RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3216
(547 letters)
>gnl|CDD|149946 pfam09069, efhand_2, EF-hand. Members of this family adopt a
helix-loop-helix motif, as per other EF hand domains.
However, since they do not contain the canonical pattern
of calcium binding residues found in many EF hand
domains, they do not bind calcium ions. The main
function of this domain is the provision of specificity
in beta-dystroglycan recognition, though in dystrophin
it serves an additional role: stabilisation of the WW
domain (pfam00397), enhancing dystroglycan binding.
Length = 89
Score = 115 bits (291), Expect = 3e-31
Identities = 50/84 (59%), Positives = 57/84 (67%), Gaps = 16/84 (19%)
Query: 249 LFRLIADPNRLVDQRKLGLLLHDCIQLPRQLGEVASFGGSNIEPS--------------A 294
LF I+D N L+DQRKLGLLLH+ +QLPRQ+GE ASFGG IEPS
Sbjct: 8 LFSQISDSNGLMDQRKLGLLLHEALQLPRQVGEGASFGG--IEPSVRSCFPQVGKPKIEL 65
Query: 295 VHFLSWLQQEPQSIVWLPVLHRLS 318
HFL WL EPQS+VWLPVLHRL+
Sbjct: 66 NHFLDWLMLEPQSLVWLPVLHRLA 89
>gnl|CDD|239074 cd02334, ZZ_dystrophin, Zinc finger, ZZ type. Zinc finger present
in dystrophin and dystrobrevin. The ZZ motif coordinates
two zinc ions and most likely participates in ligand
binding or molecular scaffolding. Dystrophin attaches
actin filaments to an integral membrane glycoprotein
complex in muscle cells. The ZZ domain in dystrophin has
been shown to be essential for binding to the membrane
protein beta-dystroglycan.
Length = 49
Score = 111 bits (279), Expect = 4e-30
Identities = 36/49 (73%), Positives = 44/49 (89%)
Query: 327 AKCNICKECPIIGFRYRCLKCFNFDMCQTCFFQGKKAKNHKLTHPMQEY 375
AKCNICKE PI GFRYRCLKCFN+D+CQ+CFF G+ +K+HK +HPM+EY
Sbjct: 1 AKCNICKEFPITGFRYRCLKCFNYDLCQSCFFSGRTSKSHKNSHPMKEY 49
>gnl|CDD|149945 pfam09068, efhand_1, EF hand. Members of this family adopt a
helix-loop-helix motif, as per other EF hand domains.
However, since they do not contain the canonical pattern
of calcium binding residues found in many EF hand
domains, they do not bind calcium ions. The main
function of this domain is the provision of specificity
in beta-dystroglycan recognition, though in dystrophin
it serves an additional role: stabilisation of the WW
domain (pfam00397), enhancing dystroglycan binding.
Length = 125
Score = 89.6 bits (223), Expect = 2e-21
Identities = 34/67 (50%), Positives = 46/67 (68%), Gaps = 1/67 (1%)
Query: 98 KMIQLMNSLSELNEVRFSAYRTALKLRTVQKRLCLDLLNLVRAIEAFDTHGLRA-QNDKL 156
KM +LM L++LN +RFSAYRTA+KLR +QK LCLDL++L IE F HGL +
Sbjct: 1 KMTELMQELADLNNIRFSAYRTAMKLRALQKALCLDLVDLWNVIEIFRRHGLNQLDSTAS 60
Query: 157 LDVSDMV 163
L V+ ++
Sbjct: 61 LSVAQLI 67
>gnl|CDD|144236 pfam00569, ZZ, Zinc finger, ZZ type. Zinc finger present in
dystrophin, CBP/p300. ZZ in dystrophin binds calmodulin.
Putative zinc finger; binding not yet shown. Four to six
cysteine residues in its sequence are responsible for
coordinating zinc ions, to reinforce the structure.
Length = 46
Score = 81.8 bits (202), Expect = 1e-19
Identities = 30/46 (65%), Positives = 37/46 (80%)
Query: 323 AKHQAKCNICKECPIIGFRYRCLKCFNFDMCQTCFFQGKKAKNHKL 368
H CNICKECPIIGFRY CL+CF++D+CQ+CFF G+KA HK+
Sbjct: 1 IHHVYTCNICKECPIIGFRYHCLRCFDYDLCQSCFFTGRKAGGHKM 46
>gnl|CDD|197633 smart00291, ZnF_ZZ, Zinc-binding domain, present in Dystrophin,
CREB-binding protein. Putative zinc-binding domain
present in dystrophin-like proteins, and CREB-binding
protein/p300 homologues. The ZZ in dystrophin appears to
bind calmodulin. A missense mutation of one of the
conserved cysteines in dystrophin results in a patient
with Duchenne muscular dystrophy.
Length = 44
Score = 71.3 bits (175), Expect = 6e-16
Identities = 18/44 (40%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 324 KHQAKCNICKECPIIGFRYRCLKCFNFDMCQTCFFQGKKAKNHK 367
H C+ C + PI+G RY CL C ++D+CQ+CF +G H
Sbjct: 2 HHSYSCDTCGK-PIVGVRYHCLVCPDYDLCQSCFAKGSAGGEHS 44
>gnl|CDD|239069 cd02249, ZZ, Zinc finger, ZZ type. Zinc finger present in
dystrophin, CBP/p300 and many other proteins. The ZZ
motif coordinates one or two zinc ions and most likely
participates in ligand binding or molecular scaffolding.
Many proteins containing ZZ motifs have other
zinc-binding motifs as well, and the majority serve as
scaffolds in pathways involving acetyltransferase,
protein kinase, or ubiqitin-related activity. ZZ
proteins can be grouped into the following functional
classes: chromatin modifying, cytoskeletal scaffolding,
ubiquitin binding or conjugating, and membrane receptor
or ion-channel modifying proteins.
Length = 46
Score = 61.3 bits (149), Expect = 2e-12
Identities = 20/47 (42%), Positives = 28/47 (59%), Gaps = 3/47 (6%)
Query: 329 CNICKECPIIGFRYRCLKCFNFDMCQTCFFQGKKAKNHKLTHPMQEY 375
C+ C + PI+G RY CL C +FD+C +C+ +GKK H H E
Sbjct: 3 CDGCLK-PIVGVRYHCLVCEDFDLCSSCYAKGKKG--HPPDHSFTEI 46
>gnl|CDD|239078 cd02338, ZZ_PCMF_like, Zinc finger, ZZ type. Zinc finger present in
potassium channel modulatory factor (PCMF) 1 and
related proteins. The ZZ motif coordinates two zinc ions
and most likely participates in ligand binding or
molecular scaffolding. Human potassium channel
modulatory factor 1 or FIGC has been shown to possess
intrinsic E3 ubiquitin ligase activity and to promote
ubiquitination.
Length = 49
Score = 58.9 bits (143), Expect = 2e-11
Identities = 17/45 (37%), Positives = 26/45 (57%)
Query: 329 CNICKECPIIGFRYRCLKCFNFDMCQTCFFQGKKAKNHKLTHPMQ 373
C+ C + G RY+CL C+++D+C C+ G + H HPMQ
Sbjct: 3 CDGCGKSNFTGRRYKCLICYDYDLCADCYDSGVTTERHLFDHPMQ 47
>gnl|CDD|239079 cd02339, ZZ_Mind_bomb, Zinc finger, ZZ type. Zinc finger present in
Drosophila Mind bomb (D-mib) and related proteins. The
ZZ motif coordinates two zinc ions and most likely
participates in ligand binding or molecular scaffolding.
Mind bomb is an E3 ubiqitin ligase that has been shown
to regulate signaling by the Notch ligand Delta in
Drosophila melanogaster.
Length = 45
Score = 54.4 bits (131), Expect = 5e-10
Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 4/47 (8%)
Query: 329 CNICKECPIIGFRYRCLKCFNFDMCQTCFFQGKKAKNHKLTHPMQEY 375
C+ C++ IIG R++C +C N+D+C TC+ K H L H Y
Sbjct: 3 CDTCRKQGIIGIRWKCAECPNYDLCTTCYHGDK----HDLEHRFYRY 45
>gnl|CDD|239075 cd02335, ZZ_ADA2, Zinc finger, ZZ type. Zinc finger present in
ADA2, a putative transcriptional adaptor, and related
proteins. The ZZ motif coordinates two zinc ions and
most likely participates in ligand binding or molecular
scaffolding.
Length = 49
Score = 49.2 bits (118), Expect = 4e-08
Identities = 13/46 (28%), Positives = 22/46 (47%)
Query: 328 KCNICKECPIIGFRYRCLKCFNFDMCQTCFFQGKKAKNHKLTHPMQ 373
C+ C + R +C +C +FD+C CF G + H+ H +
Sbjct: 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAGAEIGKHRNDHNYR 47
>gnl|CDD|239080 cd02340, ZZ_NBR1_like, Zinc finger, ZZ type. Zinc finger present in
Drosophila ref(2)P, NBR1, Human sequestosome 1 and
related proteins. The ZZ motif coordinates two zinc ions
and most likely participates in ligand binding or
molecular scaffolding. Drosophila ref(2)P appears to
control the multiplication of sigma rhabdovirus. NBR1
(Next to BRCA1 gene 1 protein) interacts with
fasciculation and elongation protein zeta-1 (FEZ1) and
calcium and integrin binding protein (CIB), and may
function in cell signalling pathways. Sequestosome 1 is
a phosphotyrosine independent ligand for the Lck SH2
domain and binds noncovalently to ubiquitin via its UBA
domain.
Length = 43
Score = 46.1 bits (110), Expect = 5e-07
Identities = 18/44 (40%), Positives = 26/44 (59%), Gaps = 7/44 (15%)
Query: 331 ICKEC--PIIGFRYRCLKCFNFDMCQTCFFQGKKAKNHKLTHPM 372
IC C PI+G RY+CL C ++D+C++C +AK H M
Sbjct: 2 ICDGCQGPIVGVRYKCLVCPDYDLCESC-----EAKGVHPEHAM 40
>gnl|CDD|239083 cd02343, ZZ_EF, Zinc finger, ZZ type. Zinc finger present in
proteins with an EF_hand motif. The ZZ motif coordinates
two zinc ions and most likely participates in ligand
binding or molecular scaffolding.
Length = 48
Score = 45.0 bits (106), Expect = 2e-06
Identities = 16/32 (50%), Positives = 22/32 (68%)
Query: 341 RYRCLKCFNFDMCQTCFFQGKKAKNHKLTHPM 372
RYRCL+C + D+C+TCF G K + H+ H M
Sbjct: 14 RYRCLQCTDMDLCKTCFLGGVKPEGHEDDHEM 45
>gnl|CDD|239085 cd02345, ZZ_dah, Zinc finger, ZZ type. Zinc finger present in
Drosophila dah and related proteins. The ZZ motif
coordinates two zinc ions and most likely participates
in ligand binding or molecular scaffolding. Dah
(discontinuous actin hexagon) is a membrane associated
protein essential for cortical furrow formation in
Drosophila. .
Length = 49
Score = 44.5 bits (105), Expect = 2e-06
Identities = 15/46 (32%), Positives = 26/46 (56%)
Query: 329 CNICKECPIIGFRYRCLKCFNFDMCQTCFFQGKKAKNHKLTHPMQE 374
C+ C++ I G R+ C C ++ +C C+ +G++ K H H M E
Sbjct: 3 CSACRKQDISGIRFPCQVCRDYSLCLGCYTKGRETKRHNSLHIMYE 48
>gnl|CDD|239084 cd02344, ZZ_HERC2, Zinc finger, ZZ type. Zinc finger present in
HERC2 and related proteins. HERC2 is a potential E3
ubiquitin protein ligase and/or guanine nucleotide
exchange factor. The ZZ motif coordinates two zinc ions
and most likely participates in ligand binding or
molecular scaffolding.
Length = 45
Score = 44.1 bits (104), Expect = 2e-06
Identities = 15/39 (38%), Positives = 21/39 (53%)
Query: 328 KCNICKECPIIGFRYRCLKCFNFDMCQTCFFQGKKAKNH 366
C+ C+ PI G R++C C +FD C+ CF K H
Sbjct: 2 TCDGCQMFPINGPRFKCRNCDDFDFCENCFKTRKHNTRH 40
>gnl|CDD|239081 cd02341, ZZ_ZZZ3, Zinc finger, ZZ type. Zinc finger present in ZZZ3
(ZZ finger containing 3) and related proteins. The ZZ
motif coordinates two zinc ions and most likely
participates in ligand binding or molecular scaffolding.
Length = 48
Score = 44.0 bits (104), Expect = 3e-06
Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 328 KCNICKECPIIGFRYRCLKCFN--FDMCQTCFFQGKKAK-NHKLT 369
KC+ C PI G RY C +C + FD+CQ C +G+ + +H L
Sbjct: 2 KCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKGESHQEDHWLV 46
>gnl|CDD|239077 cd02337, ZZ_CBP, Zinc finger, ZZ type. Zinc finger present in
CBP/p300 and related proteins. The ZZ motif coordinates
two zinc ions and most likely participates in ligand
binding or molecular scaffolding. CREB-binding protein
(CBP) is a large multidomain protein that provides
binding sites for transcriptional coactivators, the role
of the ZZ domain in CBP/p300 is unclear.
Length = 41
Score = 34.8 bits (80), Expect = 0.005
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 4/41 (9%)
Query: 329 CNICKECPIIGFRYRCLKCFNFDMCQTCFFQGKKAKNHKLT 369
CN CK + R+ C C ++D+C TC+ K HK+
Sbjct: 3 CNECKH--HVETRWHCTVCEDYDLCITCY--NTKNHPHKME 39
>gnl|CDD|133384 cd01109, HTH_YyaN, Helix-Turn-Helix DNA binding domain of the
MerR-like transcription regulators YyaN and YraB.
Putative helix-turn-helix (HTH) MerR-like transcription
regulators of Bacillus subtilis, YyaN and YraB, and
related proteins; N-terminal domain. Based on sequence
similarity, these proteins are predicted to function as
transcription regulators that mediate responses to
stress in eubacteria. They belong to the MerR
superfamily of transcription regulators that promote
transcription of various stress regulons by
reconfiguring the operator sequence located between the
-35 and -10 promoter elements. A typical MerR regulator
is comprised of distinct domains that harbor the
regulatory (effector-binding) site and the active
(DNA-binding) site. Their N-terminal domains are
homologous and contain a DNA-binding winged HTH motif,
while the C-terminal domains are often dissimilar and
bind specific coactivator molecules such as metal ions,
drugs, and organic substrates.
Length = 113
Score = 36.3 bits (85), Expect = 0.006
Identities = 11/33 (33%), Positives = 23/33 (69%)
Query: 203 AKLLRQHKGRLEARMQILEDHNRQLEAQLSQLE 235
A+L R+ + R+++LE+H +LE Q+++L+
Sbjct: 67 AELRREGDSTIPERLELLEEHREELEEQIAELQ 99
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 38.5 bits (90), Expect = 0.011
Identities = 33/152 (21%), Positives = 54/152 (35%), Gaps = 16/152 (10%)
Query: 98 KMIQLMNSLSELNEVRFSAYRTALKLRTV-------QKRLCLDLLNLVRAIEAFDTHGLR 150
++ L + L EL R +L+ ++L L L +E +
Sbjct: 696 ELRSLEDLLEELRRQLEELERQLEELKRELAALEEELEQLQSRLEELEEELEELEEELEE 755
Query: 151 AQNDKLLDVSDMVVLEEENHMLQAEYERLRGSRTTPDPSSTTTPDDLEMAAE-----AKL 205
Q ++ LEE L+ E E L R + ++LE E
Sbjct: 756 LQERLEELEEELESLEEALAKLKEEIEELEEKR----QALQEELEELEEELEEAERRLDA 811
Query: 206 LRQHKGRLEARMQILEDHNRQLEAQLSQLESK 237
L + LE R + LE +LE ++ +LE K
Sbjct: 812 LERELESLEQRRERLEQEIEELEEEIEELEEK 843
Score = 36.2 bits (84), Expect = 0.046
Identities = 48/237 (20%), Positives = 85/237 (35%), Gaps = 34/237 (14%)
Query: 1 MRLFQKSLDDLSNRLSAAESVKNTWTSVSDASQIPELREYLKKFSERLTPLQRALEDTND 60
+ ++ L++L L+A E +L+ L++ E L L+ LE+ +
Sbjct: 711 LEELERQLEELKRELAALEEELE------------QLQSRLEELEEELEELEEELEELQE 758
Query: 61 QASFFSSNNILITSNSLHKLDDLNTSHHTETTSWDHPKMIQLMNSLSELNEVRFSAYRTA 120
+ + +L KL + + L L EL E A R
Sbjct: 759 RLEELEEE-LESLEEALAKLKEEIEELEEK--------RQALQEELEELEEELEEAERRL 809
Query: 121 LKLRTVQKRLCLDLLNLVRAIEAFDTHGLRAQNDKLLDVSDMVVLEEENHMLQAEYERLR 180
L + L L + IE L + ++L + LEEE L+ E E L+
Sbjct: 810 DALERELESLEQRRERLEQEIEE-----LEEEIEELE--EKLDELEEELEELEKELEELK 862
Query: 181 GSRTTPDPSSTTTPDDLEMAAEAKLLRQHKGRLEARMQILEDHNRQLEAQLSQLESK 237
+ E+ E K L + K LE ++ LE +L+ ++ +L +
Sbjct: 863 EEL------EELEAEKEELEDELKELEEEKEELEEELRELESELAELKEEIEKLRER 913
>gnl|CDD|150420 pfam09744, Jnk-SapK_ap_N, JNK_SAPK-associated protein-1. This is
the N-terminal 200 residues of a set of proteins
conserved from yeasts to humans. Most of the proteins in
this entry have an RhoGEF pfam00621 domain at their
C-terminal end.
Length = 158
Score = 35.1 bits (81), Expect = 0.031
Identities = 30/99 (30%), Positives = 53/99 (53%), Gaps = 6/99 (6%)
Query: 137 LVRAIEAFDTHGLRAQNDKLLDVSDMVVLEEENHMLQAEYERLRGSRTTPDPSSTTTPDD 196
++R +E D+ L ++N +L +V ++ +L E+N L +YER + R + D+
Sbjct: 31 VIRVLENLDS--LASENQEL-EV-ELELLREDNERLSTQYEREKELRKQAEQKLLEFEDE 86
Query: 197 LEMAAEAKLLRQHKGRLEARMQILEDHNRQLEAQLSQLE 235
LE E K L++ LE ++ LE + L Q+S+LE
Sbjct: 87 LE--QEKKELQKKIEDLEENVRQLELKAKNLSDQVSRLE 123
>gnl|CDD|239076 cd02336, ZZ_RSC8, Zinc finger, ZZ type. Zinc finger present in RSC8
and related proteins. RSC8 is a component of the RSC
complex, which is closely related to the SWI/SNF complex
and is involved in remodeling chromatin structure. The
ZZ motif coordinates a zinc ion and most likely
participates in ligand binding or molecular scaffolding.
Length = 45
Score = 31.9 bits (73), Expect = 0.054
Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 329 CNIC-KECPIIGFRYRCLKCFNFDMCQTCFFQGK 361
C C +C RY LK +D+C +C+ +G+
Sbjct: 3 CFTCGNDC--TRVRYHNLKAKKYDLCPSCYQEGR 34
>gnl|CDD|239082 cd02342, ZZ_UBA_plant, Zinc finger, ZZ type. Zinc finger present in
plant ubiquitin-associated (UBA) proteins. The ZZ motif
coordinates a zinc ion and most likely participates in
ligand binding or molecular scaffolding.
Length = 43
Score = 31.4 bits (71), Expect = 0.087
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 328 KCNICKECPIIGFRYRCLKCFNFDMCQTCF 357
+C+ C PI G RY+ ++D+C CF
Sbjct: 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICF 31
>gnl|CDD|227445 COG5114, COG5114, Histone acetyltransferase complex SAGA/ADA,
subunit ADA2 [Chromatin structure and dynamics].
Length = 432
Score = 35.0 bits (80), Expect = 0.097
Identities = 11/43 (25%), Positives = 17/43 (39%)
Query: 329 CNICKECPIIGFRYRCLKCFNFDMCQTCFFQGKKAKNHKLTHP 371
C++C +C +C D+C CF G + H H
Sbjct: 8 CDVCFLDMTDLTFIKCNECPAVDLCLPCFVNGIETGVHSPYHG 50
>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein. Members of this
protein family have a signal peptide, a strongly
conserved SH3 domain, a variable region, and then a
C-terminal hydrophobic transmembrane alpha helix region.
Length = 198
Score = 34.2 bits (79), Expect = 0.100
Identities = 20/91 (21%), Positives = 36/91 (39%), Gaps = 19/91 (20%)
Query: 149 LRAQNDKLLDVSDMVVLEEENHMLQAEYERLRGSRTTPDPSSTTTPDDLEMAAEAKLLRQ 208
L+ +N +L LE E LQ E R++ +++A A L +
Sbjct: 92 LQQENQELKQELST--LEAELERLQKELARIK-----------------QLSANAIELDE 132
Query: 209 HKGRLEARMQILEDHNRQLEAQLSQLESKDR 239
L + L+ N LEA+ +L+ ++
Sbjct: 133 ENRELREELAELKQENEALEAENERLQENEQ 163
Score = 28.4 bits (64), Expect = 6.6
Identities = 17/90 (18%), Positives = 35/90 (38%), Gaps = 4/90 (4%)
Query: 165 LEEENHMLQAEYERLRGSRTTPDPSSTTTPDDLE-MAAEAKLLRQHKGR---LEARMQIL 220
L+EE LQ + L+ +T +LE + E ++Q L+ + L
Sbjct: 78 LQEELAELQEQLAELQQENQELKQELSTLEAELERLQKELARIKQLSANAIELDEENREL 137
Query: 221 EDHNRQLEAQLSQLESKDRSSSRFIFQNLF 250
+ +L+ + LE+++ + F
Sbjct: 138 REELAELKQENEALEAENERLQENEQRRWF 167
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 32.7 bits (75), Expect = 0.53
Identities = 34/123 (27%), Positives = 54/123 (43%), Gaps = 4/123 (3%)
Query: 118 RTALKLRTVQKRL-CLDLLNLVRAIEAFDTHGLRAQNDKLLDVSDMVV-LEEENHMLQAE 175
A + + ++ L L+L LV +E L ++L + + + L E L+ +
Sbjct: 210 EKAERYKELKAELRELELALLVLRLEELREE-LEELQEELKEAEEELEELTAELQELEEK 268
Query: 176 YERLRGSRTTPDPSSTTTPDDL-EMAAEAKLLRQHKGRLEARMQILEDHNRQLEAQLSQL 234
E LR + + +L +A E L Q K L R+ LE +LEAQL +L
Sbjct: 269 LEELRLEVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQLEEL 328
Query: 235 ESK 237
ESK
Sbjct: 329 ESK 331
Score = 31.6 bits (72), Expect = 1.4
Identities = 46/236 (19%), Positives = 84/236 (35%), Gaps = 45/236 (19%)
Query: 4 FQKSLDDLSNRLSAAESVKNTWTSVSDA--SQIPELREYLKKFSERLTPLQRALEDTNDQ 61
++ L++L L AE T+ ++ ELR + + E + LQ+ L ++
Sbjct: 237 LREELEELQEELKEAEEELEELTAELQELEEKLEELRLEVSELEEEIEELQKELYALANE 296
Query: 62 ASFFSSNNILITSNSLHKLDDLNTSHHTETTSWDHPKMIQLMNSLSELNEVRFSAYRTAL 121
S I L L+ QL S+L+E+
Sbjct: 297 ISRLEQQ-KQILRERLANLERQLEELEA-----------QLEELESKLDELAEELAELEE 344
Query: 122 KLRTVQKRLCLDLLNLVRAIEAFDTHGLRAQNDKLLDVSDMVVLEEENHMLQAEYERLRG 181
KL +++ L L A+ ++L +++ LE L+ + E LR
Sbjct: 345 KLEELKEEL----------------ESLEAELEEL--EAELEELESRLEELEEQLETLRS 386
Query: 182 SRTTPDPSSTTTPDDLEMAAEAKLLRQHKGRLEARMQILEDHNRQLEAQLSQLESK 237
++ + L RLEAR++ LED +L+ ++ +L K
Sbjct: 387 KV-------------AQLELQIASLNNEIERLEARLERLEDRRERLQQEIEELLKK 429
>gnl|CDD|217843 pfam04012, PspA_IM30, PspA/IM30 family. This family includes PspA
a protein that suppresses sigma54-dependent
transcription. The PspA protein, a negative regulator of
the Escherichia coli phage shock psp operon, is produced
when virulence factors are exported through secretins in
many Gram-negative pathogenic bacteria and its homologue
in plants, VIPP1, plays a critical role in thylakoid
biogenesis, essential for photosynthesis. Activation of
transcription by the enhancer-dependent bacterial
sigma(54) containing RNA polymerase occurs through ATP
hydrolysis-driven protein conformational changes enabled
by activator proteins that belong to the large AAA(+)
mechanochemical protein family. It has been shown that
PspA directly and specifically acts upon and binds to
the AAA(+) domain of the PspF transcription activator.
Length = 220
Score = 32.0 bits (73), Expect = 0.54
Identities = 13/40 (32%), Positives = 18/40 (45%)
Query: 198 EMAAEAKLLRQHKGRLEARMQILEDHNRQLEAQLSQLESK 237
E AE L + LE ++ QL QL+ LE+K
Sbjct: 88 EALAEIATLEKQAEALETQLTQQRSAVEQLRKQLAALETK 127
>gnl|CDD|218228 pfam04720, DUF506, Protein of unknown function (DUF506). Family of
uncharacterized plant proteins.
Length = 218
Score = 32.0 bits (73), Expect = 0.57
Identities = 23/98 (23%), Positives = 41/98 (41%), Gaps = 5/98 (5%)
Query: 160 SDMV--VLEEENHMLQAEYERLRGSRTTPDPSSTT--TPDDLEMAAEAKLLRQHKGRLEA 215
SDMV LE+ N ++ E G ++ + + D+ +++ E K L + E
Sbjct: 2 SDMVQGFLEDGNETVEDESFSGSGDDSSDEEDEEDSSSEDNGDVSDELKSLLECTLYRER 61
Query: 216 RMQILEDHNRQ-LEAQLSQLESKDRSSSRFIFQNLFRL 252
+ LE + +E + S +RS R +L R
Sbjct: 62 YRRSLEAKVARAVEEASKHVSSGNRSCLRRKVMSLLRE 99
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 32.7 bits (75), Expect = 0.60
Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 10/75 (13%)
Query: 165 LEEENHMLQAEYERLRGSRTTPDPSSTTTPDDLEMAAEAKLLRQHKGRLEARMQILEDHN 224
L EE L+ E + L + + E+ E + L K +LE +++ LE+
Sbjct: 219 LREELEKLEKEVKELEELKEEIE----------ELEKELESLEGSKRKLEEKIRELEERI 268
Query: 225 RQLEAQLSQLESKDR 239
+L+ ++ +LE K +
Sbjct: 269 EELKKEIEELEEKVK 283
>gnl|CDD|226513 COG4026, COG4026, Uncharacterized protein containing TOPRIM domain,
potential nuclease [General function prediction only].
Length = 290
Score = 31.4 bits (71), Expect = 1.1
Identities = 21/118 (17%), Positives = 39/118 (33%), Gaps = 20/118 (16%)
Query: 165 LEEENHMLQAEYERLRGSRTTPDPSSTTTPDDLEMAAEAKLLRQHKGRLEARMQILEDHN 224
L +E L+AEYE ++ K L RLE ++ L
Sbjct: 154 LLKELEELEAEYEEVQ--------------------ERLKRLEVENSRLEEMLKKLPGEV 193
Query: 225 RQLEAQLSQLESKDRSSSRFIFQNLFRLIADPNRLVDQRKLGLLLHDCIQLPRQLGEV 282
L+ + +LE + +L + + + + + D ++ LG V
Sbjct: 194 YDLKKRWDELEPGVELPEEELISDLVKETLNLAPKDIEGQGYIYAEDEKEVEILLGTV 251
>gnl|CDD|238103 cd00176, SPEC, Spectrin repeats, found in several proteins
involved in cytoskeletal structure; family members
include spectrin, alpha-actinin and dystrophin; the
spectrin repeat forms a three helix bundle with the
second helix interrupted by proline in some sequences;
the repeats are independent folding units; tandem
repeats are found in differing numbers and arrange in
an antiparallel manner to form dimers; the repeats are
defined by a characteristic tryptophan (W) residue in
helix A and a leucine (L) at the carboxyl end of helix
C and separated by a linker of 5 residues; two copies
of the repeat are present here.
Length = 213
Score = 30.9 bits (70), Expect = 1.2
Identities = 14/84 (16%), Positives = 29/84 (34%)
Query: 2 RLFQKSLDDLSNRLSAAESVKNTWTSVSDASQIPELREYLKKFSERLTPLQRALEDTNDQ 61
+ F + D+L LS E + ++ D + L + + L + +E N+
Sbjct: 3 QQFLRDADELEAWLSEKEELLSSTDYGDDLESVEALLKKHEALEAELAAHEERVEALNEL 62
Query: 62 ASFFSSNNILITSNSLHKLDDLNT 85
+L++LN
Sbjct: 63 GEQLIEEGHPDAEEIQERLEELNQ 86
>gnl|CDD|215179 PLN02314, PLN02314, pectinesterase.
Length = 586
Score = 31.3 bits (71), Expect = 1.5
Identities = 27/94 (28%), Positives = 41/94 (43%), Gaps = 9/94 (9%)
Query: 3 LFQKSLDDLSNRLSAAESVKNTWTSVSDASQIPELREYLKKFSERLTPLQRALEDTNDQA 62
L +DDL LSA + + T DA Q EL + S ++ A+ ++ +
Sbjct: 169 LSSSKIDDLKTWLSATITDQET---CIDALQ--ELSQNKYANSTLTNEVKTAMSNSTE-- 221
Query: 63 SFFSSNNILITSNSLHKLDDLNTSHHTETTSWDH 96
F+SN++ I S L L DL H S+ H
Sbjct: 222 --FTSNSLAIVSKILGILSDLGIPIHRRLLSFHH 253
>gnl|CDD|202539 pfam03107, C1_2, C1 domain. This short domain is rich in cysteines
and histidines. The pattern of conservation is similar
to that found in pfam00130, therefore we have termed
this domain DC1 for divergent C1 domain. This domain
probably also binds to two zinc ions. The function of
proteins with this domain is uncertain, however this
domain may bind to molecules such as diacylglycerol (A
Bateman pers. obs.). This family are found in plant
proteins.
Length = 30
Score = 27.2 bits (61), Expect = 1.7
Identities = 11/30 (36%), Positives = 15/30 (50%), Gaps = 3/30 (10%)
Query: 328 KCNICKECPIIGF-RYRCLKCFNFDMCQTC 356
C++C+ I GF Y C KC F + C
Sbjct: 2 WCSVCRRK-IDGFYFYTCKKC-CFTLHVRC 29
>gnl|CDD|235315 PRK04841, PRK04841, transcriptional regulator MalT; Provisional.
Length = 903
Score = 31.1 bits (71), Expect = 1.8
Identities = 25/104 (24%), Positives = 39/104 (37%), Gaps = 24/104 (23%)
Query: 215 ARMQILEDHNRQLEAQLSQLESKDRSSSRFIFQNLFRLIADPNR----------LVDQRK 264
AR QIL + E L +L RS RL++D NR ++
Sbjct: 698 ARAQILLGQFDEAEIILEELNENARS---------LRLMSDLNRNLILLNQLYWQQGRKS 748
Query: 265 LGL-LLHDCIQLPRQLGEVASFGGSNIEPSAV-HFLSWLQQEPQ 306
+L + ++L + G ++ F IE A+ L L Q
Sbjct: 749 EAQRVLLEALKLANRTGFISHF---VIEGEAMAQQLRQLIQLNT 789
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 30.9 bits (71), Expect = 2.0
Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 12/71 (16%)
Query: 167 EENHMLQAEYERLRGSRTTPDPSSTTTPDDLEMAAEAKLLRQHKGRLEARMQILEDHNRQ 226
EE H L+ E+E+ R E+ K L Q + L+ ++++LE +
Sbjct: 64 EEIHKLRNEFEKELRERRN------------ELQKLEKRLLQKEENLDRKLELLEKREEE 111
Query: 227 LEAQLSQLESK 237
LE + +LE K
Sbjct: 112 LEKKEKELEQK 122
>gnl|CDD|132021 TIGR02976, phageshock_pspB, phage shock protein B. This model
describes the PspB protein of the psp (phage shock
protein) operon, as found in Escherichia coli and many
related species. Expression of a phage protein called
secretin protein IV, and a number of other stresses
including ethanol, heat shock, and defects in protein
secretion trigger sigma-54-dependent expression of the
phage shock regulon. PspB is both a regulator and an
effector protein of the phage shock response [Cellular
processes, Adaptations to atypical conditions].
Length = 75
Score = 28.5 bits (64), Expect = 2.0
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 3/39 (7%)
Query: 183 RTTPDPSSTTTPDDLEMAAEAKLLRQHKGRLEARMQILE 221
R+ +++ + DD + E L RLE R+ LE
Sbjct: 27 RSKRKTAASLSTDDQALLQE---LYAKADRLEERIDTLE 62
>gnl|CDD|225701 COG3159, COG3159, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 218
Score = 30.4 bits (69), Expect = 2.1
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 4/57 (7%)
Query: 214 EARMQILEDHNRQLEAQLSQLESKDRSSSRFIFQNLFRLIADPNRLVDQRKLGLLLH 270
E ++ L + R+LE +L+ L R++ R +F L L D L+D R L LL
Sbjct: 44 ERQLARLRNRIRELEEELAALMENARANER-LFYRLHALQLD---LLDARSLDDLLR 96
>gnl|CDD|218661 pfam05622, HOOK, HOOK protein. This family consists of several
HOOK1, 2 and 3 proteins from different eukaryotic
organisms. The different members of the human gene
family are HOOK1, HOOK2 and HOOK3. Different domains
have been identified in the three human HOOK proteins,
and it was demonstrated that the highly conserved
NH2-domain mediates attachment to microtubules, whereas
the central coiled-coil motif mediates homodimerisation
and the more divergent C-terminal domains are involved
in binding to specific organelles (organelle-binding
domains). It has been demonstrated that endogenous HOOK3
binds to Golgi membranes, whereas both HOOK1 and HOOK2
are localised to discrete but unidentified cellular
structures. In mice the Hook1 gene is predominantly
expressed in the testis. Hook1 function is necessary for
the correct positioning of microtubular structures
within the haploid germ cell. Disruption of Hook1
function in mice causes abnormal sperm head shape and
fragile attachment of the flagellum to the sperm head.
Length = 713
Score = 30.5 bits (69), Expect = 2.6
Identities = 17/74 (22%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 164 VLEEENHMLQAEYERLRGSRTTPDPSSTTTPDDLEMAAEAKLLRQHKGRLEARMQILEDH 223
L++EN LQ +L G ++ P+ + + ++ + L++ RLEA
Sbjct: 211 SLQQENEKLQERLAQLEG--SSLGPNQLGSKKYNLLQSQLEQLQEENFRLEAARDDYRIK 268
Query: 224 NRQLEAQLSQLESK 237
+LE +L++L+ +
Sbjct: 269 CEELEKELAELQHR 282
>gnl|CDD|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain.
Transcription of the anti-viral guanylate-binding
protein (GBP) is induced by interferon-gamma during
macrophage induction. This family contains GBP1 and
GPB2, both GTPases capable of binding GTP, GDP and GMP.
Length = 297
Score = 29.9 bits (68), Expect = 3.3
Identities = 12/40 (30%), Positives = 17/40 (42%), Gaps = 3/40 (7%)
Query: 198 EMAAEAKLLRQHKGRLEARMQILEDHNRQLEAQLSQLESK 237
AE +LLR+ + E M E R + + QL K
Sbjct: 215 AAEAEQELLREKQKEEEQMM---EAQERSYQEHVKQLIEK 251
>gnl|CDD|234714 PRK00286, xseA, exodeoxyribonuclease VII large subunit; Reviewed.
Length = 438
Score = 30.2 bits (69), Expect = 3.4
Identities = 20/87 (22%), Positives = 35/87 (40%), Gaps = 14/87 (16%)
Query: 193 TPDDLEMAAEAKLLRQHKGRLEARMQ-ILEDHNRQLEAQLSQLESKDRSSSRFIFQNLFR 251
PD E+ L+Q + RL M+ LE ++L+ + R FQ+ R
Sbjct: 259 VPDRAELLQR---LQQLQQRLARAMRRRLEQKRQRLDQL----------ARRLKFQSPER 305
Query: 252 LIADPNRLVDQRKLGLLLHDCIQLPRQ 278
L+A + +D+ + L +L
Sbjct: 306 LLAQQQQRLDRLQQRLQRALERRLRLA 332
>gnl|CDD|173841 cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar
to fadE6, fadE17, and fadE26. Putative acyl-CoA
dehydrogenases (ACAD). Mitochondrial acyl-CoA
dehydrogenases (ACAD) catalyze the alpha, beta
dehydrogenation of the corresponding trans-enoyl-CoA by
FAD, which becomes reduced. The reduced form of ACAD is
reoxidized in the oxidative half-reaction by
electron-transferring flavoprotein (ETF), from which the
electrons are transferred to the mitochondrial
respiratory chain coupled with ATP synthesis. The ACD
family includes the eukaryotic beta-oxidation, as well
as amino acid catabolism enzymes. These enzymes share
high sequence similarity, but differ in their substrate
specificities. The mitochondrial ACD's are generally
homotetramers and have an active site glutamate at a
conserved position.
Length = 380
Score = 29.6 bits (67), Expect = 4.1
Identities = 22/86 (25%), Positives = 32/86 (37%), Gaps = 13/86 (15%)
Query: 159 VSDMVVLEEENH-----MLQAEYER--LRGSRTTPDP-----SSTTTPDDLEMAAEAKLL 206
V D + E N M +ER + GS T T D + + L+
Sbjct: 216 VPDANRVGEVNDGWKVAMTTLNFERVSIGGSAATFFELLLARLLLLTRDGRPLIDDP-LV 274
Query: 207 RQHKGRLEARMQILEDHNRQLEAQLS 232
RQ RLEA + L +L + L+
Sbjct: 275 RQRLARLEAEAEALRLLVFRLASALA 300
>gnl|CDD|224755 COG1842, PspA, Phage shock protein A (IM30), suppresses
sigma54-dependent transcription [Transcription / Signal
transduction mechanisms].
Length = 225
Score = 29.2 bits (66), Expect = 4.4
Identities = 14/40 (35%), Positives = 20/40 (50%)
Query: 198 EMAAEAKLLRQHKGRLEARMQILEDHNRQLEAQLSQLESK 237
E E + L LEA +Q E+ +L+ QL+ LE K
Sbjct: 89 EALEEKQSLEDLAKALEAELQQAEEQVEKLKKQLAALEQK 128
>gnl|CDD|162489 TIGR01690, ICE_RAQPRD, integrative conjugative element protein,
RAQPRD family. This model represents a small family of
proteins about 100 amino acids in length, including a
predicted signal sequence and a perfectly conserved
motif RAQPRD towards the C-terminus. Members are found
in the Pseudomonas putida TOL plasmid pWW0 and in
cryptic plasmid regions of Salmonella enterica subsp.
enterica serovar Typhi and Pseudomonas syringae DC3000.
The function is unknown [Mobile and extrachromosomal
element functions, Plasmid functions].
Length = 94
Score = 27.7 bits (62), Expect = 4.7
Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 485 IVPVPRSPVQVMHAIDADQREELEVMISVLNPTLQTRSVTASQLATDSP 533
++ + A A +RE+L I L+ L+ + A+ +A SP
Sbjct: 4 LLALALLVAASALADQASEREQLAAAIRQLD-ALERSAQRAAVVAPQSP 51
>gnl|CDD|234342 TIGR03752, conj_TIGR03752, integrating conjugative element protein,
PFL_4705 family. Members of this protein family are
found occasionally on plasmids such as the Pseudomonas
putida toluene catabolic TOL plasmid pWWO_p085. Usually,
however, they are found on the bacterial main chromosome
in regions flanked by markers of conjugative transfer
and/or transposition [Mobile and extrachromosomal
element functions, Plasmid functions].
Length = 472
Score = 29.6 bits (67), Expect = 4.8
Identities = 18/75 (24%), Positives = 33/75 (44%), Gaps = 5/75 (6%)
Query: 160 SDMVVLEEENHMLQAEYERLRGSRTTPDPSSTTTPDDLEMAAEAKLLRQHKGRLEARMQI 219
+ L EN L+AE ERL+ S + +E + L + +L++ Q
Sbjct: 73 KRLAKLISENEALKAENERLQKRE-----QSIDQQIQQAVQSETQELTKEIEQLKSERQQ 127
Query: 220 LEDHNRQLEAQLSQL 234
L+ QL+ +L+ +
Sbjct: 128 LQGLIDQLQRRLAGV 142
>gnl|CDD|176888 cd08879, RHO_alpha_C_AntDO-like, C-terminal catalytic domain of the
oxygenase alpha subunit of Pseudomonas resinovorans
strain CA10 anthranilate 1,2-dioxygenase and related
aromatic ring hydroxylating dioxygenases. C-terminal
catalytic domain of the oxygenase alpha subunit of
anthranilate 1,2-dioxygenase (AntDO) and related
Rieske-type non-heme iron aromatic ring-hydroxylating
oxygenases (RHOs, also known as aromatic ring
hydroxylating dioxygenases). RHOs utilize non-heme
Fe(II) to catalyze the addition of hydroxyl groups to
the aromatic ring, an initial step in the oxidative
degradation of aromatic compounds. RHOs are composed of
either two or three protein components, and are
comprised of an electron transport chain (ETC) and an
oxygenase. The ETC transfers reducing equivalents from
the electron donor to the oxygenase component, which in
turn transfers electrons to the oxygen molecules. The
oxygenase components are oligomers, either (alpha)n or
(alpha)n(beta)n. The alpha subunits are the catalytic
components and have an N-terminal domain, which binds a
Rieske-like 2Fe-2S cluster, and the C-terminal catalytic
domain which binds the non-heme Fe(II). The Fe(II) is
co-ordinated by conserved His and Asp residues.
Oxygenases belonging to this subgroup include the alpha
subunits of AntDO, aniline dioxygenase, Acinetobacter
calcoaceticus benzoate 1,2-dioxygenase, 2-halobenzoate
1,2-dioxygenase from Pseudomonas cepacia 2CBS,
2,4,5-trichlorophenoxyacetic acid oxygenase from
Pseudomonas cepacia AC1100, 2,4-dichlorophenoxyacetic
acid oxygenase from Bradyrhizobium sp. strain HW13,
p-cumate 2,3-dioxygenase, 2-halobenzoate 1,2-dioxygenase
form Pseudomonas cepacia 2CBS, and Pseudomonas putida
IacC, which may be involved in the catabolism of the
plant hormone indole 3-acetic acid. This subfamily
belongs to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket.
Length = 237
Score = 29.2 bits (66), Expect = 5.0
Identities = 12/22 (54%), Positives = 12/22 (54%)
Query: 178 RLRGSRTTPDPSSTTTPDDLEM 199
RLR S PS TPDDLE
Sbjct: 161 RLRYSEDFFGPSGFATPDDLEA 182
>gnl|CDD|215197 PLN02347, PLN02347, GMP synthetase.
Length = 536
Score = 29.7 bits (67), Expect = 5.4
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 4/47 (8%)
Query: 395 KFKSKRYFKKHPRVGYLPVQTVLEGDALES---PAPSPQHSHTIGPH 438
+F K K + +L VQ L D +ES P HSHTI H
Sbjct: 323 EFAHKLEQKLGKKPAFL-VQGTLYPDVIESCPPPGSGRTHSHTIKSH 368
>gnl|CDD|107207 cd06446, Trp-synth_B, Tryptophan synthase-beta: Trptophan
synthase is a bifunctional enzyme that catalyses the
last two steps in the biosynthesis of L-tryptophan via
its alpha and beta reactions. In the alpha reaction,
indole 3-glycerol phosphate is cleaved reversibly to
glyceraldehyde 3-phosphate and indole at the active
site of the alpha subunit. In the beta reaction, indole
undergoes a PLP-dependent reaction with L-serine to
form L-tryptophan at the active site of the beta
subunit. Members of this CD, Trp-synth_B, are found in
all three major phylogenetic divisions.
Length = 365
Score = 29.4 bits (67), Expect = 5.4
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 17 AAESVKNTWTSVSDASQIP-ELREYLKKFSERLTPLQRA 54
A E ++ ++ P ELRE K + R TPL RA
Sbjct: 2 ALEELEQEFSKERYDPDFPEELRELYKDYVGRPTPLYRA 40
>gnl|CDD|131493 TIGR02440, FadJ, fatty oxidation complex, alpha subunit FadJ.
Members represent alpha subunit of multifunctional
enzyme complex of the fatty acid degradation cycle.
Plays a minor role in aerobic beta-oxidation of fatty
acids. FadJI complex is necessary for anaerobic growth
on short-chain acids with nitrate as an electron
acceptor. Activities include: enoyl-CoA hydratase (EC
4.2.1.17),3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35),
3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A
representative is E. coli FadJ (aka YfcX). This model
excludes the FadB of TIGR02437 equivalog model [Fatty
acid and phospholipid metabolism, Degradation].
Length = 699
Score = 29.4 bits (66), Expect = 5.9
Identities = 8/29 (27%), Positives = 15/29 (51%)
Query: 37 LREYLKKFSERLTPLQRALEDTNDQASFF 65
L ++ +R TP QR + ++ SF+
Sbjct: 671 LERLQTQYGDRFTPCQRLVAMAAEKQSFY 699
>gnl|CDD|130902 TIGR01843, type_I_hlyD, type I secretion membrane fusion protein,
HlyD family. Type I secretion is an ABC transport
process that exports proteins, without cleavage of any
signal sequence, from the cytosol to extracellular
medium across both inner and outer membranes. The
secretion signal is found in the C-terminus of the
transported protein. This model represents the adaptor
protein between the ATP-binding cassette (ABC) protein
of the inner membrane and the outer membrane protein,
and is called the membrane fusion protein. This model
selects a subfamily closely related to HlyD; it is
defined narrowly and excludes, for example, colicin V
secretion protein CvaA and multidrug efflux proteins
[Protein fate, Protein and peptide secretion and
trafficking].
Length = 423
Score = 29.2 bits (66), Expect = 6.0
Identities = 29/111 (26%), Positives = 49/111 (44%), Gaps = 9/111 (8%)
Query: 160 SDMVVLEEENHMLQAEYERLRGSRTTPDPSSTTTPDDL---EMAAEAKLLRQHKGRLEAR 216
+D LE + L+AE RLR + + PDDL E A +L++ + E+R
Sbjct: 81 ADAAELESQVLRLEAEVARLRAEADSQA--AIEFPDDLLSAEDPAVPELIKGQQSLFESR 138
Query: 217 MQILEDHNRQLEAQLSQLESKDRSSSRFI--FQNLFRLIADPNRLVDQRKL 265
L + AQ+ QLE++ + + +I++ L +RKL
Sbjct: 139 KSTLRAQLELILAQIKQLEAELAGLQAQLQALRQQLEVISE--ELEARRKL 187
>gnl|CDD|193531 cd05654, M20_ArgE_RocB, M20 Peptidase Arginine utilization protein,
RocB. Peptidase M20 family, ArgE RocB (Arginine
utilization protein, RocB; arginine degradation protein,
RocB) subfamily. This group of proteins is possibly
related to acetylornithine deacetylase (ArgE) and may be
involved in the arginine and/or ornithine degradation
pathway. In Bacillus subtilis, RocB is one of the three
genes found in the rocABC operon, which is sigma L
dependent and induced by arginine. The function of
members of this family is as yet unknown, although they
are predicted as deacetylases.
Length = 535
Score = 29.5 bits (67), Expect = 6.0
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 7/47 (14%)
Query: 378 TTTSGEDVRDFTRALRNKFKSKRYFKKHP-RVGYLPVQTVLEGDALE 423
T T GE R+ + K YFK++P ++G P LE D L
Sbjct: 17 TGTEGE--REIADFIYEYLKEIPYFKENPEQLGRQP----LENDPLG 57
>gnl|CDD|218674 pfam05644, Miff, Mitochondrial and peroxisomal fission factor Mff.
This protein has a role in mitochondrial and peroxisomal
fission.
Length = 243
Score = 29.0 bits (65), Expect = 6.4
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 177 ERLRGSRTTPDPSSTTTPDDLEMAAEAKLLRQHKGRLEARMQILEDHNRQ 226
LR T D S DD E+ A L RQ +L R+ +LE+ N++
Sbjct: 169 RSLREGTPTLDGSLEGLTDDEELVDAASLRRQ-IAKLNRRLLLLEEENKE 217
>gnl|CDD|147119 pfam04802, SMK-1, Component of IIS longevity pathway SMK-1. SMK-1
is a component of the IIs longevity pathway which
regulates aging in C.elegans. Specifically, SMK-1
influences DAF-16-dependant regulation of the aging
process by regulating the transcriptional specificity of
DAF-16 activity. SMK-1 plays a role in longevity by
modulating the transcriptional specificity of DAF-16.
Length = 193
Score = 28.7 bits (65), Expect = 6.8
Identities = 10/36 (27%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 245 IFQNLFRLIADPNRLVDQRK-LGLLLHDCIQLPRQL 279
+ LF L+ D + ++R+ L L LH+ + + L
Sbjct: 146 FLEELFALLTDSSTSDERRRDLVLFLHEFCNIAKSL 181
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 29.3 bits (66), Expect = 7.7
Identities = 9/39 (23%), Positives = 21/39 (53%)
Query: 198 EMAAEAKLLRQHKGRLEARMQILEDHNRQLEAQLSQLES 236
E+ A+ + R+ L+A+++ LE+ ++E + E
Sbjct: 907 ELEAQIEKKRKRLSELKAKLEALEEELSEIEDPKGEDEE 945
>gnl|CDD|178238 PLN02631, PLN02631, ferric-chelate reductase.
Length = 699
Score = 28.9 bits (64), Expect = 7.8
Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 5/49 (10%)
Query: 430 QHSHTIGPHDMHSRLEMYASRLAEVELR-----TRSNSTPDSEDEHQLI 473
+H H + D+ L++ S ++ + LR TR + P++ D+H+L+
Sbjct: 455 KHYHDLAFLDLIFPLDISVSDISRLNLRIEAYITREDKKPETTDDHRLL 503
>gnl|CDD|133382 cd01107, HTH_BmrR, Helix-Turn-Helix DNA binding domain of the BmrR
transcription regulator. Helix-turn-helix (HTH)
multidrug-efflux transporter transcription regulator,
BmrR and YdfL of Bacillus subtilis, and related
proteins; N-terminal domain. Bmr is a membrane protein
which causes the efflux of a variety of toxic substances
and antibiotics. BmrR is comprised of two distinct
domains that harbor a regulatory (effector-binding) site
and an active (DNA-binding) site. The conserved
N-terminal domain contains a winged HTH motif that
mediates DNA binding, while the C-terminal domain binds
coactivating, toxic compounds. BmrR shares the
N-terminal DNA binding domain with other transcription
regulators of the MerR superfamily that promote
transcription by reconfiguring the spacer between the
-35 and -10 promoter elements.
Length = 108
Score = 27.1 bits (61), Expect = 8.6
Identities = 14/40 (35%), Positives = 20/40 (50%)
Query: 195 DDLEMAAEAKLLRQHKGRLEARMQILEDHNRQLEAQLSQL 234
D KLLR+ LEA ++ L+ R LE +L Q+
Sbjct: 69 DADNDDELRKLLREKLAELEAEIEELQRILRLLEDRLKQI 108
>gnl|CDD|203098 pfam04827, Plant_tran, Plant transposon protein. This family
contains plant transposases which are putative members
of the PIF / Ping-Pong family.
Length = 205
Score = 28.4 bits (63), Expect = 8.6
Identities = 16/50 (32%), Positives = 26/50 (52%)
Query: 226 QLEAQLSQLESKDRSSSRFIFQNLFRLIADPNRLVDQRKLGLLLHDCIQL 275
+L AQ + KD + + Q F+++A P RL +Q L ++ CI L
Sbjct: 144 KLFAQQQEACRKDVERAFGVLQARFKIVATPARLWNQSDLSNIMTACIIL 193
>gnl|CDD|200576 cd10952, CE4_MrCDA_like, Catalytic NodB homology domain of Mucor
rouxii chitin deacetylase and similar proteins. This
family is represented by the chitin deacetylase (MrCDA,
EC 3.5.1.41) encoded from the fungus Mucor rouxii (also
known as Amylomyces rouxii). MrCDA is an acidic
glycoprotein with a very stringent specificity for
beta1-4-linked N-acetylglucosamine homopolymers. It
requires at least four residues (chitotetraose) for
catalysis, and can achieve extensive deacetylation on
chitin polymers. MrCDA shows high sequence similarity to
Colletotrichum lindemuthianum chitin deacetylase
(endo-chitin de-N-acetylase, ClCDA), which consists of a
single catalytic domain similar to the deformed
(beta/alpha)8 barrel fold adopted by the carbohydrate
esterase 4 (CE4) superfamily, which encompasses a
mononuclear metalloenzyme employing a conserved
His-His-Asp zinc-binding triad closely associated with
the conserved catalytic base (aspartic acid) and acid
(histidine) to carry out acid/base catalysis. The family
also includes some uncharacterized eukaryotic and
bacterial homologs of MrCDA.
Length = 178
Score = 28.1 bits (63), Expect = 8.7
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 9/58 (15%)
Query: 51 LQRALEDTNDQASFFSSNNILITSNSLHKLDDL----NTSHHTETTSWDHPKMIQLMN 104
L L+ N +A+FF +I SN ++ D L H +W HP M L N
Sbjct: 18 LLDYLKSHNQKATFF-----VIGSNVVNNPDILQRALEAGHEIGVHTWSHPAMTTLTN 70
>gnl|CDD|220441 pfam09849, DUF2076, Uncharacterized protein conserved in bacteria
(DUF2076). This domain, found in various hypothetical
prokaryotic proteins, has no known function. The domain,
however, is found in various periplasmic ligand-binding
sensor proteins.
Length = 234
Score = 28.5 bits (64), Expect = 8.8
Identities = 20/99 (20%), Positives = 34/99 (34%), Gaps = 30/99 (30%)
Query: 167 EENHMLQAEYERLRGSRTTP-DPSSTTTPDDLEMAAEAKLLRQHKGR------------- 212
+E ++ + RL+ + P D AEA L+ + R
Sbjct: 4 QERQLIDGLFSRLKQAEGAPRDA-----------EAEA-LIAEALRRQPDAPYYLVQTIL 51
Query: 213 -LEARMQILEDHNRQLEAQLSQLESKDRSSSRFIFQNLF 250
EA ++ +LEAQ + +SS F +F
Sbjct: 52 VQEAALKQANARIEELEAQAQH--PQSQSSGGF-LSGMF 87
>gnl|CDD|237738 PRK14508, PRK14508, 4-alpha-glucanotransferase; Provisional.
Length = 497
Score = 28.6 bits (65), Expect = 9.9
Identities = 20/54 (37%), Positives = 26/54 (48%), Gaps = 12/54 (22%)
Query: 262 QRKLGLLLHDCI-QLPRQLGEVASFGGSNIEPSAVHFLSWLQQEPQSIVW--LP 312
+RK G+LLH I LP G + FG A F+ +L + QS W LP
Sbjct: 4 KRKSGILLH--ITSLPGSYG-IGDFG-----KGAYEFIDFLAEAGQSY-WQILP 48
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.131 0.381
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,064,593
Number of extensions: 2608150
Number of successful extensions: 3232
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3190
Number of HSP's successfully gapped: 115
Length of query: 547
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 445
Effective length of database: 6,413,494
Effective search space: 2854004830
Effective search space used: 2854004830
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 61 (27.2 bits)