug resistance protein MEXB; DDM, RND, membr	84.45
3ne5_A	1054	Cation efflux system protein CUSA; transmembrane h	84.14
3ne5_A	1054	Cation efflux system protein CUSA; transmembrane h	81.89

>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=97.03  E-value=0.00041  Score=57.78  Aligned_cols=84  Identities=10%  Similarity=-0.037  Sum_probs=71.1

Q ss_pred             hhhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhcc-CCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhcc
Q psy16375          5 TQFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISI-PSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTF   83 (89)
Q Consensus         5 ~~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t-~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t~   83 (89)
                      -++++++|...++..-.-+.+.+++++||-+++...+++. ....+.++++.+++++.+.+|+.+.+|-+..|..-++..
T Consensus       313 ~~~l~l~g~~l~l~~i~glil~iGi~VD~~I~i~eri~e~~~~g~~~~~Ai~~~~~~~~~~Il~s~lTt~i~f~~L~~~~  392 (741)
T 3aqp_A          313 LGLLSGLGATLTLPGIAGLVLTLGAAVDGNVLSFERIKEELRAGKKLRQAIPEGFRHSTLTIMDVNIAHLLAAAALYQYA  392 (741)
T ss_dssp             HHHHHHHCCBCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHCCCccHHHHHHHHHHHHHHHhchhhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            4667888999888777788999999999999999877643 345678999999999999999999999999998888877


Q ss_pred             CCccc
Q psy16375         84 FPVIQ   88 (89)
Q Consensus        84 ~Pavq   88 (89)
                      .|.+|
T Consensus       393 ~~~~~  397 (741)
T 3aqp_A          393 TGPVR  397 (741)
T ss_dssp             CTHHH
T ss_pred             ccccc
Confidence            66543

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

Probab=92.55  E-value=0.021  Score=48.58  Aligned_cols=77  Identities=6%  Similarity=0.015  Sum_probs=60.8

Q ss_pred             hhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhcc--CCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhc
Q psy16375          6 QFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISI--PSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLT   82 (89)
Q Consensus         6 ~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t--~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t   82 (89)
                      ++..++|...+.++-+-..+.+++++||-+++...+.+.  ....+.++++.++.++.+.+|+.+.+|-++.|.-=++.
T Consensus       381 ~~l~~~g~~ln~~s~~gl~~~iGi~vd~aI~~~~~~~~~~~~~g~~~~~A~~~a~~~~~~pil~t~ltt~~~f~pl~~~  459 (1052)
T 2v50_A          381 GVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLSPREAARKSMGQIQGALVGIAMVLSAVFLPMAFF  459 (1052)
T ss_dssp             HHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHTTSSTTHHHHHHHHHTTHHHHTC
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHHhhccceEEEehHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            345667877777776777788889999999999887543  34567899999999999999999999998887544433

>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=92.21  E-value=0.047  Score=45.43  Aligned_cols=80  Identities=13%  Similarity=-0.008  Sum_probs=58.0

Q ss_pred             hhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhcc---CCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhc
Q psy16375          6 QFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISI---PSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLT   82 (89)
Q Consensus         6 ~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t---~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t   82 (89)
                      +++.++|...+..+-+-..+++++++||-.++.+-.++.   ....+.++.+.+++++.+..++.|+++-++.|..=++.
T Consensus       610 g~l~l~g~~l~~~~i~~~l~liGisvd~~I~l~~r~re~~~~~~g~~~~eav~~a~~~~~~~il~Tsltt~~g~~~L~~~  689 (741)
T 3aqp_A          610 GMYSLLGLEFSIPTIAALLTIVGYSINDSIVVSDRIRENQKLLRHLPYAELVNRSINQTLSRTVMTSLTTLLPILALLFL  689 (741)
T ss_dssp             HHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCccHHHHHHHHHHHHHhhcceEEehHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            556777876666332223345899999999988876542   23468999999999999999999999988877554444


Q ss_pred             cCC
Q psy16375         83 FFP   85 (89)
Q Consensus        83 ~~P   85 (89)
                      ..+
T Consensus       690 g~~  692 (741)
T 3aqp_A          690 GGS  692 (741)
T ss_dssp             CCH
T ss_pred             ccH
Confidence            433

>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=89.91  E-value=0.12  Score=43.83  Aligned_cols=71  Identities=8%  Similarity=0.049  Sum_probs=56.9

Q ss_pred             hhhhcccchhhhhhccceeeEeeecchhhhHhhhhhcc-C-CCCCHHHHHHHHHhhhchHHHHHHHHHHHHHH
Q psy16375          7 FRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISI-P-SHLDSKIRIAQGLSKEGWSITKNFFLELTVLT   77 (89)
Q Consensus         7 ~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t-~-~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~   77 (89)
                      ++.++|...++++-.-.-+.+++++||-+++.....+. . ...+.++.+.++.++.+.+|+.+.+|-++.|.
T Consensus       382 ~l~~~g~~ln~~sl~gl~~~iGi~vd~aIv~~~~~~~~~~~~g~~~~~A~~~a~~~~~~pi~~t~ltt~~~f~  454 (1057)
T 4dx5_A          382 VLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFV  454 (1057)
T ss_dssp             HHHHTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHhCCcHHHHHHHHHHHHeeccccceEEeHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45567777777666666778888899999998876643 2 26789999999999999999999999888774

>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=86.27  E-value=0.41  Score=40.67  Aligned_cols=71  Identities=7%  Similarity=-0.114  Sum_probs=54.5

Q ss_pred             hhhcccchhhhhhccceeeEeeecchhhhHhhhhhc--cCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHH
Q psy16375          8 RKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIIS--IPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTA   78 (89)
Q Consensus         8 ~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~--t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~i   78 (89)
                      +.++|...++.+-+-.-+++++|+||-+++..-.++  .....+.++.+.++..+.+..|+.|.+|-++.|.-
T Consensus       916 l~~~g~~l~~~~~~g~i~l~Gi~vd~~I~lv~~~~~~~~~~g~~~~~Ai~~a~~~~~rpil~t~ltt~~g~~p  988 (1057)
T 4dx5_A          916 ATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMP  988 (1057)
T ss_dssp             HHHHTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHTHH
T ss_pred             HHHHCCCccHHHHHHHHHHHHHHHcCeEEEehHHhHHHHHcCCCHHHHHHHHHHHhHhHHHHHHHHHHHHHHH
Confidence            345666666644444446679999999998877654  34578899999999999999999999998887643

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

Probab=84.45  E-value=0.49  Score=40.30  Aligned_cols=75  Identities=7%  Similarity=-0.081  Sum_probs=55.0

Q ss_pred             hhcccchhhhhhccceeeEeeecchhhhHhhhhhcc-CCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhcc
Q psy16375          9 KPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISI-PSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLTF   83 (89)
Q Consensus         9 s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t-~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t~   83 (89)
                      .++|...++.+-+.-.+.+++|+||-+++.+-..+. ....+.++.+.++.++.+..|+.|.+|-++.|.-=++..
T Consensus       916 ~~~g~~l~~~~~~g~~~l~Gi~vd~~I~lv~~~~~~~~~g~~~~~Ai~~a~~~~~rpil~t~~tt~~g~~pl~~~~  991 (1052)
T 2v50_A          916 SMRGLSNDVFFQVGLLTTIGLSAKNAILIVEFAKELHEQGKGIVEAAIEACRMRLRPIVMTSLAFILGVVPLAIST  991 (1052)
T ss_dssp             HHTTCCBSHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCHHHHHHHHHHHHHHHHHHHHHHHHTTSHHHHTCC
T ss_pred             HHHCCCccHHHHHHHHHHHHHHHcCeEEEeehHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHhcC
Confidence            445655554333334456799999999998877653 345789999999999999999999999887765444443

>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=84.14  E-value=0.18  Score=42.78  Aligned_cols=70  Identities=6%  Similarity=-0.034  Sum_probs=53.7

Q ss_pred             hhhhcccchhhhhhccceeeEeeecchhhhHhhhhhccC-C-----------CCCHHHHHHHHHhhhchHHHHHHHHHHH
Q psy16375          7 FRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISIP-S-----------HLDSKIRIAQGLSKEGWSITKNFFLELT   74 (89)
Q Consensus         7 ~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t~-~-----------~~~v~~RIa~~ls~~G~SIt~t~ltei~   74 (89)
                      ++.++|...+..+-.-.-+.+++++||-+++.....+.- .           ..+.++.+.++.++.++.++.+.+|-++
T Consensus       387 ~l~~~g~~ln~~sl~gl~l~iGi~vd~aIvvve~~~~~~~~~~~~~~~~~~~g~~~~~a~~~a~~~~~~~i~~s~ltt~~  466 (1054)
T 3ne5_A          387 VMHFQGLNANIMSLGGIAIAVGAMVDAAIVMIENAHKRLEEWQHQHPDATLDNKTRWQVITDASVEVGPALFISLLIITL  466 (1054)
T ss_dssp             HHHHHTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHSCSSCCCTTHHHHHHHTTTTTHHHHHHHHHHHHHH
T ss_pred             HHHHhCCCHHHHHHHHHHHHhhheecCcEEEeeHHHHHHhhccccccccccccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445677777776656566778888999999988765422 2           4568899999999999999999998876


Q ss_pred             HH
Q psy16375         75 VL   76 (89)
Q Consensus        75 ~f   76 (89)
                      .|
T Consensus       467 ~f  468 (1054)
T 3ne5_A          467 SF  468 (1054)
T ss_dssp             TT
T ss_pred             HH
Confidence            54

>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=81.89  E-value=0.47  Score=40.30  Aligned_cols=71  Identities=8%  Similarity=-0.188  Sum_probs=51.3

Q ss_pred             hhhcccchhhhhhccceeeEeeecchhhhHhhhhhccCC------------CCCHHHHHHHHHhhhchHHHHHHHHHHHH
Q psy16375          8 RKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIISIPS------------HLDSKIRIAQGLSKEGWSITKNFFLELTV   75 (89)
Q Consensus         8 ~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~t~~------------~~~v~~RIa~~ls~~G~SIt~t~ltei~~   75 (89)
                      +.++|...++.+-+-..+++++++||-+++..-..+...            ..+.++.+.++..+.+..|+.|.+|-++.
T Consensus       922 l~l~g~~l~~~~~~g~i~l~Gi~vd~~I~lv~~~~~~~~~~~~~~~~~~~~g~~~~~Ai~~a~~~~~rpil~t~ltti~g 1001 (1054)
T 3ne5_A          922 LWWMGFHLSVATGTGFIALAGVAAEFGVVMLMYLRHAIEAVPSLNNPQTFSEQKLDEALYHGAVLRVRPKAMTVAVIIAG 1001 (1054)
T ss_dssp             HHHHTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTHHHHTTTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCccHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhhhhhhcccccCCCCHHHHHHHHHHHhHhHHHHHHHHHHHH
Confidence            345666666644444456779999999998843332211            45678999999999999999999998887


Q ss_pred             HHH
Q psy16375         76 LTA   78 (89)
Q Consensus        76 f~i   78 (89)
                      |.-
T Consensus      1002 ~~p 1004 (1054)
T 3ne5_A         1002 LLP 1004 (1054)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            753

---

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	89
d1iwga7	199	Multidrug efflux transporter AcrB transmembrane do	96.64
d1iwga8	222	Multidrug efflux transporter AcrB transmembrane do	94.69

>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=96.64  E-value=0.00021  Score=48.93  Aligned_cols=79  Identities=8%  Similarity=-0.027  Sum_probs=64.4

Q ss_pred             hhhhhhcccchhhhhhccceeeEeeecchhhhHhhhhhc--cCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHhhhc
Q psy16375          5 TQFRKPNGVLPYFIIIVLPYFIIIVGLENILVLTKSIIS--IPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLTAGLLT   82 (89)
Q Consensus         5 ~~~~s~~gv~~tli~eViPFLVl~IGvDniflit~av~~--t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~iG~~t   82 (89)
                      .+....+|.+.+...-..+-+.+++|+||...+.+...+  .....+.+|++.++.++.|.++..+.+|-+..|.--++.
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            456677888888888888889999999999998876532  235667899999999999999999999999888655554


Q ss_pred             c
Q psy16375         83 F   83 (89)
Q Consensus        83 ~   83 (89)
                      +
T Consensus       161 ~  161 (199)
T d1iwga7         161 G  161 (199)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=94.69  E-value=0.0083  Score=41.22  Aligned_cols=68  Identities=7%  Similarity=-0.119  Sum_probs=55.1

Q ss_pred             hcccchhhhhhccceeeEeeecchhhhHhhhhhc--cCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHH
Q psy16375         10 PNGVLPYFIIIVLPYFIIIVGLENILVLTKSIIS--IPSHLDSKIRIAQGLSKEGWSITKNFFLELTVLT   77 (89)
Q Consensus        10 ~~gv~~tli~eViPFLVl~IGvDniflit~av~~--t~~~~~v~~RIa~~ls~~G~SIt~t~ltei~~f~   77 (89)
                      ..|......+-.-.-+.+++++||-.+++....+  .....+.++.+.++.++.+.+|..+.+|-+..|.
T Consensus       104 ~~g~~~~~~~~~g~i~l~Gi~v~~~i~~~~~~~~~~~~~g~~~~~Ai~~a~~~~~~~i~~t~ltti~gf~  173 (222)
T d1iwga8         104 FRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVM  173 (222)
T ss_dssp             HTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSCCCTTHHHHHHHHTTHHHHHHHHHHHHHHHH
T ss_pred             HcCCchhhhhcccccchhhhhhhHHHHHHHHhccccccccCCHHHHHHHHHHHHhhhhhhhHHHHHHHHH
Confidence            4455555556666667889999999999998765  4556788999999999999999999999888774