Query 018438
Match_columns 356
No_of_seqs 79 out of 81
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 09:01:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018438.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018438hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12937 F-box-like: F-box-lik 98.9 1.3E-09 2.8E-14 76.5 4.3 44 94-137 2-45 (47)
2 PF00646 F-box: F-box domain; 98.7 7.2E-09 1.6E-13 72.0 2.2 47 91-137 1-47 (48)
3 smart00256 FBOX A Receptor for 98.5 1E-07 2.3E-12 63.1 3.9 40 96-135 1-40 (41)
4 KOG2997 F-box protein FBX9 [Ge 95.8 0.0071 1.5E-07 60.6 3.2 52 92-143 106-162 (366)
5 KOG2120 SCF ubiquitin ligase, 95.3 0.017 3.7E-07 58.3 3.9 50 87-136 92-141 (419)
6 PF06881 Elongin_A: RNA polyme 95.1 0.027 6E-07 46.6 4.0 60 93-154 4-66 (109)
7 PF13013 F-box-like_2: F-box-l 93.3 0.11 2.3E-06 44.4 4.0 44 91-136 20-63 (109)
8 PLN03215 ascorbic acid mannose 93.1 0.087 1.9E-06 53.1 3.5 39 91-129 2-41 (373)
9 KOG0281 Beta-TrCP (transducin 85.8 1 2.2E-05 46.6 4.4 68 93-160 75-149 (499)
10 KOG3926 F-box proteins [Amino 84.9 1.2 2.6E-05 44.5 4.3 65 89-153 198-270 (332)
11 KOG0274 Cdc4 and related F-box 83.8 0.58 1.3E-05 48.9 1.7 54 91-144 106-159 (537)
12 PF04970 LRAT: Lecithin retino 77.6 1.3 2.7E-05 36.9 1.4 16 296-311 3-18 (125)
13 PF00018 SH3_1: SH3 domain; I 75.1 1.6 3.6E-05 30.7 1.3 24 299-326 15-38 (48)
14 smart00743 Agenet Tudor-like d 73.0 2.3 5.1E-05 31.2 1.7 26 299-328 2-28 (61)
15 PF14250 AbrB-like: AbrB-like 71.3 2.8 6.2E-05 34.1 1.9 21 292-312 45-65 (71)
16 PF07653 SH3_2: Variant SH3 do 70.6 1.9 4.1E-05 31.2 0.7 24 299-325 17-40 (55)
17 KOG4408 Putative Mg2+ and Co2+ 67.8 1.3 2.7E-05 45.3 -0.9 52 90-141 5-56 (386)
18 cd05829 Sortase_E Sortase E (S 64.5 3.3 7.2E-05 35.9 1.1 22 295-316 68-89 (144)
19 COG1064 AdhP Zn-dependent alco 62.5 4.7 0.0001 40.6 1.9 48 283-340 57-110 (339)
20 PF00855 PWWP: PWWP domain; I 59.9 7.5 0.00016 29.8 2.2 40 301-350 2-41 (86)
21 KOG1708 Mitochondrial/chloropl 58.3 7.9 0.00017 37.4 2.5 38 268-312 47-85 (236)
22 PF07886 BA14K: BA14K-like pro 52.5 5.3 0.00011 27.8 0.3 23 242-267 6-28 (31)
23 PF12969 DUF3857: Domain of Un 52.5 8.9 0.00019 32.4 1.7 23 295-317 85-107 (177)
24 TIGR03784 marine_sortase sorta 47.6 8.5 0.00018 35.0 0.9 22 295-316 104-125 (174)
25 PF00970 FAD_binding_6: Oxidor 44.7 7.3 0.00016 30.2 0.0 18 292-309 74-91 (99)
26 PF09372 PRANC: PRANC domain; 43.4 23 0.00049 28.5 2.6 27 90-116 69-95 (97)
27 PF03489 SapB_2: Saposin-like 42.5 26 0.00056 23.3 2.4 23 98-120 13-35 (35)
28 smart00306 HintN Hint (Hedgeho 42.4 13 0.00028 28.3 1.0 25 285-309 68-99 (100)
29 smart00326 SH3 Src homology 3 41.5 21 0.00046 23.9 1.9 22 299-324 20-41 (58)
30 PF14604 SH3_9: Variant SH3 do 40.5 17 0.00036 26.3 1.3 22 299-324 14-35 (49)
31 PF07497 Rho_RNA_bind: Rho ter 38.0 31 0.00068 28.2 2.7 38 278-315 16-58 (78)
32 cd04459 Rho_CSD Rho_CSD: Rho p 37.9 35 0.00076 27.1 2.9 36 279-314 15-55 (68)
33 COG1018 Hmp Flavodoxin reducta 36.0 22 0.00047 34.1 1.7 28 292-320 79-107 (266)
34 cd00174 SH3 Src homology 3 dom 33.3 35 0.00075 22.7 1.9 23 299-325 17-39 (54)
35 PF11270 DUF3070: Protein of u 33.1 29 0.00063 24.6 1.5 24 282-305 2-26 (32)
36 TIGR03635 S17_bact 30S ribosom 30.1 41 0.00088 26.9 2.1 13 297-309 46-58 (71)
37 PF11604 CusF_Ec: Copper bindi 29.6 40 0.00088 26.2 2.0 27 289-315 32-58 (70)
38 PF14890 Intein_splicing: Inte 29.2 18 0.00039 34.4 0.0 21 297-317 80-102 (323)
39 cd06166 Sortase_D_5 Sortase D 28.3 23 0.0005 29.8 0.5 18 294-311 59-76 (126)
40 PF13550 Phage-tail_3: Putativ 27.9 40 0.00086 28.1 1.8 14 298-311 138-151 (164)
41 cd05162 PWWP The PWWP domain, 27.8 37 0.0008 26.6 1.5 29 300-333 1-29 (87)
42 PF04225 OapA: Opacity-associa 27.4 32 0.00069 27.9 1.1 16 295-310 38-53 (85)
43 cd05767 IgC_MHC_II_alpha Class 27.2 36 0.00078 27.7 1.4 17 298-315 25-41 (94)
44 KOG0162 Myosin class I heavy c 27.0 79 0.0017 36.1 4.2 27 299-329 1069-1095(1106)
45 cd07699 IgC_L Immunoglobulin C 26.4 29 0.00064 28.0 0.7 20 295-315 23-43 (100)
46 PF03658 Ub-RnfH: RnfH family 26.3 34 0.00073 28.4 1.1 10 299-308 61-70 (84)
47 cd05847 IgC_CH2_IgE CH2 domain 25.9 31 0.00067 27.9 0.8 21 294-315 19-40 (94)
48 cd04453 S1_RNase_E S1_RNase_E: 25.8 33 0.00071 27.6 0.9 15 298-312 55-69 (88)
49 TIGR02988 YaaA_near_RecF S4 do 25.7 41 0.00089 24.8 1.4 10 299-308 49-58 (59)
50 COG1545 Predicted nucleic-acid 25.7 1E+02 0.0022 27.1 4.0 95 219-321 35-131 (140)
51 PRK06944 sulfur carrier protei 25.5 43 0.00093 24.7 1.4 10 299-308 49-58 (65)
52 PRK05863 sulfur carrier protei 25.1 43 0.00093 25.4 1.4 9 300-308 50-58 (65)
53 cd00081 Hint Hedgehog/Intein d 25.0 36 0.00078 27.5 1.0 25 285-309 68-99 (136)
54 PRK08053 sulfur carrier protei 23.4 49 0.0011 25.1 1.4 10 299-308 50-59 (66)
55 cd05835 Dnmt3b_related The PWW 23.3 50 0.0011 26.6 1.5 23 301-328 2-24 (87)
56 PRK07440 hypothetical protein; 23.3 49 0.0011 25.8 1.4 10 299-308 54-63 (70)
57 cd03470 Rieske_cytochrome_bc1 23.1 33 0.00073 29.5 0.5 18 297-314 6-23 (126)
58 COG3086 RseC Positive regulato 22.7 52 0.0011 30.3 1.7 15 295-309 54-68 (150)
59 PF10530 Toxin_35: Toxin with 22.0 42 0.00091 22.3 0.7 15 325-339 2-16 (23)
60 cd05770 IgC_beta2m Class I maj 21.6 38 0.00082 27.6 0.5 17 298-315 25-41 (93)
61 PRK06437 hypothetical protein; 21.6 55 0.0012 25.2 1.4 10 299-308 51-60 (67)
62 PRK11798 ClpXP protease specif 21.2 37 0.00081 30.7 0.4 21 228-252 91-111 (138)
63 PRK05610 rpsQ 30S ribosomal pr 20.9 76 0.0016 26.2 2.1 18 292-309 46-63 (84)
64 PHA03095 ankyrin-like protein; 20.8 79 0.0017 30.7 2.6 24 94-117 443-466 (471)
65 cd05828 Sortase_D_4 Sortase D 20.7 44 0.00096 28.1 0.8 17 295-311 57-73 (127)
66 PF09917 DUF2147: Uncharacteri 20.7 75 0.0016 26.3 2.1 46 223-278 69-114 (114)
67 PRK06083 sulfur carrier protei 20.5 59 0.0013 26.6 1.4 9 300-308 69-77 (84)
68 PRK06488 sulfur carrier protei 20.3 62 0.0013 24.2 1.4 10 299-308 49-58 (65)
No 1
>PF12937 F-box-like: F-box-like; PDB: 1P22_A 2OVP_B 2OVR_B 2OVQ_B 1FS1_A 1FS2_C 1FQV_I 1LDK_E 2AST_B 2ASS_B.
Probab=98.92 E-value=1.3e-09 Score=76.54 Aligned_cols=44 Identities=27% Similarity=0.506 Sum_probs=40.0
Q ss_pred CCCcHHHHHHHHccCChhhHHHHHhhcHHHHHhccCchHHHHhh
Q 018438 94 LDLPELVLECILEKLPPSGLCNMAAVCSSLRDRCMSDHLWEKHM 137 (356)
Q Consensus 94 LDLPeelLd~ILs~LSP~DLcrmAaVCrsLRerc~SD~LWeklV 137 (356)
.+||+|++..|+++|+|.||++++.||+.+|+.+.++.||.++.
T Consensus 2 ~~LP~Eil~~If~~L~~~dl~~~~~vcr~w~~~~~~~~lW~~~~ 45 (47)
T PF12937_consen 2 SSLPDEILLEIFSYLDPRDLLRLSLVCRRWRRIANDNSLWRRLC 45 (47)
T ss_dssp CCS-HHHHHHHHTTS-HHHHHHHTTSSHHHHHHHTCCCHHHHHC
T ss_pred hHhHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHCChhhhhhhc
Confidence 58999999999999999999999999999999999999999864
No 2
>PF00646 F-box: F-box domain; InterPro: IPR001810 The F-box domain was first described as a sequence motif found in cyclin-F that interacts with the protein SKP1 [, ]. This relatively conserved structural motif is present in numerous proteins and serves as a link between a target protein and a ubiquitin-conjugating enzyme. The SCF complex (e.g., Skp1-Cullin-F-box) plays a similar role as an E3 ligase in the ubiquitin protein degradation pathway [, ]. Different F-box proteins as a part of SCF complex recruit particular substrates for ubiquitination through specific protein-protein interaction domains. Many mammalian F-box domains contain leucine-rich or WD-40 repeats (IPR001680 from INTERPRO). However, several F-box proteins either have other previously described domains such as Sec7 domain found in FBS protein or do not contain defined protein-protein interaction domains or motifs.; GO: 0005515 protein binding; PDB: 2E32_A 2E31_A 3V7D_B 1NEX_B 3MKS_D 3L2O_B.
Probab=98.70 E-value=7.2e-09 Score=71.96 Aligned_cols=47 Identities=32% Similarity=0.526 Sum_probs=40.9
Q ss_pred CCCCCCcHHHHHHHHccCChhhHHHHHhhcHHHHHhccCchHHHHhh
Q 018438 91 MSVLDLPELVLECILEKLPPSGLCNMAAVCSSLRDRCMSDHLWEKHM 137 (356)
Q Consensus 91 ~sLLDLPeelLd~ILs~LSP~DLcrmAaVCrsLRerc~SD~LWeklV 137 (356)
+++.+||++++..|+++|++.|+++++.||+.+|+.+.++.+|.+..
T Consensus 1 ~~~~~LP~~il~~Il~~l~~~~~~~l~~vsk~~~~~~~~~~~~~~~~ 47 (48)
T PF00646_consen 1 FPLSDLPDEILQEILSYLDPKDLLRLSLVSKRWRSLVDSPRLWKKII 47 (48)
T ss_dssp -HHHHS-HHHHHHHHHTS-HHHHHHHCTT-HHHHHHHTTHHHHHHHH
T ss_pred CCHHHCCHHHHHHHHHHCcHHHHHHHHHHhhHHHHHHcCCCccHHHh
Confidence 36789999999999999999999999999999999999999998864
No 3
>smart00256 FBOX A Receptor for Ubiquitination Targets.
Probab=98.53 E-value=1e-07 Score=63.10 Aligned_cols=40 Identities=40% Similarity=0.620 Sum_probs=38.7
Q ss_pred CcHHHHHHHHccCChhhHHHHHhhcHHHHHhccCchHHHH
Q 018438 96 LPELVLECILEKLPPSGLCNMAAVCSSLRDRCMSDHLWEK 135 (356)
Q Consensus 96 LPeelLd~ILs~LSP~DLcrmAaVCrsLRerc~SD~LWek 135 (356)
||++++..|+++|++.|++++++||+.+|..+.++.+|.+
T Consensus 1 lP~~ll~~I~~~l~~~d~~~~~~vc~~~~~~~~~~~~~~~ 40 (41)
T smart00256 1 LPDEILEEILSKLPPKDLLRLRKVSRRWRSLIDSHDFWFK 40 (41)
T ss_pred CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcChhhhhc
Confidence 7999999999999999999999999999999999999975
No 4
>KOG2997 consensus F-box protein FBX9 [General function prediction only]
Probab=95.79 E-value=0.0071 Score=60.62 Aligned_cols=52 Identities=25% Similarity=0.406 Sum_probs=44.6
Q ss_pred CCCCCcHHHHHHHHccCC-----hhhHHHHHhhcHHHHHhccCchHHHHhhhhhhcc
Q 018438 92 SVLDLPELVLECILEKLP-----PSGLCNMAAVCSSLRDRCMSDHLWEKHMKQKWGR 143 (356)
Q Consensus 92 sLLDLPeelLd~ILs~LS-----P~DLcrmAaVCrsLRerc~SD~LWeklV~~kwp~ 143 (356)
.+..||+|+|=.|+...= -.+|-++|+||+.|+..|+.|.||...--+-|++
T Consensus 106 ~~~~LPdEvLm~I~~~vv~~~~d~rsL~~~s~vCr~F~~~~R~~~lwR~aC~KvW~~ 162 (366)
T KOG2997|consen 106 SISVLPDEVLMRIFRWVVSSLLDLRSLEQLSLVCRGFYKCARDPELWRLACLKVWQR 162 (366)
T ss_pred hhhhCCHHHHHHHHHHHHhhhcchhhHHHhHhhHHHHHHHHcChHHHHHHHHHHHHH
Confidence 368899999999887654 4999999999999999999999999877655553
No 5
>KOG2120 consensus SCF ubiquitin ligase, Skp2 component [Posttranslational modification, protein turnover, chaperones]
Probab=95.31 E-value=0.017 Score=58.35 Aligned_cols=50 Identities=22% Similarity=0.361 Sum_probs=45.5
Q ss_pred CCCCCCCCCCcHHHHHHHHccCChhhHHHHHhhcHHHHHhccCchHHHHh
Q 018438 87 GGAEMSVLDLPELVLECILEKLPPSGLCNMAAVCSSLRDRCMSDHLWEKH 136 (356)
Q Consensus 87 ~~~~~sLLDLPeelLd~ILs~LSP~DLcrmAaVCrsLRerc~SD~LWekl 136 (356)
--.+.+.-.||+|++.+|.+.|.-.||.+|+.||+.+..-+....+|..+
T Consensus 92 ~npgv~~~slpDEill~IFs~L~kk~LL~~~~VC~Rfyr~~~de~lW~~l 141 (419)
T KOG2120|consen 92 NNPGVSWDSLPDEILLGIFSCLCKKELLKVSGVCKRFYRLASDESLWQTL 141 (419)
T ss_pred cCCCCCcccCCHHHHHHHHHhccHHHHHHHHHHHHHHhhccccccceeee
Confidence 34556788999999999999999999999999999999999999999764
No 6
>PF06881 Elongin_A: RNA polymerase II transcription factor SIII (Elongin) subunit A; InterPro: IPR010684 This family represents a conserved region within RNA polymerase II transcription factor SIII (Elongin) subunit A. In mammals, the Elongin complex activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin is a heterotrimer composed of A, B, and C subunits of 110, 18, and 15 kilodaltons, respectively. Subunit A has been shown to function as the transcriptionally active component of Elongin [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus, 0016021 integral to membrane
Probab=95.10 E-value=0.027 Score=46.64 Aligned_cols=60 Identities=30% Similarity=0.496 Sum_probs=51.0
Q ss_pred CCCCcHHHHHHHHccCChhhHHHHHhhcHHHHHhccCchHHHHhhhhhhccc---cCccccchhh
Q 018438 93 VLDLPELVLECILEKLPPSGLCNMAAVCSSLRDRCMSDHLWEKHMKQKWGRI---VGPAAYREWQ 154 (356)
Q Consensus 93 LLDLPeelLd~ILs~LSP~DLcrmAaVCrsLRerc~SD~LWeklV~~kwp~v---Lgpaa~~eWq 154 (356)
+.++|-.+|.-||...+|..|.++-.-|..|.+. +|.||.+|+++..|.- -.|...++|.
T Consensus 4 vG~~py~ll~piL~~~~~~QL~~iE~~np~l~~~--tdeLW~~~i~rdFp~~~~~~~~~~~~~Wr 66 (109)
T PF06881_consen 4 VGDVPYHLLRPILEKCSPEQLRRIEDNNPHLIED--TDELWKKLIKRDFPEESKRQKPKEPESWR 66 (109)
T ss_pred cCCCCHHHHHHHHccCCHHHHHHHHHhCCCcchh--hHHHHHHHHHhHCcChhhcccccccchHH
Confidence 6789999999999999999999999999888765 8999999999999952 2444445773
No 7
>PF13013 F-box-like_2: F-box-like domain
Probab=93.35 E-value=0.11 Score=44.42 Aligned_cols=44 Identities=25% Similarity=0.435 Sum_probs=37.7
Q ss_pred CCCCCCcHHHHHHHHccCChhhHHHHHhhcHHHHHhccCchHHHHh
Q 018438 91 MSVLDLPELVLECILEKLPPSGLCNMAAVCSSLRDRCMSDHLWEKH 136 (356)
Q Consensus 91 ~sLLDLPeelLd~ILs~LSP~DLcrmAaVCrsLRerc~SD~LWekl 136 (356)
..++|||+|+++.|+++-.+.++..+..+|+.+|.+.. +.|..+
T Consensus 20 ltl~DLP~ELl~~I~~~C~~~~l~~l~~~~~~~r~~r~--~~~~~L 63 (109)
T PF13013_consen 20 LTLLDLPWELLQLIFDYCNDPILLALSRTCRAYRSWRD--HIWYLL 63 (109)
T ss_pred cchhhChHHHHHHHHhhcCcHHHHHHHHHHHHHHHHHH--HHHHHh
Confidence 46999999999999999999999999999999987643 455544
No 8
>PLN03215 ascorbic acid mannose pathway regulator 1; Provisional
Probab=93.05 E-value=0.087 Score=53.12 Aligned_cols=39 Identities=26% Similarity=0.366 Sum_probs=35.6
Q ss_pred CCCCCCcHHHHHHHHccC-ChhhHHHHHhhcHHHHHhccC
Q 018438 91 MSVLDLPELVLECILEKL-PPSGLCNMAAVCSSLRDRCMS 129 (356)
Q Consensus 91 ~sLLDLPeelLd~ILs~L-SP~DLcrmAaVCrsLRerc~S 129 (356)
++.-+||+++|+.|..+| +..|+.++++||++-|.+...
T Consensus 2 ~~Ws~Lp~dll~~i~~~l~~~~d~~~~~~vC~sWr~a~~~ 41 (373)
T PLN03215 2 ADWSTLPEELLHMIAGRLFSNVELKRFRSICRSWRSSVSG 41 (373)
T ss_pred CChhhCCHHHHHHHHhhCCcHHHHHHHHhhhhhHHHhccc
Confidence 356799999999999999 889999999999999998775
No 9
>KOG0281 consensus Beta-TrCP (transducin repeats containing)/Slimb proteins [Function unknown]
Probab=85.76 E-value=1 Score=46.56 Aligned_cols=68 Identities=25% Similarity=0.447 Sum_probs=58.3
Q ss_pred CCCCc----HHHHHHHHccCChhhHHHHHhhcHHHHHhccCchHHHHhhhhhhccc-c--Cccccchhhhhhhcc
Q 018438 93 VLDLP----ELVLECILEKLPPSGLCNMAAVCSSLRDRCMSDHLWEKHMKQKWGRI-V--GPAAYREWQWHLASR 160 (356)
Q Consensus 93 LLDLP----eelLd~ILs~LSP~DLcrmAaVCrsLRerc~SD~LWeklV~~kwp~v-L--gpaa~~eWq~h~a~~ 160 (356)
...|| +++-+.||+||...|||+--.||+.-+......-+|.+++.+++... + |-+.++.|..++-..
T Consensus 75 i~~lP~~gl~hi~e~ilsyld~~sLc~celv~k~W~r~l~dg~~WKkLie~~vr~dslWrgl~e~rqw~~~lf~~ 149 (499)
T KOG0281|consen 75 ITALPEQGLDHIAENILSYLDALSLCACELVCKEWKRVLSDGMLWKKLIERMVRTDSLWRGLSERRQWDQYLFKN 149 (499)
T ss_pred HHhcccccHHHHHHHHHHhcchhhhhHHHHHHHHHHHHhccchHHHHHHHHhcchHHHHhhhhhccCcchhhccC
Confidence 34688 99999999999999999999999999999999999999999998733 2 777778887766543
No 10
>KOG3926 consensus F-box proteins [Amino acid transport and metabolism]
Probab=84.93 E-value=1.2 Score=44.54 Aligned_cols=65 Identities=22% Similarity=0.391 Sum_probs=52.1
Q ss_pred CCCCCCCCcHHHHHHHHccCC-hhhHHHHHhhcHHHHHhccCchHHHHhhh-----hhhcccc--Cccccchh
Q 018438 89 AEMSVLDLPELVLECILEKLP-PSGLCNMAAVCSSLRDRCMSDHLWEKHMK-----QKWGRIV--GPAAYREW 153 (356)
Q Consensus 89 ~~~sLLDLPeelLd~ILs~LS-P~DLcrmAaVCrsLRerc~SD~LWeklV~-----~kwp~vL--gpaa~~eW 153 (356)
.+.-|.|||+|++-.||-+|| -.||..+|+|=.+|.+-...+.+|.++-+ .+..+.+ +..--.+|
T Consensus 198 ~~ltl~dLP~e~vl~Il~rlsDh~dL~s~aqa~etl~~l~~e~~iWkkLcqfHF~erQi~~~l~l~k~~q~dW 270 (332)
T KOG3926|consen 198 AGLTLHDLPLECVLNILLRLSDHRDLESLAQAWETLAKLSEERRIWKKLCQFHFNERQIHTILILSKKGQKDW 270 (332)
T ss_pred CCCCcccchHHHHHHHHHHccCcchHHHHHHhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHhhhhccccchhH
Confidence 457799999999999999998 48999999999999999999999998754 2333222 54444667
No 11
>KOG0274 consensus Cdc4 and related F-box and WD-40 proteins [General function prediction only]
Probab=83.79 E-value=0.58 Score=48.95 Aligned_cols=54 Identities=22% Similarity=0.283 Sum_probs=49.1
Q ss_pred CCCCCCcHHHHHHHHccCChhhHHHHHhhcHHHHHhccCchHHHHhhhhhhccc
Q 018438 91 MSVLDLPELVLECILEKLPPSGLCNMAAVCSSLRDRCMSDHLWEKHMKQKWGRI 144 (356)
Q Consensus 91 ~sLLDLPeelLd~ILs~LSP~DLcrmAaVCrsLRerc~SD~LWeklV~~kwp~v 144 (356)
--+..||.|+.-.|+.+|++.+|+++++||+..++.+..|..|-+...+.-+..
T Consensus 106 dfi~~lp~el~~~il~~Ld~~~l~~~~~v~~~w~~~~~~~~~~~~~~~~~~~~~ 159 (537)
T KOG0274|consen 106 DFLSLLPSELSLHILSFLDGRDLLAVRQVCRNWNKLLDDDKVWWRMCRELIGRL 159 (537)
T ss_pred chhhcccchhcccccccCCHHHhhhhhhhcchhhhhhhccchhhhhhhhhcccC
Confidence 358899999999999999999999999999999999999999998887776653
No 12
>PF04970 LRAT: Lecithin retinol acyltransferase; InterPro: IPR007053 This entry represents a conserved sequence region found in proteins from viruses, bacteria and eukaryotes. It contains a well-conserved NCEHF motif, though its function in these proteins is unknown.; PDB: 2KYT_A 4DOT_A 4FA0_A.
Probab=77.57 E-value=1.3 Score=36.91 Aligned_cols=16 Identities=44% Similarity=0.680 Sum_probs=8.6
Q ss_pred ccCCCCCCCeeEEEee
Q 018438 296 CLNDLHPGDHIEIQWR 311 (356)
Q Consensus 296 cl~dLkPGDHIEIQWR 311 (356)
+...|+||||||++-.
T Consensus 3 ~~~~~~~GD~I~~~r~ 18 (125)
T PF04970_consen 3 DKKRLKPGDHIEVPRG 18 (125)
T ss_dssp ---S--TT-EEEEEET
T ss_pred cccCCCCCCEEEEecC
Confidence 4578999999999754
No 13
>PF00018 SH3_1: SH3 domain; InterPro: IPR001452 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. The crystal structure of the SH3 domain of the cytoskeletal protein spectrin, and the solution structures of SH3 domains of phospholipase C (PLC-y) and phosphatidylinositol 3-kinase p85 alpha-subunit, have been determined [, , ]. In spite of relatively limited sequence similarity, their overall structures are similar. The domains belong to the alpha+beta structural class, with 5 to 8 beta-strands forming 2 tightly-packed, anti-parallel beta-sheets arranged in a barrel-like structure, and intervening loops sometimes forming helices. Conserved aliphatic and aromatic residues form a hydrophobic core (A11, L23, A29, V34, W42, L52 and V59 in PLC-y []) and a hydrophobic pocket on the molecular surface (L12, F13, W53 and P55 in PLC-y). The conserved core is believed to stabilise the fold, while the pocket is thought to serve as a binding site for target proteins. Conserved carboxylic amino acids located in the loops, on the periphery of the pocket (D14 and E22), may be involved in protein-protein interactions via proline-rich regions. The N- and C-termini are packed in close proximity, indicating that they are independent structural modules.; GO: 0005515 protein binding; PDB: 1UHF_A 1W1F_A 1WA7_A 1SEM_A 1KFZ_A 2SEM_B 1K76_A 3SEM_B 1X2Q_A 2J06_B ....
Probab=75.14 E-value=1.6 Score=30.69 Aligned_cols=24 Identities=29% Similarity=0.642 Sum_probs=18.6
Q ss_pred CCCCCCeeEEEeeccCCCCccchhhhhc
Q 018438 299 DLHPGDHIEIQWRRNKEFPYGWWYGVVG 326 (356)
Q Consensus 299 dLkPGDHIEIQWRrnkefPYgWWYgvVG 326 (356)
.++.||.|+|-=+.+. |||+|-..
T Consensus 15 s~~~Gd~i~v~~~~~~----~Ww~~~~~ 38 (48)
T PF00018_consen 15 SFKKGDIIEVLEKSDD----GWWKVRNE 38 (48)
T ss_dssp EB-TTEEEEEEEESSS----SEEEEEET
T ss_pred eEECCCEEEEEEecCC----CEEEEEEC
Confidence 3799999999877666 99998643
No 14
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=73.05 E-value=2.3 Score=31.16 Aligned_cols=26 Identities=35% Similarity=0.726 Sum_probs=20.7
Q ss_pred CCCCCCeeEEEeeccCCCCccchhhhh-ccc
Q 018438 299 DLHPGDHIEIQWRRNKEFPYGWWYGVV-GHL 328 (356)
Q Consensus 299 dLkPGDHIEIQWRrnkefPYgWWYgvV-GHl 328 (356)
+++.||.||++|+- --+||-|+| ..+
T Consensus 2 ~~~~G~~Ve~~~~~----~~~W~~a~V~~~~ 28 (61)
T smart00743 2 DFKKGDRVEVFSKE----EDSWWEAVVTKVL 28 (61)
T ss_pred CcCCCCEEEEEECC----CCEEEEEEEEEEC
Confidence 58999999999985 468999955 443
No 15
>PF14250 AbrB-like: AbrB-like transcriptional regulator
Probab=71.27 E-value=2.8 Score=34.13 Aligned_cols=21 Identities=33% Similarity=0.439 Sum_probs=17.1
Q ss_pred ccccccCCCCCCCeeEEEeec
Q 018438 292 HISDCLNDLHPGDHIEIQWRR 312 (356)
Q Consensus 292 h~Sdcl~dLkPGDHIEIQWRr 312 (356)
|+..=.-+|+|||.+||+=.|
T Consensus 45 ~AYT~~m~L~PGdEFeI~Lgr 65 (71)
T PF14250_consen 45 SAYTKQMGLKPGDEFEIKLGR 65 (71)
T ss_pred HHHHHHhCCCCCCEEEEEeCc
Confidence 456667799999999999765
No 16
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=70.60 E-value=1.9 Score=31.23 Aligned_cols=24 Identities=38% Similarity=0.819 Sum_probs=17.1
Q ss_pred CCCCCCeeEEEeeccCCCCccchhhhh
Q 018438 299 DLHPGDHIEIQWRRNKEFPYGWWYGVV 325 (356)
Q Consensus 299 dLkPGDHIEIQWRrnkefPYgWWYgvV 325 (356)
.++.||.|+|. +.++-+ |||+|..
T Consensus 17 s~~~Gd~i~v~--~~~~~~-~ww~~~~ 40 (55)
T PF07653_consen 17 SFKKGDVIEVL--GEKDDD-GWWLGEN 40 (55)
T ss_dssp EB-TTEEEEEE--EEECST-SEEEEEE
T ss_pred EEecCCEEEEE--EeecCC-CEEEEEE
Confidence 47899999998 333333 9999976
No 17
>KOG4408 consensus Putative Mg2+ and Co2+ transporter CorD [Inorganic ion transport and metabolism]
Probab=67.82 E-value=1.3 Score=45.31 Aligned_cols=52 Identities=25% Similarity=0.241 Sum_probs=47.2
Q ss_pred CCCCCCCcHHHHHHHHccCChhhHHHHHhhcHHHHHhccCchHHHHhhhhhh
Q 018438 90 EMSVLDLPELVLECILEKLPPSGLCNMAAVCSSLRDRCMSDHLWEKHMKQKW 141 (356)
Q Consensus 90 ~~sLLDLPeelLd~ILs~LSP~DLcrmAaVCrsLRerc~SD~LWeklV~~kw 141 (356)
.+.+-+||..+++.||+++-+.+|.+.|.|.+.|.+-++-+.+|.++-+..|
T Consensus 5 ~~~le~~~~~~l~~vls~~~~~~~~~~a~vs~rLk~~~s~~~lw~r~c~k~l 56 (386)
T KOG4408|consen 5 PLGLEWLPRDPLHLVLSFLLYRDLINCAYVSRRLKELGSHLPLWNRPCKKYL 56 (386)
T ss_pred ccchhhcccccceeeecccchhhhhcceeechHHhhhhhccccccccccccc
Confidence 3667889999999999999999999999999999999999999998875444
No 18
>cd05829 Sortase_E Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function of Sortase E is unknown. In two different sortase families, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one sortase and it is thought that the different sortases anchor different surface protein classes. The sortase domain is a modified beta-barrel flanked by two (SrtA) or three (SrtB) short alpha-helices.
Probab=64.50 E-value=3.3 Score=35.86 Aligned_cols=22 Identities=27% Similarity=0.382 Sum_probs=16.9
Q ss_pred cccCCCCCCCeeEEEeeccCCC
Q 018438 295 DCLNDLHPGDHIEIQWRRNKEF 316 (356)
Q Consensus 295 dcl~dLkPGDHIEIQWRrnkef 316 (356)
.-|++|++||.|.|+....+.+
T Consensus 68 ~~L~~l~~GD~I~v~~~~g~~~ 89 (144)
T cd05829 68 FRLGDLRKGDKVEVTRADGQTA 89 (144)
T ss_pred cchhcCCCCCEEEEEECCCCEE
Confidence 3467999999999999654433
No 19
>COG1064 AdhP Zn-dependent alcohol dehydrogenases [General function prediction only]
Probab=62.52 E-value=4.7 Score=40.55 Aligned_cols=48 Identities=29% Similarity=0.549 Sum_probs=36.4
Q ss_pred CCCCCCccccc-----ccccCCCCCCCeeEEEeeccCCCCccchhhhhccccccC-CCCCceee
Q 018438 283 PVDTSPHDLHI-----SDCLNDLHPGDHIEIQWRRNKEFPYGWWYGVVGHLESCD-GNENFCHC 340 (356)
Q Consensus 283 PvdT~~hdlh~-----Sdcl~dLkPGDHIEIQWRrnkefPYgWWYgvVGHlesCd-gn~~~C~C 340 (356)
++-+|-|..=- -.=...+|+||.+=| ||++.-.||=|.|. |+||+|+=
T Consensus 57 ~P~ipGHEivG~V~~vG~~V~~~k~GDrVgV----------~~~~~~Cg~C~~C~~G~E~~C~~ 110 (339)
T COG1064 57 LPLIPGHEIVGTVVEVGEGVTGLKVGDRVGV----------GWLVISCGECEYCRSGNENLCPN 110 (339)
T ss_pred CCccCCcceEEEEEEecCCCccCCCCCEEEe----------cCccCCCCCCccccCcccccCCC
Confidence 45567776541 122237999999998 78999999999997 89999864
No 20
>PF00855 PWWP: PWWP domain; InterPro: IPR000313 Upon characterisation of WHSC1, a gene mapping to the Wolf-Hirschhornsyndrome critical region and at its C terminus similar to the Drosophila melanogaster ASH1/trithorax group proteins, a novel protein domain designated PWWP domain was identified []. The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. It is present in proteins of nuclear origin and plays a role in cell growth and differentiation. Due to its position, the composition of amino acids close to the PWWP motif and the pattern of other domains present it has been suggested that the domain is involved in protein-protein interactions [].; PDB: 3LYI_B 2L89_A 2NLU_A 1RI0_A 1KHC_A 3QKJ_C 2DAQ_A 1N27_A 3PFS_B 3QJ6_A ....
Probab=59.92 E-value=7.5 Score=29.78 Aligned_cols=40 Identities=25% Similarity=0.646 Sum_probs=28.1
Q ss_pred CCCCeeEEEeeccCCCCccchhhhhccccccCCCCCceeeccCCeEEEEE
Q 018438 301 HPGDHIEIQWRRNKEFPYGWWYGVVGHLESCDGNENFCHCHNSGKSVKLM 350 (356)
Q Consensus 301 kPGDHIEIQWRrnkefPYgWWYgvVGHlesCdgn~~~C~Ch~sdtvvlEf 350 (356)
+|||.| |=|-+.|| ||=|+|=+.+.+.++ -...+.+.|.|
T Consensus 2 ~~GdlV---WaK~~g~p--wWPa~V~~~~~~~~~-----~~~~~~~~V~F 41 (86)
T PF00855_consen 2 RPGDLV---WAKLKGYP--WWPARVCDPDEKSKK-----KRKDGHVLVRF 41 (86)
T ss_dssp STTEEE---EEEETTSE--EEEEEEEECCHCTSC-----SSSSTEEEEEE
T ss_pred CCCCEE---EEEeCCCC--CCceEEeeccccccc-----CCCCCEEEEEe
Confidence 678766 66778887 999999888866553 23455555555
No 21
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=58.26 E-value=7.9 Score=37.41 Aligned_cols=38 Identities=32% Similarity=0.655 Sum_probs=30.0
Q ss_pred eeeecCCCccccccCCCCCC-CcccccccccCCCCCCCeeEEEeec
Q 018438 268 IAIECGVPWERLRAAPVDTS-PHDLHISDCLNDLHPGDHIEIQWRR 312 (356)
Q Consensus 268 ~~ie~~i~WdRlRapPvdT~-~hdlh~Sdcl~dLkPGDHIEIQWRr 312 (356)
.+...+-+|+|.|.+|++-. -||.| +.+||.|||-==|
T Consensus 47 ~~~qk~~~w~rrr~~~~e~i~d~dw~-------ff~GDtVeVlvGk 85 (236)
T KOG1708|consen 47 LVLQKNKPWERRRCVPVEPIIDEDWH-------FFFGDTVEVLVGK 85 (236)
T ss_pred hHHhhcCccccccCCCCCCcccccee-------EecCCEEEEEecc
Confidence 34456789999999999877 47888 7899999995433
No 22
>PF07886 BA14K: BA14K-like protein; InterPro: IPR012413 The sequences found in this family are similar to the BA14K proteins expressed by Brucella abortus (Q44701 from SWISSPROT) and by Brucella suis (Q8FVU0 from SWISSPROT). BA14K was found to be strongly immunoreactive; it induces both humoral and cellular responses in hosts throughout the infective process [].
Probab=52.55 E-value=5.3 Score=27.75 Aligned_cols=23 Identities=35% Similarity=0.562 Sum_probs=18.2
Q ss_pred ecceeeeeecCCCceeecCCCCCCCc
Q 018438 242 CYDAELSYDQSTDTFQARYPPHGRRP 267 (356)
Q Consensus 242 CYDA~lsYd~~TDTF~ARYpphGrr~ 267 (356)
|.+--=|||++|+|||.. .|+|.
T Consensus 6 C~~rYRSy~p~~~Ty~~~---~G~r~ 28 (31)
T PF07886_consen 6 CARRYRSYDPRDNTYQPY---DGPRR 28 (31)
T ss_pred HHHHhcCCCCCCCcEeCC---CCccc
Confidence 555666999999999987 67664
No 23
>PF12969 DUF3857: Domain of Unknown Function with PDB structure (DUF3857); InterPro: IPR024618 This domain is based on the first domain of the PDB structure 3KD4 (residues 1-228). It is structurally similar to domains in other hydrolases, eg. M1 family aminopeptidase, despite lack of any significant sequence similarity. The domain is N-terminal to a transglutaminase domain, which is found in many proteins known to have transglutaminase activity. The function of this domain is unknown. ; PDB: 3KD4_A.
Probab=52.47 E-value=8.9 Score=32.37 Aligned_cols=23 Identities=26% Similarity=0.388 Sum_probs=13.8
Q ss_pred cccCCCCCCCeeEEEeeccCCCC
Q 018438 295 DCLNDLHPGDHIEIQWRRNKEFP 317 (356)
Q Consensus 295 dcl~dLkPGDHIEIQWRrnkefP 317 (356)
--+.+|+|||-||++++....-|
T Consensus 85 ~~~p~v~~GdiIe~~y~~~~~~p 107 (177)
T PF12969_consen 85 FAFPDVRVGDIIEYSYTIKSKNP 107 (177)
T ss_dssp EE--S--TT-EEEEEEEEEE-TT
T ss_pred EEcCCCCCCcEEEEEEEEEecCC
Confidence 56889999999999999864444
No 24
>TIGR03784 marine_sortase sortase, marine proteobacterial type. Members of this protein family are sortase enzymes, cysteine transpeptidases involved in protein sorting activities. Members of this family tend to be found in proteobacteria, rather than in Gram-positive bacteria where sortases attach proteins to the Gram-positive cell wall or participate in pilin cross-linking. Many species with this sortase appear to contain a signal target sequence, a protein with a Vault protein inter-alpha-trypsin domain (pfam08487) and a von Willebrand factor type A domain (pfam00092), encoded by an adjacent gene. These sortases are designated subfamily 6 according to Comfort and Clubb (2004).
Probab=47.63 E-value=8.5 Score=34.96 Aligned_cols=22 Identities=32% Similarity=0.426 Sum_probs=18.1
Q ss_pred cccCCCCCCCeeEEEeeccCCC
Q 018438 295 DCLNDLHPGDHIEIQWRRNKEF 316 (356)
Q Consensus 295 dcl~dLkPGDHIEIQWRrnkef 316 (356)
.-|++|++||.|+||-..++.+
T Consensus 104 ~~L~~L~~GD~I~v~~~~g~~~ 125 (174)
T TIGR03784 104 AFLQELRPGDVIRLQTPDGQWQ 125 (174)
T ss_pred CChhhCCCCCEEEEEECCCeEE
Confidence 3489999999999998776654
No 25
>PF00970 FAD_binding_6: Oxidoreductase FAD-binding domain; InterPro: IPR008333 These sequences contain an oxidoreductase FAD-binding domain. To date, the 3D-structures of the flavoprotein domain of Zea mays (Maize) nitrate reductase [] and of pig NADH:cytochrome b5 reductase [] have been solved. The overall fold is similar to that of ferredoxin:NADP+ reductase []: the FAD-binding domain (N-terminal) has the topology of an anti-parallel beta-barrel, while the NAD(P)-binding domain (C-terminal) has the topology of a classical pyridine dinucleotide-binding fold (i.e. a central parallel beta-sheet flanked by 2 helices on each side).; PDB: 1JB9_A 3LVB_A 3LO8_A 1FRN_A 1FND_A 1BX1_A 1FNC_A 1FNB_A 1BX0_A 1FRQ_A ....
Probab=44.73 E-value=7.3 Score=30.22 Aligned_cols=18 Identities=44% Similarity=0.875 Sum_probs=15.4
Q ss_pred ccccccCCCCCCCeeEEE
Q 018438 292 HISDCLNDLHPGDHIEIQ 309 (356)
Q Consensus 292 h~Sdcl~dLkPGDHIEIQ 309 (356)
.+|..|++|++||.|+|-
T Consensus 74 ~~S~~L~~l~~Gd~v~i~ 91 (99)
T PF00970_consen 74 RVSRYLHQLKPGDEVEIR 91 (99)
T ss_dssp HHHHHHHTSCTTSEEEEE
T ss_pred HHHHHHHhCCCCCEEEEE
Confidence 357889999999999985
No 26
>PF09372 PRANC: PRANC domain; InterPro: IPR018272 This presumed domain is found at the C terminus of a variety of Pox virus proteins. The PRANC (Pox proteins Repeats of ANkyrin, C-terminal) domain is also found on its own in some proteins []. The function of this domain is unknown, but it appears to be related to the F-box domain and may play a similar role.
Probab=43.35 E-value=23 Score=28.52 Aligned_cols=27 Identities=26% Similarity=0.089 Sum_probs=24.8
Q ss_pred CCCCCCCcHHHHHHHHccCChhhHHHH
Q 018438 90 EMSVLDLPELVLECILEKLPPSGLCNM 116 (356)
Q Consensus 90 ~~sLLDLPeelLd~ILs~LSP~DLcrm 116 (356)
...+-.||.|+-..||++|+-.||..+
T Consensus 69 ~~~w~~LP~EIk~~Il~~L~~~dL~~l 95 (97)
T PF09372_consen 69 NNYWNILPIEIKYKILEYLSNKDLKKL 95 (97)
T ss_pred CCchhhCCHHHHHHHHHcCCHHHHHHH
Confidence 467999999999999999999999876
No 27
>PF03489 SapB_2: Saposin-like type B, region 2; InterPro: IPR008138 Saposins are small lysosomal proteins that serve as activators of various lysosomal lipid-degrading enzymes []. They probably act by isolating the lipid substrate from the membrane surroundings, thus making it more accessible to the soluble degradative enzymes. All mammalian saposins are synthesized as a single precursor molecule (prosaposin) which contains four Saposin-B domains, yielding the active saposins after proteolytic cleavage, and two Saposin-A domains that are removed in the activation reaction. The Saposin-B domains also occur in other proteins, many of them active in the lysis of membranes [, ].; PDB: 3BQQ_A 2RB3_B 2R0R_A 3BQP_A 2R1Q_A 1NKL_A 1L9L_A 1QDM_C 3RFI_A 4DDJ_A ....
Probab=42.53 E-value=26 Score=23.34 Aligned_cols=23 Identities=17% Similarity=0.626 Sum_probs=20.3
Q ss_pred HHHHHHHHccCChhhHHHHHhhc
Q 018438 98 ELVLECILEKLPPSGLCNMAAVC 120 (356)
Q Consensus 98 eelLd~ILs~LSP~DLcrmAaVC 120 (356)
+.+++.+.+.++|.++|.+-..|
T Consensus 13 ~~ii~~l~~~~~p~~iC~~i~~C 35 (35)
T PF03489_consen 13 PQIIQLLEKQLDPQQICTKIGLC 35 (35)
T ss_dssp HHHHHHHHTTSTHHHHHHHTTSS
T ss_pred HHHHHHHHhcCChHHHHHHcCCC
Confidence 47899999999999999987776
No 28
>smart00306 HintN Hint (Hedgehog/Intein) domain N-terminal region. Hedgehog/Intein domain, N-terminal region. Domain has been split to accommodate large insertions of endonucleases.
Probab=42.44 E-value=13 Score=28.35 Aligned_cols=25 Identities=32% Similarity=0.465 Sum_probs=20.0
Q ss_pred CCCCcccccccc-------cCCCCCCCeeEEE
Q 018438 285 DTSPHDLHISDC-------LNDLHPGDHIEIQ 309 (356)
Q Consensus 285 dT~~hdlh~Sdc-------l~dLkPGDHIEIQ 309 (356)
-|+-|-+.+.+- ..+|++||+|-+|
T Consensus 68 ~T~~H~~~~~~~~~~~w~~a~~l~~gd~v~~~ 99 (100)
T smart00306 68 LTPDHLLLVRDGGKLVWVFASELKPGDYVLVP 99 (100)
T ss_pred ECCCCEEEEecCCcEEEEEHHHCCCCCEEEec
Confidence 477787777666 7899999999875
No 29
>smart00326 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
Probab=41.45 E-value=21 Score=23.91 Aligned_cols=22 Identities=32% Similarity=0.746 Sum_probs=17.8
Q ss_pred CCCCCCeeEEEeeccCCCCccchhhh
Q 018438 299 DLHPGDHIEIQWRRNKEFPYGWWYGV 324 (356)
Q Consensus 299 dLkPGDHIEIQWRrnkefPYgWWYgv 324 (356)
.|++||.|+|-=+. .-|||+|.
T Consensus 20 ~~~~Gd~v~v~~~~----~~~w~~~~ 41 (58)
T smart00326 20 SFKKGDIITVLEKS----DDGWWKGR 41 (58)
T ss_pred CCCCCCEEEEEEcC----CCCeEEEE
Confidence 58999999998554 45999875
No 30
>PF14604 SH3_9: Variant SH3 domain; PDB: 2CRE_A 2E5K_A 2CT3_A 2DE0_X 2D8H_A 2DA9_A 2X3X_E 2X3W_D 2KRN_A 2ED0_A ....
Probab=40.54 E-value=17 Score=26.26 Aligned_cols=22 Identities=36% Similarity=0.859 Sum_probs=16.5
Q ss_pred CCCCCCeeEEEeeccCCCCccchhhh
Q 018438 299 DLHPGDHIEIQWRRNKEFPYGWWYGV 324 (356)
Q Consensus 299 dLkPGDHIEIQWRrnkefPYgWWYgv 324 (356)
.|+.||.|+|--+ -.=|||+|.
T Consensus 14 s~~~Gd~i~v~~~----~~~~W~~g~ 35 (49)
T PF14604_consen 14 SFKKGDVITVLEK----SDDGWWYGR 35 (49)
T ss_dssp EB-TTEEEEEEEE----SSTSEEEEE
T ss_pred eEcCCCEEEEEEe----CCCCEEEEE
Confidence 4799999999844 346999986
No 31
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=37.98 E-value=31 Score=28.20 Aligned_cols=38 Identities=34% Similarity=0.363 Sum_probs=23.9
Q ss_pred ccccC--CCCCCCccccccccc---CCCCCCCeeEEEeeccCC
Q 018438 278 RLRAA--PVDTSPHDLHISDCL---NDLHPGDHIEIQWRRNKE 315 (356)
Q Consensus 278 RlRap--PvdT~~hdlh~Sdcl---~dLkPGDHIEIQWRrnke 315 (356)
-||.+ --.+.+.|.|+|--+ ..||.||.|+=|=|..|+
T Consensus 16 FLR~~~~~y~~~~~DvYVs~~qIrrf~LR~GD~V~G~vr~p~~ 58 (78)
T PF07497_consen 16 FLRSPDNNYLPSPDDVYVSPSQIRRFGLRTGDLVEGQVRPPRE 58 (78)
T ss_dssp EEE-GGGTTS-STTSEEE-CCCCCCTT--TTEEEEEEEE--ST
T ss_pred EeECCCcCCCCCCCCEEECHHHHHHcCCCCCCEEEEEEeCCCC
Confidence 36666 555678899988876 589999999988887654
No 32
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=37.87 E-value=35 Score=27.14 Aligned_cols=36 Identities=31% Similarity=0.368 Sum_probs=27.3
Q ss_pred cccCCC--CCCCccccccccc---CCCCCCCeeEEEeeccC
Q 018438 279 LRAAPV--DTSPHDLHISDCL---NDLHPGDHIEIQWRRNK 314 (356)
Q Consensus 279 lRapPv--dT~~hdlh~Sdcl---~dLkPGDHIEIQWRrnk 314 (356)
||.+-. ...+-|.++|--+ ..||+||.|+=+=|..+
T Consensus 15 LR~~~~~y~~~~~DvyVs~~~Irr~~LR~GD~V~G~vr~p~ 55 (68)
T cd04459 15 LRSSGYNYLPGPDDIYVSPSQIRRFNLRTGDTVVGQIRPPK 55 (68)
T ss_pred EecCCcCCCCCCCCEEECHHHHHHhCCCCCCEEEEEEeCCC
Confidence 555533 5677888888776 68999999999988644
No 33
>COG1018 Hmp Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]
Probab=36.02 E-value=22 Score=34.11 Aligned_cols=28 Identities=25% Similarity=0.275 Sum_probs=22.1
Q ss_pred ccccccC-CCCCCCeeEEEeeccCCCCccc
Q 018438 292 HISDCLN-DLHPGDHIEIQWRRNKEFPYGW 320 (356)
Q Consensus 292 h~Sdcl~-dLkPGDHIEIQWRrnkefPYgW 320 (356)
=.|..|+ +|||||.|+| =.-..+|++..
T Consensus 79 ~~S~~Lh~~lk~Gd~l~v-~~P~G~F~l~~ 107 (266)
T COG1018 79 GGSNWLHDHLKVGDTLEV-SAPAGDFVLDD 107 (266)
T ss_pred cccHHHHhcCCCCCEEEE-ecCCCCccCCC
Confidence 3688898 9999999999 56666777653
No 34
>cd00174 SH3 Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
Probab=33.30 E-value=35 Score=22.69 Aligned_cols=23 Identities=35% Similarity=0.874 Sum_probs=17.3
Q ss_pred CCCCCCeeEEEeeccCCCCccchhhhh
Q 018438 299 DLHPGDHIEIQWRRNKEFPYGWWYGVV 325 (356)
Q Consensus 299 dLkPGDHIEIQWRrnkefPYgWWYgvV 325 (356)
.|++||-|.|-=+.+. |||+|-.
T Consensus 17 ~~~~Gd~v~v~~~~~~----~w~~~~~ 39 (54)
T cd00174 17 SFKKGDIIEVLEKSDD----GWWEGRL 39 (54)
T ss_pred CCCCCCEEEEEEcCCC----CeEEEEE
Confidence 5899999999866332 8998753
No 35
>PF11270 DUF3070: Protein of unknown function (DUF3070); InterPro: IPR021423 This eukaryotic family of proteins has no known function.
Probab=33.13 E-value=29 Score=24.59 Aligned_cols=24 Identities=33% Similarity=0.553 Sum_probs=18.4
Q ss_pred CCCCCC-CcccccccccCCCCCCCe
Q 018438 282 APVDTS-PHDLHISDCLNDLHPGDH 305 (356)
Q Consensus 282 pPvdT~-~hdlh~Sdcl~dLkPGDH 305 (356)
+||+.| +-|-|..--.+++.||||
T Consensus 2 aPa~~Pp~Eeaheap~~s~~~~~d~ 26 (32)
T PF11270_consen 2 APAEEPPAEEAHEAPHDSDLYPSDH 26 (32)
T ss_pred CcccCCChhhhccCcccccCCCCCc
Confidence 444444 678888888899999998
No 36
>TIGR03635 S17_bact 30S ribosomal protein S17. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.
Probab=30.09 E-value=41 Score=26.88 Aligned_cols=13 Identities=31% Similarity=0.404 Sum_probs=11.3
Q ss_pred cCCCCCCCeeEEE
Q 018438 297 LNDLHPGDHIEIQ 309 (356)
Q Consensus 297 l~dLkPGDHIEIQ 309 (356)
-|+.+.||-|+|+
T Consensus 46 ~~~~k~GD~V~I~ 58 (71)
T TIGR03635 46 NNECKVGDVVRII 58 (71)
T ss_pred CCCCCCCCEEEEE
Confidence 3589999999997
No 37
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=29.62 E-value=40 Score=26.23 Aligned_cols=27 Identities=22% Similarity=0.439 Sum_probs=17.6
Q ss_pred cccccccccCCCCCCCeeEEEeeccCC
Q 018438 289 HDLHISDCLNDLHPGDHIEIQWRRNKE 315 (356)
Q Consensus 289 hdlh~Sdcl~dLkPGDHIEIQWRrnke 315 (356)
..+--+--+.+|+|||.|+++-.+..+
T Consensus 32 F~v~~~~~l~~l~~Gd~V~F~~~~~~~ 58 (70)
T PF11604_consen 32 FPVADPVDLAGLKPGDKVRFTFERTDD 58 (70)
T ss_dssp EE--TTSEESS-STT-EEEEEEEEETT
T ss_pred EEcCChhhhhcCCCCCEEEEEEEECCC
Confidence 333345568899999999999888654
No 38
>PF14890 Intein_splicing: Intein splicing domain; PDB: 1MI8_A 2CW7_A 2CW8_A.
Probab=29.21 E-value=18 Score=34.44 Aligned_cols=21 Identities=33% Similarity=0.838 Sum_probs=12.7
Q ss_pred cCCCCCCCeeEEE--eeccCCCC
Q 018438 297 LNDLHPGDHIEIQ--WRRNKEFP 317 (356)
Q Consensus 297 l~dLkPGDHIEIQ--WRrnkefP 317 (356)
+.+|+|||.|-|+ .++...+|
T Consensus 80 ~~~Lk~GD~I~v~~~~~~~~~~p 102 (323)
T PF14890_consen 80 LEELKPGDRIAVPLSYKEPIRLP 102 (323)
T ss_dssp CCC--TT-EEEEES-TCGCEEEE
T ss_pred hHHhhccccccccccccccccCC
Confidence 4569999999999 45555566
No 39
>cd06166 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5, represented by Clostridium perfringens CPE2315. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=28.25 E-value=23 Score=29.75 Aligned_cols=18 Identities=22% Similarity=0.499 Sum_probs=15.2
Q ss_pred ccccCCCCCCCeeEEEee
Q 018438 294 SDCLNDLHPGDHIEIQWR 311 (356)
Q Consensus 294 Sdcl~dLkPGDHIEIQWR 311 (356)
-.-|++|++||.|.|+..
T Consensus 59 F~~L~~l~~Gd~v~v~~~ 76 (126)
T cd06166 59 FNRLDEVEKGDEIKVTTK 76 (126)
T ss_pred cCChHHCCCCCEEEEEEC
Confidence 345889999999999886
No 40
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=27.90 E-value=40 Score=28.09 Aligned_cols=14 Identities=36% Similarity=0.465 Sum_probs=12.3
Q ss_pred CCCCCCCeeEEEee
Q 018438 298 NDLHPGDHIEIQWR 311 (356)
Q Consensus 298 ~dLkPGDHIEIQWR 311 (356)
-.|.|||.|+|++-
T Consensus 138 ~~l~pGDvi~l~~~ 151 (164)
T PF13550_consen 138 LALEPGDVIALSDD 151 (164)
T ss_pred ccCCCCCEEEEEeC
Confidence 45999999999986
No 41
>cd05162 PWWP The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes. The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes. Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors.
Probab=27.82 E-value=37 Score=26.61 Aligned_cols=29 Identities=31% Similarity=0.845 Sum_probs=22.0
Q ss_pred CCCCCeeEEEeeccCCCCccchhhhhccccccCC
Q 018438 300 LHPGDHIEIQWRRNKEFPYGWWYGVVGHLESCDG 333 (356)
Q Consensus 300 LkPGDHIEIQWRrnkefPYgWWYgvVGHlesCdg 333 (356)
++|||.| |=+-+.|| ||=|+|=+......
T Consensus 1 f~~GdlV---waK~~g~p--wWPa~V~~~~~~~~ 29 (87)
T cd05162 1 FRPGDLV---WAKMKGYP--WWPALVVDPPKDSK 29 (87)
T ss_pred CCCCCEE---EEeCCCCC--CCCEEEccccccch
Confidence 4789877 65666666 99999988877643
No 42
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=27.44 E-value=32 Score=27.87 Aligned_cols=16 Identities=38% Similarity=0.634 Sum_probs=9.1
Q ss_pred cccCCCCCCCeeEEEe
Q 018438 295 DCLNDLHPGDHIEIQW 310 (356)
Q Consensus 295 dcl~dLkPGDHIEIQW 310 (356)
.-|..|||||.|+++=
T Consensus 38 k~L~~L~pGq~l~f~~ 53 (85)
T PF04225_consen 38 KPLTRLKPGQTLEFQL 53 (85)
T ss_dssp --GGG--TT-EEEEEE
T ss_pred chHhhCCCCCEEEEEE
Confidence 4788999999998764
No 43
>cd05767 IgC_MHC_II_alpha Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain. IgC_MHC_II_alpha: Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. In both humans and in mice these molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), for example on B-lymphocytes, monocytes, and macrophages. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from protelytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosom
Probab=27.18 E-value=36 Score=27.67 Aligned_cols=17 Identities=18% Similarity=0.622 Sum_probs=14.0
Q ss_pred CCCCCCCeeEEEeeccCC
Q 018438 298 NDLHPGDHIEIQWRRNKE 315 (356)
Q Consensus 298 ~dLkPGDHIEIQWRrnke 315 (356)
.++-|+| |+|+|+||..
T Consensus 25 ~gFyP~~-I~v~W~~~g~ 41 (94)
T cd05767 25 DNFFPPV-LNVTWLKNGV 41 (94)
T ss_pred EEEECCc-CEEEEEECCe
Confidence 4678988 9999999854
No 44
>KOG0162 consensus Myosin class I heavy chain [Cytoskeleton]
Probab=27.04 E-value=79 Score=36.06 Aligned_cols=27 Identities=44% Similarity=0.887 Sum_probs=22.2
Q ss_pred CCCCCCeeEEEeeccCCCCccchhhhhcccc
Q 018438 299 DLHPGDHIEIQWRRNKEFPYGWWYGVVGHLE 329 (356)
Q Consensus 299 dLkPGDHIEIQWRrnkefPYgWWYgvVGHle 329 (356)
-++-||.|||- +|=|=|||-|-+|-.|
T Consensus 1069 s~~~~diIei~----~edpSGWw~gk~~~ke 1095 (1106)
T KOG0162|consen 1069 SFKKGDIIEIM----REDPSGWWLGKLNGKE 1095 (1106)
T ss_pred cccCCCEEEEe----ccCCCcchhhccCCcc
Confidence 36899999995 6779999999876554
No 45
>cd07699 IgC_L Immunoglobulin Constant domain. IgC_L: Immunoglobulin (Ig) light chain constant (C) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains.
Probab=26.36 E-value=29 Score=28.00 Aligned_cols=20 Identities=40% Similarity=0.858 Sum_probs=15.1
Q ss_pred ccc-CCCCCCCeeEEEeeccCC
Q 018438 295 DCL-NDLHPGDHIEIQWRRNKE 315 (356)
Q Consensus 295 dcl-~dLkPGDHIEIQWRrnke 315 (356)
.|+ .++.|.| |+|.|+||..
T Consensus 23 ~C~~~gfyP~~-i~v~W~~~g~ 43 (100)
T cd07699 23 VCLINDFYPGF-ATVQWKVDGA 43 (100)
T ss_pred EEEEEeEECCC-CEEEEEECCE
Confidence 454 4678966 9999999864
No 46
>PF03658 Ub-RnfH: RnfH family Ubiquitin; InterPro: IPR005346 This is a small family of proteins of unknown function.; PDB: 2HJ1_B.
Probab=26.34 E-value=34 Score=28.43 Aligned_cols=10 Identities=50% Similarity=0.787 Sum_probs=6.2
Q ss_pred CCCCCCeeEE
Q 018438 299 DLHPGDHIEI 308 (356)
Q Consensus 299 dLkPGDHIEI 308 (356)
-|+.||.|||
T Consensus 61 ~L~~GDRVEI 70 (84)
T PF03658_consen 61 VLRDGDRVEI 70 (84)
T ss_dssp B--TT-EEEE
T ss_pred cCCCCCEEEE
Confidence 4889999998
No 47
>cd05847 IgC_CH2_IgE CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE). IgC_CH2_IgE: The second constant domain of the heavy chain of immunoglobulin E (IgE). The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) and three (in alpha, delta, and gamma) or four (in epsilon and mu) constant domains (CH1 to CH4). The different classes of antibodies vary in their heavy chains; the IgE class has the epsilon type. This domain (Cepsilon2) of IgE is in place of the flexible hinge region found in IgG.
Probab=25.95 E-value=31 Score=27.93 Aligned_cols=21 Identities=33% Similarity=0.786 Sum_probs=15.9
Q ss_pred cccc-CCCCCCCeeEEEeeccCC
Q 018438 294 SDCL-NDLHPGDHIEIQWRRNKE 315 (356)
Q Consensus 294 Sdcl-~dLkPGDHIEIQWRrnke 315 (356)
=-|+ .++.|.| |+|+|+||.+
T Consensus 19 L~C~a~gFyP~~-I~vtW~~dg~ 40 (94)
T cd05847 19 LLCLISGYTPGT-IEVEWLVDGQ 40 (94)
T ss_pred EEEEEEeEECCC-CEEEEEECCE
Confidence 3454 4788985 9999998865
No 48
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=25.77 E-value=33 Score=27.59 Aligned_cols=15 Identities=27% Similarity=0.310 Sum_probs=12.8
Q ss_pred CCCCCCCeeEEEeec
Q 018438 298 NDLHPGDHIEIQWRR 312 (356)
Q Consensus 298 ~dLkPGDHIEIQWRr 312 (356)
+.|+.||.|++|=-+
T Consensus 55 ~~~~~Gd~v~VqV~~ 69 (88)
T cd04453 55 KLLKEGQEILVQVVK 69 (88)
T ss_pred HcCCCCCEEEEEEEE
Confidence 459999999999765
No 49
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=25.74 E-value=41 Score=24.77 Aligned_cols=10 Identities=70% Similarity=1.026 Sum_probs=7.0
Q ss_pred CCCCCCeeEE
Q 018438 299 DLHPGDHIEI 308 (356)
Q Consensus 299 dLkPGDHIEI 308 (356)
-|++||+|+|
T Consensus 49 ~l~~Gd~v~i 58 (59)
T TIGR02988 49 KLYPGDVIEI 58 (59)
T ss_pred CCCCCCEEEe
Confidence 4677777776
No 50
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=25.67 E-value=1e+02 Score=27.10 Aligned_cols=95 Identities=21% Similarity=0.203 Sum_probs=50.5
Q ss_pred cccccccceeeeccCCeeeeeeeecceeeeeecCCCceeecCCCC-CCCceeeecCCCccccccCCCCCCCccccccc-c
Q 018438 219 TGRFWFPAQVYNRENGHVGFMLSCYDAELSYDQSTDTFQARYPPH-GRRPIAIECGVPWERLRAAPVDTSPHDLHISD-C 296 (356)
Q Consensus 219 sG~FWFPAQVYnRenghvGfmLSCYDA~lsYd~~TDTF~ARYpph-Grr~~~ie~~i~WdRlRapPvdT~~hdlh~Sd-c 296 (356)
||+--||.|.|.-..|--+ -+ -..+|+=.-.=.||+.=|.+- |-+. +....=.-++..- ...--.|+.| -
T Consensus 35 CG~v~~PPr~~Cp~C~~~~-~~--E~vels~~G~V~t~Tv~~~~~~~~~~---~~P~viaiV~l~~--~~~i~~~i~~~~ 106 (140)
T COG1545 35 CGRVYFPPRAYCPKCGSET-EL--EWVELSGEGKVETYTVVYVKPPGFSL---EEPYVIAIVELEE--GGRILGQLVDVD 106 (140)
T ss_pred CCeEEcCCcccCCCCCCCC-ce--EEEEeCCCeEEEEEEEEeeCCCCccc---CCCEEEEEEEeCC--CCceEEEEEecC
Confidence 6889999999986655443 11 223333333333444433222 1110 0000001111111 1133456666 4
Q ss_pred cCCCCCCCeeEEEeeccCCCCccch
Q 018438 297 LNDLHPGDHIEIQWRRNKEFPYGWW 321 (356)
Q Consensus 297 l~dLkPGDHIEIQWRrnkefPYgWW 321 (356)
-.+++.|+-||..||+..+-.+..+
T Consensus 107 p~~v~iGm~V~~v~~~~~~~~~~~~ 131 (140)
T COG1545 107 PDDVEIGMKVEAVFRKREEDGGRGY 131 (140)
T ss_pred cccccCCCEEEEEEEEccccCCceE
Confidence 6799999999999999888776544
No 51
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=25.53 E-value=43 Score=24.71 Aligned_cols=10 Identities=30% Similarity=0.780 Sum_probs=8.6
Q ss_pred CCCCCCeeEE
Q 018438 299 DLHPGDHIEI 308 (356)
Q Consensus 299 dLkPGDHIEI 308 (356)
.|+.||.|||
T Consensus 49 ~L~~gD~vei 58 (65)
T PRK06944 49 ALAAGDRLDL 58 (65)
T ss_pred cCCCCCEEEE
Confidence 3888999998
No 52
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=25.09 E-value=43 Score=25.41 Aligned_cols=9 Identities=33% Similarity=0.752 Sum_probs=8.4
Q ss_pred CCCCCeeEE
Q 018438 300 LHPGDHIEI 308 (356)
Q Consensus 300 LkPGDHIEI 308 (356)
|+.||.|||
T Consensus 50 L~~gD~ieI 58 (65)
T PRK05863 50 LRDGARLEV 58 (65)
T ss_pred cCCCCEEEE
Confidence 899999998
No 53
>cd00081 Hint Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein, and the flanking polypeptide sequences - the exteins - are joined by a peptide bond. In addition to the autocatalytic splicing domain, many inteins contain an inserted endonuclease domain, which plays a role in spreading inteins. Hedgehog proteins are a major class of intercellular signaling molecules, which control inductive interactions during animal development. The mature signaling forms of hedgehog proteins are the N-terminal fragments, which are covalently linked to cholesterol at their C-termini. This modification is the result of an autoprocessing step catalyzed by the C-terminal fragments, which are aligned here.
Probab=25.02 E-value=36 Score=27.46 Aligned_cols=25 Identities=32% Similarity=0.448 Sum_probs=22.2
Q ss_pred CCCCcccccccc-------cCCCCCCCeeEEE
Q 018438 285 DTSPHDLHISDC-------LNDLHPGDHIEIQ 309 (356)
Q Consensus 285 dT~~hdlh~Sdc-------l~dLkPGDHIEIQ 309 (356)
-|+-|-+.+.+. ..+|++||.|-+|
T Consensus 68 ~T~~H~~~~~~~~~~~~~~a~~l~~gd~l~~~ 99 (136)
T cd00081 68 LTPDHLLFVLEDGELKWVFASDLKPGDYVLVP 99 (136)
T ss_pred EcCCCEEEEEeCCeEEEEEHHHCCCCCEEEEc
Confidence 488899998885 7999999999998
No 54
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=23.42 E-value=49 Score=25.05 Aligned_cols=10 Identities=30% Similarity=0.501 Sum_probs=8.5
Q ss_pred CCCCCCeeEE
Q 018438 299 DLHPGDHIEI 308 (356)
Q Consensus 299 dLkPGDHIEI 308 (356)
-|+.||.|||
T Consensus 50 ~L~~gD~Iei 59 (66)
T PRK08053 50 IVQDGDQILL 59 (66)
T ss_pred ccCCCCEEEE
Confidence 4889999997
No 55
>cd05835 Dnmt3b_related The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of Dnmt3b has been identified in patients with ICF syndrome (immunodeficiency, centromeric instability, and facial anomalies), a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=23.29 E-value=50 Score=26.60 Aligned_cols=23 Identities=43% Similarity=1.080 Sum_probs=18.6
Q ss_pred CCCCeeEEEeeccCCCCccchhhhhccc
Q 018438 301 HPGDHIEIQWRRNKEFPYGWWYGVVGHL 328 (356)
Q Consensus 301 kPGDHIEIQWRrnkefPYgWWYgvVGHl 328 (356)
++||.| |=+-|.|| ||=|.|=+.
T Consensus 2 ~vGDlV---WaK~kg~p--wWP~~V~~~ 24 (87)
T cd05835 2 NVGDLV---WGKIKGFP--WWPGRVVSI 24 (87)
T ss_pred CCCCEE---EEecCCCC--CCCeEEech
Confidence 688876 77888888 999998665
No 56
>PRK07440 hypothetical protein; Provisional
Probab=23.26 E-value=49 Score=25.78 Aligned_cols=10 Identities=50% Similarity=1.125 Sum_probs=8.2
Q ss_pred CCCCCCeeEE
Q 018438 299 DLHPGDHIEI 308 (356)
Q Consensus 299 dLkPGDHIEI 308 (356)
.|+.||.|||
T Consensus 54 ~L~~gD~IEI 63 (70)
T PRK07440 54 QVQPGDRLEI 63 (70)
T ss_pred ecCCCCEEEE
Confidence 3788999987
No 57
>cd03470 Rieske_cytochrome_bc1 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including uni- and multi-cellular eukaryotes, plants (in their mitochondria) and bacteria. The cytochrome bc(1) and b6f complexes are central components of the respiratory and photosynthetic electron transport chains, respectively, which carry out similar core electron and proton transfer steps. The bc(1) and b6f complexes share a common core structure of three catalytic subunits: cyt b, the Rieske ISP, and either a cyt c1 in the bc(1) complex or cyt f in the b6f complex, which are arranged in an integral membrane-bound dimeric complex. While the core of the b6f complex is similar to that of the bc(1) complex, the domain arrangement outside the core and the complement of prosthetic groups are strikingly different.
Probab=23.09 E-value=33 Score=29.52 Aligned_cols=18 Identities=28% Similarity=0.750 Sum_probs=15.4
Q ss_pred cCCCCCCCeeEEEeeccC
Q 018438 297 LNDLHPGDHIEIQWRRNK 314 (356)
Q Consensus 297 l~dLkPGDHIEIQWRrnk 314 (356)
+.+|.||.-.++.||+..
T Consensus 6 l~~l~~G~~~~v~w~Gkp 23 (126)
T cd03470 6 LSKIEEGQLITVEWRGKP 23 (126)
T ss_pred hhhCCCCCEEEEEECCeE
Confidence 578999999999998764
No 58
>COG3086 RseC Positive regulator of sigma E activity [Signal transduction mechanisms]
Probab=22.72 E-value=52 Score=30.26 Aligned_cols=15 Identities=27% Similarity=0.601 Sum_probs=13.5
Q ss_pred cccCCCCCCCeeEEE
Q 018438 295 DCLNDLHPGDHIEIQ 309 (356)
Q Consensus 295 dcl~dLkPGDHIEIQ 309 (356)
-|...|+|||.|||-
T Consensus 54 ~t~~pL~~Gq~VeiG 68 (150)
T COG3086 54 ETDEPLEPGQKVELG 68 (150)
T ss_pred ecCCcCCCCCEEEEc
Confidence 688999999999984
No 59
>PF10530 Toxin_35: Toxin with inhibitor cystine knot ICK or Knottin scaffold; InterPro: IPR019553 Spider toxins of the CSTX family are ion channel toxins containing an inhibitor cystine knot (ICK) structural motif or Knottin scaffold. The four disulphide bonds present in the CSTX spider toxin family are arranged in the following pattern: 1-4, 2-5, 3-8 and 6-7. CSTX-1 is the most important component of Cupiennius salei (Wandering spider) venom in terms of relative abundance and toxicity and therefore is likely to contribute significantly to the overall toxicity of the whole venom. CSTX-1 blocked rat neuronal L-type, but no other types of HVA Cav channels []. Interestingly, the omega-toxins from Phoneutria nigriventer (Brazilian armed spider) venom (another South American species also belonging to the Ctenidae family) are included as they carry the same disulphide bond arrangement. suggested that CSTX-1 may interact with Cav channels. Calcium ion voltage channel heteromultimer containing an L-type pore-forming alpha1-subunit is the most probable candidate for the molecular target of CSTX-1 these toxins [].
Probab=21.97 E-value=42 Score=22.35 Aligned_cols=15 Identities=27% Similarity=0.676 Sum_probs=13.0
Q ss_pred hccccccCCCCCcee
Q 018438 325 VGHLESCDGNENFCH 339 (356)
Q Consensus 325 VGHlesCdgn~~~C~ 339 (356)
|||-+||..|.|-|-
T Consensus 2 I~~~~sC~~dk~gCC 16 (23)
T PF10530_consen 2 IGKRHSCTHDKHGCC 16 (23)
T ss_pred CccccccccCCCCce
Confidence 799999999988774
No 60
>cd05770 IgC_beta2m Class I major histocompatibility complex (MHC) beta2-microglobulin. IgC_beta2m: Immunoglobulin-like domain in beta2-Microglobulin (beta2m). Beta2m is the non-covalently bound light chain of the human class I major histocompatibility complex (MHC-I). Beta2m is structured as a beta-sandwich domain composed of two facing beta-sheets (four stranded and three stranded), that is typical of the C-type immunoglobulin superfamily. This structure is stabilized by an intramolecular disulfide bridge connecting two Cys residues in the facing beta -sheets. In vivo, MHC-I continuously exposes beta2m on the cell surface, where it may be released to plasmatic fluids, transported to the kidneys, degraded and then excreted.
Probab=21.61 E-value=38 Score=27.64 Aligned_cols=17 Identities=41% Similarity=0.647 Sum_probs=14.6
Q ss_pred CCCCCCCeeEEEeeccCC
Q 018438 298 NDLHPGDHIEIQWRRNKE 315 (356)
Q Consensus 298 ~dLkPGDHIEIQWRrnke 315 (356)
.+.-|.| |+|+|+||.+
T Consensus 25 ~gFyP~~-i~v~W~~dg~ 41 (93)
T cd05770 25 TGFHPPD-IEIRLLKNGV 41 (93)
T ss_pred EEEeCCC-CEEEEEECCE
Confidence 5678998 9999999975
No 61
>PRK06437 hypothetical protein; Provisional
Probab=21.55 E-value=55 Score=25.23 Aligned_cols=10 Identities=20% Similarity=0.421 Sum_probs=8.8
Q ss_pred CCCCCCeeEE
Q 018438 299 DLHPGDHIEI 308 (356)
Q Consensus 299 dLkPGDHIEI 308 (356)
-|++||.|||
T Consensus 51 ~L~dgD~Vei 60 (67)
T PRK06437 51 NVKKEDDVLI 60 (67)
T ss_pred EcCCCCEEEE
Confidence 5889999998
No 62
>PRK11798 ClpXP protease specificity-enhancing factor; Provisional
Probab=21.15 E-value=37 Score=30.67 Aligned_cols=21 Identities=48% Similarity=1.050 Sum_probs=15.9
Q ss_pred eeeccCCeeeeeeeecceeeeeecC
Q 018438 228 VYNRENGHVGFMLSCYDAELSYDQS 252 (356)
Q Consensus 228 VYnRenghvGfmLSCYDA~lsYd~~ 252 (356)
+|.||||+ |+|+ +.|..|+..
T Consensus 91 IyArEnGq-Gm~F---~~e~~~~~~ 111 (138)
T PRK11798 91 IYARENGQ-GMMF---EPEAAYDED 111 (138)
T ss_pred hhhhccCC-ceec---CCCcccccc
Confidence 78999999 8776 677666544
No 63
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=20.89 E-value=76 Score=26.18 Aligned_cols=18 Identities=33% Similarity=0.423 Sum_probs=13.4
Q ss_pred ccccccCCCCCCCeeEEE
Q 018438 292 HISDCLNDLHPGDHIEIQ 309 (356)
Q Consensus 292 h~Sdcl~dLkPGDHIEIQ 309 (356)
|+-|=-++.+.||-|+|+
T Consensus 46 ~aHD~~n~~k~GD~V~I~ 63 (84)
T PRK05610 46 HAHDENNEAKIGDVVRIM 63 (84)
T ss_pred EEECCCCCCCCCCEEEEE
Confidence 333444589999999997
No 64
>PHA03095 ankyrin-like protein; Provisional
Probab=20.79 E-value=79 Score=30.66 Aligned_cols=24 Identities=33% Similarity=0.463 Sum_probs=21.9
Q ss_pred CCCcHHHHHHHHccCChhhHHHHH
Q 018438 94 LDLPELVLECILEKLPPSGLCNMA 117 (356)
Q Consensus 94 LDLPeelLd~ILs~LSP~DLcrmA 117 (356)
-.||.|+...||++|+-.||..+.
T Consensus 443 ~~lP~Ei~~~Il~~l~~~dl~~~~ 466 (471)
T PHA03095 443 CALPPEIVMRILDFLPDDDLRNLL 466 (471)
T ss_pred CCCCHHHHHHHHHhCCHHHHHHHh
Confidence 789999999999999999997653
No 65
>cd05828 Sortase_D_4 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-4. These sortases recognize a unique sorting signal (LPXTA) and they constitute a specialized sorting pathway found in bacilli. Their substrates are predicted to be predominantly enzymes such as 5'-nucleotidases, glycosyl hydrolase, and subtilase.
Probab=20.75 E-value=44 Score=28.11 Aligned_cols=17 Identities=41% Similarity=0.605 Sum_probs=14.6
Q ss_pred cccCCCCCCCeeEEEee
Q 018438 295 DCLNDLHPGDHIEIQWR 311 (356)
Q Consensus 295 dcl~dLkPGDHIEIQWR 311 (356)
.-|++|++||-|+|+..
T Consensus 57 ~~L~~l~~Gd~i~v~~~ 73 (127)
T cd05828 57 RFLGELEPGDIITLQTL 73 (127)
T ss_pred hChhcCCCCCEEEEEEC
Confidence 35788999999999986
No 66
>PF09917 DUF2147: Uncharacterized protein conserved in bacteria (DUF2147); InterPro: IPR019223 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=20.73 E-value=75 Score=26.32 Aligned_cols=46 Identities=26% Similarity=0.575 Sum_probs=32.1
Q ss_pred cccceeeeccCCeeeeeeeecceeeeeecCCCceeecCCCCCCCceeeecCCCccc
Q 018438 223 WFPAQVYNRENGHVGFMLSCYDAELSYDQSTDTFQARYPPHGRRPIAIECGVPWER 278 (356)
Q Consensus 223 WFPAQVYnRenghvGfmLSCYDA~lsYd~~TDTF~ARYpphGrr~~~ie~~i~WdR 278 (356)
|==..|||.++|+. |++.+.-+.. ||...|=- .|-. .+.....|.|
T Consensus 69 w~~G~iydP~~Gkt------Y~~~i~l~~~-~~L~v~G~-~g~~--~~gks~tW~R 114 (114)
T PF09917_consen 69 WKGGKIYDPEDGKT------YSAKITLSGN-DTLKVRGC-VGIS--LLGKSQTWTR 114 (114)
T ss_pred ccCcEEEeCCCCCE------EEEEEEECCC-CEEEEEEE-Eccc--cccCCcEEeC
Confidence 44468999999986 9999998877 78877731 1111 3556667765
No 67
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=20.53 E-value=59 Score=26.57 Aligned_cols=9 Identities=44% Similarity=0.804 Sum_probs=7.6
Q ss_pred CCCCCeeEE
Q 018438 300 LHPGDHIEI 308 (356)
Q Consensus 300 LkPGDHIEI 308 (356)
|+.||.|||
T Consensus 69 L~egD~IEI 77 (84)
T PRK06083 69 LSSGDAISL 77 (84)
T ss_pred CCCCCEEEE
Confidence 788888887
No 68
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=20.27 E-value=62 Score=24.21 Aligned_cols=10 Identities=70% Similarity=1.002 Sum_probs=8.2
Q ss_pred CCCCCCeeEE
Q 018438 299 DLHPGDHIEI 308 (356)
Q Consensus 299 dLkPGDHIEI 308 (356)
-|+.||.|||
T Consensus 49 ~L~dgD~Iei 58 (65)
T PRK06488 49 VLHEGDRIEI 58 (65)
T ss_pred ccCCCCEEEE
Confidence 4788999987
Done!