Query 037135
Match_columns 124
No_of_seqs 106 out of 229
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 08:59:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037135.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037135hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03791 KNOX2: KNOX2 domain ; 100.0 5.4E-30 1.2E-34 164.0 7.2 49 65-113 4-52 (52)
2 PF03790 KNOX1: KNOX1 domain ; 99.9 7.4E-26 1.6E-30 141.1 4.6 44 10-53 1-44 (45)
3 KOG0773 Transcription factor M 98.3 1.3E-07 2.8E-12 78.0 0.3 106 10-115 50-163 (342)
4 PF13097 CENP-U: CENP-A nucleo 84.2 3.4 7.3E-05 32.5 5.7 45 68-112 101-148 (175)
5 PF03792 PBC: PBC domain; Int 81.8 6.4 0.00014 31.4 6.5 43 6-48 23-76 (191)
6 PF11288 DUF3089: Protein of u 79.4 0.63 1.4E-05 37.1 0.1 29 9-41 110-138 (207)
7 PF06295 DUF1043: Protein of u 74.0 6.9 0.00015 28.6 4.3 35 78-112 36-70 (128)
8 KOG0774 Transcription factor P 73.0 26 0.00057 29.8 8.0 43 6-48 25-78 (334)
9 COG3105 Uncharacterized protei 66.8 20 0.00043 27.3 5.5 41 72-112 39-79 (138)
10 PRK11677 hypothetical protein; 65.6 13 0.00028 27.9 4.3 41 71-111 33-73 (134)
11 PF07425 Pardaxin: Pardaxin; 64.6 4.8 0.0001 23.2 1.4 17 13-29 6-22 (33)
12 PF12057 DUF3538: Domain of un 60.8 18 0.00039 26.8 4.3 41 72-112 15-69 (120)
13 COG1497 Predicted transcriptio 59.3 8.2 0.00018 32.1 2.5 41 2-42 171-212 (260)
14 PF05190 MutS_IV: MutS family 55.3 15 0.00032 23.9 2.8 24 67-90 1-24 (92)
15 PF11348 DUF3150: Protein of u 54.0 51 0.0011 26.9 6.3 19 71-89 100-118 (257)
16 PF05016 Plasmid_stabil: Plasm 50.4 43 0.00094 21.1 4.4 22 96-117 24-45 (90)
17 PF02290 SRP14: Signal recogni 46.7 18 0.00039 25.2 2.2 17 69-85 72-88 (93)
18 PF15225 IL32: Interleukin 32 46.2 1.1E+02 0.0024 22.0 6.4 50 41-94 2-62 (104)
19 KOG4460 Nuclear pore complex, 45.9 45 0.00097 31.1 5.1 37 73-112 569-605 (741)
20 KOG1338 Uncharacterized conser 45.7 37 0.00079 30.4 4.4 64 17-83 122-187 (466)
21 cd00669 Asp_Lys_Asn_RS_core As 44.0 23 0.0005 28.7 2.8 36 5-40 199-238 (269)
22 PF08335 GlnD_UR_UTase: GlnD P 40.3 58 0.0013 23.5 4.2 47 74-120 39-101 (142)
23 PF10152 DUF2360: Predicted co 37.6 1.2E+02 0.0027 22.5 5.7 42 72-113 1-49 (148)
24 KOG4445 Uncharacterized conser 36.4 93 0.002 27.0 5.3 42 71-112 135-178 (368)
25 PF01563 Alpha_E3_glycop: Alph 34.9 20 0.00044 23.4 0.9 25 10-34 26-50 (56)
26 PF03401 TctC: Tripartite tric 34.9 63 0.0014 25.9 4.0 16 35-50 212-227 (274)
27 PF11014 DUF2852: Protein of u 34.4 28 0.00061 25.6 1.7 34 40-78 78-112 (115)
28 PF13713 BRX_N: Transcription 34.0 57 0.0012 19.6 2.7 19 95-113 8-26 (39)
29 COG5661 Predicted secreted Zn- 33.1 1.3E+02 0.0029 24.3 5.4 43 67-112 109-151 (210)
30 cd00776 AsxRS_core Asx tRNA sy 32.6 53 0.0012 27.2 3.3 36 5-40 256-291 (322)
31 KOG3489 Mitochondrial import i 32.5 77 0.0017 22.3 3.6 32 67-103 9-40 (86)
32 PRK03826 5'-nucleotidase; Prov 32.4 1.1E+02 0.0024 23.9 4.9 10 70-79 172-181 (195)
33 PF01533 Tospo_nucleocap: Tosp 32.3 41 0.00089 27.9 2.5 37 7-47 113-162 (248)
34 PRK13895 conjugal transfer pro 31.9 1.6E+02 0.0035 22.6 5.5 46 44-94 4-59 (144)
35 PF13865 FoP_duplication: C-te 31.8 34 0.00073 22.8 1.7 7 70-76 47-53 (74)
36 KOG4278 Protein tyrosine kinas 31.2 1.3E+02 0.0028 29.2 5.8 42 66-112 1084-1125(1157)
37 COG1084 Predicted GTPase [Gene 29.3 2.3E+02 0.005 24.6 6.6 83 18-111 75-161 (346)
38 PLN02372 violaxanthin de-epoxi 29.0 3.4E+02 0.0074 24.4 7.7 65 38-111 328-395 (455)
39 PF12878 SICA_beta: SICA extra 28.8 63 0.0014 24.9 2.9 24 67-92 95-118 (169)
40 PF14689 SPOB_a: Sensor_kinase 27.5 1.7E+02 0.0036 18.5 5.7 36 77-112 10-57 (62)
41 PHA02698 hypothetical protein; 26.2 2.3E+02 0.0051 19.8 5.3 36 71-111 49-85 (89)
42 COG0365 Acs Acyl-coenzyme A sy 25.5 67 0.0015 28.9 2.9 21 18-38 71-91 (528)
43 PF10112 Halogen_Hydrol: 5-bro 25.2 1.8E+02 0.0038 22.1 4.9 43 70-112 125-173 (199)
44 smart00787 Spc7 Spc7 kinetocho 24.9 1.5E+02 0.0032 25.0 4.6 43 68-110 47-95 (312)
45 PLN02850 aspartate-tRNA ligase 24.5 83 0.0018 28.3 3.3 36 5-40 460-495 (530)
46 PF04711 ApoA-II: Apolipoprote 24.5 2.4E+02 0.0053 19.4 5.1 46 68-113 3-54 (76)
47 PRK05159 aspC aspartyl-tRNA sy 24.5 80 0.0017 27.4 3.1 36 5-40 367-402 (437)
48 PF06238 Borrelia_lipo_2: Borr 23.0 2.7E+02 0.0057 20.4 5.1 38 68-111 34-71 (111)
49 PF14591 AF0941-like: AF0941-l 22.9 59 0.0013 24.4 1.7 34 78-111 65-98 (127)
50 PF07337 CagY_M: DC-EC Repeat; 22.3 35 0.00076 20.0 0.3 16 27-42 1-17 (33)
51 KOG1733 Mitochondrial import i 22.0 1.2E+02 0.0025 21.8 3.0 24 70-93 68-91 (97)
52 KOG1992 Nuclear export recepto 21.8 1.6E+02 0.0034 28.8 4.6 34 72-105 232-297 (960)
53 TIGR00457 asnS asparaginyl-tRN 21.7 1E+02 0.0022 27.0 3.2 35 6-40 384-418 (453)
54 KOG2070 Guanine nucleotide exc 21.7 57 0.0012 30.1 1.7 74 15-93 135-215 (661)
55 TIGR02609 doc_partner putative 21.6 1.4E+02 0.0029 19.6 3.1 23 70-92 48-71 (74)
56 PF07165 DUF1397: Protein of u 21.4 1.4E+02 0.003 23.6 3.6 58 31-88 19-82 (213)
57 KOG1856 Transcription elongati 20.8 2.2E+02 0.0048 28.8 5.4 80 13-94 1102-1206(1299)
58 KOG4014 Uncharacterized conser 20.7 1.4E+02 0.003 24.6 3.5 24 79-102 36-59 (248)
59 PF06340 TcpF: Vibrio cholerae 20.6 50 0.0011 28.0 1.0 21 17-42 24-44 (311)
60 PTZ00401 aspartyl-tRNA synthet 20.6 95 0.0021 28.2 2.9 36 5-40 480-515 (550)
No 1
>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=99.96 E-value=5.4e-30 Score=164.03 Aligned_cols=49 Identities=69% Similarity=1.050 Sum_probs=47.4
Q ss_pred CCCCCCchhhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhhC
Q 037135 65 STNKDPELDQFMEAYYDMLVKYREELTRPIQEAMDFIRRIETQLNMLSN 113 (124)
Q Consensus 65 ~~~~dpELDqFMeaYc~~L~kykeeL~~p~~EA~~f~~~iE~QL~~L~~ 113 (124)
.+|.||||||||++||.||+||||||+|||+||++|||+||+||++|||
T Consensus 4 ~~~~dpELDqFMeaYc~~L~kykeeL~~p~~EA~~f~~~ie~qL~~Lt~ 52 (52)
T PF03791_consen 4 SIGADPELDQFMEAYCDMLVKYKEELQRPFQEAMEFCREIEQQLSSLTG 52 (52)
T ss_pred CCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 3689999999999999999999999999999999999999999999997
No 2
>PF03790 KNOX1: KNOX1 domain ; InterPro: IPR005540 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=99.92 E-value=7.4e-26 Score=141.09 Aligned_cols=44 Identities=70% Similarity=1.027 Sum_probs=41.2
Q ss_pred HHHHHHHhhCCCcHHHHHHHHhhhhcCCchhHHHHHHHHHHHHH
Q 037135 10 EAIKAKIISHPQYSSLLEAYVDCQKVGAPPEVVARLAAARQEFE 53 (124)
Q Consensus 10 ~~iKa~I~sHPlYp~LL~A~i~C~KVGaP~e~~~~L~~~~~~~~ 53 (124)
+.|||+|++||+||+||+|||+|+|||||||++++||++.++++
T Consensus 1 e~iKA~I~~HP~Y~~Ll~Ayi~C~KVGAP~e~~~~L~e~~~~~~ 44 (45)
T PF03790_consen 1 EAIKAKIASHPLYPRLLAAYIDCQKVGAPPEVVARLDEILAESQ 44 (45)
T ss_pred ChHHHHHHcCCCcHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhc
Confidence 46999999999999999999999999999999999999988753
No 3
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=98.32 E-value=1.3e-07 Score=78.01 Aligned_cols=106 Identities=18% Similarity=0.163 Sum_probs=82.7
Q ss_pred HHHHHHHhhCCCcHHHHHHHHhhhhcCCchhHHHHHHHHHHHHHH--hhhcccC---C-CCCCCCCCchhhHHHHHHHHH
Q 037135 10 EAIKAKIISHPQYSSLLEAYVDCQKVGAPPEVVARLAAARQEFES--RQRSSLN---S-RDSTNKDPELDQFMEAYYDML 83 (124)
Q Consensus 10 ~~iKa~I~sHPlYp~LL~A~i~C~KVGaP~e~~~~L~~~~~~~~~--~~~~~~~---~-~~~~~~dpELDqFMeaYc~~L 83 (124)
..+|..+.+||+|..++.+|++|++++.|.+.+.+.+........ ..+...+ . .-..+.+++++.||..|+.+|
T Consensus 50 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~s~~~~~~~~~~~~~~~~~k~~~~l 129 (342)
T KOG0773|consen 50 ASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRSPASLSPPEDKGARRGNATRESATLKAWLEEHRLNPYPSKLEKIL 129 (342)
T ss_pred ccccccccchhHHhHHhhccccccccccCcCccccccccccCccccccccccccccccccccchhhhhhccCchHHHHHH
Confidence 347899999999999999999999999999998886554332111 0010000 0 002357899999999999999
Q ss_pred HHHHHHhhhhH--HHHHHHHHHHHHHHHHhhCCC
Q 037135 84 VKYREELTRPI--QEAMDFIRRIETQLNMLSNGP 115 (124)
Q Consensus 84 ~kykeeL~~p~--~EA~~f~~~iE~QL~~L~~~~ 115 (124)
..++..|+..+ ++++.+.++++..+...++.+
T Consensus 130 l~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~ 163 (342)
T KOG0773|consen 130 LAVITKLTLTQVSTWFANARRRLKKELKMTWGPT 163 (342)
T ss_pred HHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCc
Confidence 99999999999 699999999999999988653
No 4
>PF13097 CENP-U: CENP-A nucleosome associated complex (NAC) subunit
Probab=84.15 E-value=3.4 Score=32.51 Aligned_cols=45 Identities=24% Similarity=0.468 Sum_probs=39.1
Q ss_pred CC-CchhhHHHHHHHHHHHHHHHhhhhH-HHHH-HHHHHHHHHHHHhh
Q 037135 68 KD-PELDQFMEAYYDMLVKYREELTRPI-QEAM-DFIRRIETQLNMLS 112 (124)
Q Consensus 68 ~d-pELDqFMeaYc~~L~kykeeL~~p~-~EA~-~f~~~iE~QL~~L~ 112 (124)
.| -|||-...++-.++..||+.++-.+ ++|+ .|+..+..||-.+-
T Consensus 101 SDItELDVvL~~FEk~~~eYkq~ieS~~cr~AI~~F~~~~keqL~~~i 148 (175)
T PF13097_consen 101 SDITELDVVLSAFEKTALEYKQSIESKICRKAINKFYSNFKEQLIEMI 148 (175)
T ss_pred ccchHHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHH
Confidence 35 5999999999999999999998877 6777 78999999987764
No 5
>PF03792 PBC: PBC domain; InterPro: IPR005542 Pbx proteins are members of the TALE (three-amino-acid loop extension) family of atypical homeodomain proteins, whose members are characterised by a three-residue insertion in the first helix of the homeodomain involved in their interaction with Hox proteins. Examination of Pbx1 has shown that, in addition to the homeodomain, a short 16-residue C-terminal tail is essential for maximal cooperative interactions with Hox partners as well as for maximal monomeric binding of Pbx1 to DNA. The PBX domain is a bipartite acidic domain [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005634 nucleus
Probab=81.78 E-value=6.4 Score=31.39 Aligned_cols=43 Identities=23% Similarity=0.334 Sum_probs=32.2
Q ss_pred hhhHHHHHHHHhhCCCcHHHHHHHHhhh-hcCC---------chh-HHHHHHHH
Q 037135 6 SSETEAIKAKIISHPQYSSLLEAYVDCQ-KVGA---------PPE-VVARLAAA 48 (124)
Q Consensus 6 ~~e~~~iKa~I~sHPlYp~LL~A~i~C~-KVGa---------P~e-~~~~L~~~ 48 (124)
-++....|-.|-+||+||.|-+..++-. |++- ||| ++.|||-+
T Consensus 23 LDeaqa~K~~l~~hr~k~ALfsVLcE~KEkt~LSir~~qee~p~dpQl~RLDNM 76 (191)
T PF03792_consen 23 LDEAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRNIQEEDPPDPQLMRLDNM 76 (191)
T ss_pred HhHHHHhchhhcCCCCchhhHHHHHHHHhhcCccccccCCcCCCchhhhhhhcc
Confidence 3456789999999999999999987765 3221 444 77888865
No 6
>PF11288 DUF3089: Protein of unknown function (DUF3089); InterPro: IPR021440 This family of proteins has no known function.
Probab=79.44 E-value=0.63 Score=37.12 Aligned_cols=29 Identities=31% Similarity=0.548 Sum_probs=26.6
Q ss_pred HHHHHHHHhhCCCcHHHHHHHHhhhhcCCchhH
Q 037135 9 TEAIKAKIISHPQYSSLLEAYVDCQKVGAPPEV 41 (124)
Q Consensus 9 ~~~iKa~I~sHPlYp~LL~A~i~C~KVGaP~e~ 41 (124)
...||.+|..+|++.+||+||+ ||.|.-.
T Consensus 110 ~~LL~e~~~~~pl~~rLVAAYl----iG~~v~~ 138 (207)
T PF11288_consen 110 LRLLKEEIAGDPLRKRLVAAYL----IGYPVTV 138 (207)
T ss_pred HHHHHHHhcCchHHhhhheeee----cCccccH
Confidence 4679999999999999999999 9998776
No 7
>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=73.96 E-value=6.9 Score=28.60 Aligned_cols=35 Identities=11% Similarity=0.283 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhh
Q 037135 78 AYYDMLVKYREELTRPIQEAMDFIRRIETQLNMLS 112 (124)
Q Consensus 78 aYc~~L~kykeeL~~p~~EA~~f~~~iE~QL~~L~ 112 (124)
.=-.-|..||.++..||..+...+++|...-+.|-
T Consensus 36 ~~k~el~~yk~~V~~HF~~ta~Ll~~l~~~Y~~l~ 70 (128)
T PF06295_consen 36 QAKQELEQYKQEVNDHFAQTAELLDNLTQDYQKLY 70 (128)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44456899999999999999988888877666653
No 8
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=72.96 E-value=26 Score=29.75 Aligned_cols=43 Identities=23% Similarity=0.343 Sum_probs=32.3
Q ss_pred hhhHHHHHHHHhhCCCcHHHHHHHHhhh-hcC---------Cchh-HHHHHHHH
Q 037135 6 SSETEAIKAKIISHPQYSSLLEAYVDCQ-KVG---------APPE-VVARLAAA 48 (124)
Q Consensus 6 ~~e~~~iKa~I~sHPlYp~LL~A~i~C~-KVG---------aP~e-~~~~L~~~ 48 (124)
-++..+.|-.|-+||+||.|.+--..-. |++ .||| ++-|||.+
T Consensus 25 lDeaqa~K~~lnch~mk~AlfsVLcE~KeKt~lsir~~qdeep~dpqlmRLDnM 78 (334)
T KOG0774|consen 25 LDEAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRGMQDEEPPDPQLMRLDNM 78 (334)
T ss_pred cchHHhhhhccccccchHHHHHHHHHhhhhheeeeccccccCCCChHHHHHHHH
Confidence 3456688999999999999998766543 222 3777 88899875
No 9
>COG3105 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=66.84 E-value=20 Score=27.27 Aligned_cols=41 Identities=20% Similarity=0.352 Sum_probs=33.4
Q ss_pred hhhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhh
Q 037135 72 LDQFMEAYYDMLVKYREELTRPIQEAMDFIRRIETQLNMLS 112 (124)
Q Consensus 72 LDqFMeaYc~~L~kykeeL~~p~~EA~~f~~~iE~QL~~L~ 112 (124)
|-.=|+.--.-|..||+||.+||.+..+.+++|-+.-+.|-
T Consensus 39 ~q~ELe~~K~~ld~~rqel~~HFa~sAeLlktl~~dYqkly 79 (138)
T COG3105 39 LQYELEKVKAQLDEYRQELVKHFARSAELLKTLAQDYQKLY 79 (138)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33445666777899999999999999999999988777664
No 10
>PRK11677 hypothetical protein; Provisional
Probab=65.63 E-value=13 Score=27.86 Aligned_cols=41 Identities=20% Similarity=0.316 Sum_probs=30.3
Q ss_pred chhhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHh
Q 037135 71 ELDQFMEAYYDMLVKYREELTRPIQEAMDFIRRIETQLNML 111 (124)
Q Consensus 71 ELDqFMeaYc~~L~kykeeL~~p~~EA~~f~~~iE~QL~~L 111 (124)
+|.+=.+.=-.-|..||.|+..||.++...+++|-.+=+.|
T Consensus 33 ~le~eLe~~k~ele~YkqeV~~HFa~TA~Ll~~L~~~Y~~L 73 (134)
T PRK11677 33 ALQYELEKNKAELEEYRQELVSHFARSAELLDTMAKDYRQL 73 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444445556699999999999999998887776665554
No 11
>PF07425 Pardaxin: Pardaxin; InterPro: IPR009990 This family consists of several Pardaxin proteins. Pardaxin, a 33-amino-acid pore-forming polypeptide toxin isolated from the Red Sea Moses sole Pardachirus marmoratus, has a helix-hinge-helix structure. This is a common structural motif found both in antibacterial peptides that can act selectively on bacterial membranes (e.g., cecropin), and in cytotoxic peptides that can lyse both mammalian and bacterial cells (e.g., melittin). Pardaxin possesses a high antibacterial activity with a significantly reduced haemolytic activity towards human red blood cells compared with melittin []. Pardaxin has also been found to have a shark repellent action [].; GO: 0005576 extracellular region; PDB: 1XC0_A 2KNS_A.
Probab=64.61 E-value=4.8 Score=23.24 Aligned_cols=17 Identities=47% Similarity=0.659 Sum_probs=14.6
Q ss_pred HHHHhhCCCcHHHHHHH
Q 037135 13 KAKIISHPQYSSLLEAY 29 (124)
Q Consensus 13 Ka~I~sHPlYp~LL~A~ 29 (124)
--||++.|++..||+|-
T Consensus 6 ipkiissplfktllsav 22 (33)
T PF07425_consen 6 IPKIISSPLFKTLLSAV 22 (33)
T ss_dssp HHHHCCTTTCHHHHHHH
T ss_pred hhHHHccHHHHHHHHHH
Confidence 35899999999999874
No 12
>PF12057 DUF3538: Domain of unknown function (DUF3538); InterPro: IPR021925 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 120 amino acids in length. This domain is found associated with PF00240 from PFAM. This domain has a conserved SDL sequence motif.
Probab=60.77 E-value=18 Score=26.82 Aligned_cols=41 Identities=34% Similarity=0.567 Sum_probs=30.4
Q ss_pred hhhHHHHHHHHHH-----HH------HHHhhhhHH---HHHHHHHHHHHHHHHhh
Q 037135 72 LDQFMEAYYDMLV-----KY------REELTRPIQ---EAMDFIRRIETQLNMLS 112 (124)
Q Consensus 72 LDqFMeaYc~~L~-----ky------keeL~~p~~---EA~~f~~~iE~QL~~L~ 112 (124)
|-=||+.|+++|. .| +|+=+|-|+ ||..++..-...|++|.
T Consensus 15 L~Pflery~~iL~~~~~~e~~~~~~~re~~QRi~d~VsEalh~lsHA~hAlSDL~ 69 (120)
T PF12057_consen 15 LQPFLERYHEILQEDPSFEYENNTQEREEDQRIFDLVSEALHYLSHAYHALSDLM 69 (120)
T ss_pred HhHHHHHHHHHHhcCCCCCCCCCccchhhHhHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3447778888776 34 566677775 88888888888888875
No 13
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=59.29 E-value=8.2 Score=32.10 Aligned_cols=41 Identities=22% Similarity=0.366 Sum_probs=32.5
Q ss_pred CCCchhhHHHHHHHHhhCCCcHHH-HHHHHhhhhcCCchhHH
Q 037135 2 EGNESSETEAIKAKIISHPQYSSL-LEAYVDCQKVGAPPEVV 42 (124)
Q Consensus 2 ~~~~~~e~~~iKa~I~sHPlYp~L-L~A~i~C~KVGaP~e~~ 42 (124)
||...-+.+++|+.+.+||..... ..||+.|.|+|--||+-
T Consensus 171 GGsr~~dld~~~el~~s~d~iaAmG~~a~va~rklgiePdi~ 212 (260)
T COG1497 171 GGSRKVDLDRLKELSASEDIIAAMGTEALVALRKLGIEPDIE 212 (260)
T ss_pred CcccccchHHHHHhhcccchhhhhhHHHHHHHHHcCCCCCee
Confidence 344566789999999999954443 57899999999999863
No 14
>PF05190 MutS_IV: MutS family domain IV C-terminus.; InterPro: IPR007861 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the clamp domain (domain 4) found in proteins of the MutS family. The clamp domain is inserted within the core domain at the top of the lever helices. It has a beta-sheet structure [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B 1WBD_A 1WB9_A 3K0S_A 1OH6_A ....
Probab=55.29 E-value=15 Score=23.87 Aligned_cols=24 Identities=33% Similarity=0.434 Sum_probs=17.6
Q ss_pred CCCCchhhHHHHHHHHHHHHHHHh
Q 037135 67 NKDPELDQFMEAYYDMLVKYREEL 90 (124)
Q Consensus 67 ~~dpELDqFMeaYc~~L~kykeeL 90 (124)
|-||+||...+.|..+-....+.+
T Consensus 1 g~d~~Ld~~~~~~~~~~~~l~~~~ 24 (92)
T PF05190_consen 1 GFDEELDELREEYEEIEEELEELL 24 (92)
T ss_dssp TSSHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHH
Confidence 468999999999887765554443
No 15
>PF11348 DUF3150: Protein of unknown function (DUF3150); InterPro: IPR021496 This bacterial family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=53.98 E-value=51 Score=26.85 Aligned_cols=19 Identities=16% Similarity=0.438 Sum_probs=13.7
Q ss_pred chhhHHHHHHHHHHHHHHH
Q 037135 71 ELDQFMEAYYDMLVKYREE 89 (124)
Q Consensus 71 ELDqFMeaYc~~L~kykee 89 (124)
+-++|+..|=..+..+..+
T Consensus 100 ~k~~Fl~~Yd~~i~~w~~~ 118 (257)
T PF11348_consen 100 EKQDFLANYDQAIEEWIDR 118 (257)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 5677777777777777666
No 16
>PF05016 Plasmid_stabil: Plasmid stabilisation system protein; InterPro: IPR007712 Members of this family are involved in plasmid stabilisation. The exact molecular function of this protein is not known.; PDB: 3KXE_A 1WMI_A 3KIQ_y 3KIX_y 2KC9_A 3KHA_B 3KIS_y 3KIU_y 2KC8_A 1Z8M_A ....
Probab=50.36 E-value=43 Score=21.13 Aligned_cols=22 Identities=36% Similarity=0.474 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHhhCCCcc
Q 037135 96 EAMDFIRRIETQLNMLSNGPVR 117 (124)
Q Consensus 96 EA~~f~~~iE~QL~~L~~~~~~ 117 (124)
-|..|...|+.++..|...|..
T Consensus 24 ~a~~~~~~i~~~i~~l~~~P~~ 45 (90)
T PF05016_consen 24 AAERFIDAIEKAIERLSENPEM 45 (90)
T ss_dssp HHHHHHHHHHHHHHHHHCCCCT
T ss_pred HHHHHHHHHHHHHHhccccccc
Confidence 3899999999999999977654
No 17
>PF02290 SRP14: Signal recognition particle 14kD protein; InterPro: IPR003210 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the 14 kDa SRP14 component. Both SRP9 and SRP14 have the same (beta)-alpha-beta(3)-alpha fold. The heterodimer has pseudo two-fold symmetry and is saddle-like, consisting of a curved six-stranded beta-sheet that has four helices packed on the convex side and an exposed concave surface lined with positively charged residues. The SRP9/SRP14 heterodimer is essential for SRP RNA binding, mediating the pausing of synthesis of ribosome associated nascent polypeptides that have been engaged by the targeting domain of SRP [].; GO: 0008312 7S RNA binding, 0030942 endoplasmic reticulum signal peptide binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0005786 signal recognition particle, endoplasmic reticulum targeting; PDB: 1914_A 1RY1_D 1E8O_B 2W9J_B.
Probab=46.66 E-value=18 Score=25.15 Aligned_cols=17 Identities=29% Similarity=0.620 Sum_probs=14.6
Q ss_pred CCchhhHHHHHHHHHHH
Q 037135 69 DPELDQFMEAYYDMLVK 85 (124)
Q Consensus 69 dpELDqFMeaYc~~L~k 85 (124)
-.+||.|..+|+.+|..
T Consensus 72 ~~~l~~F~~~Y~~v~K~ 88 (93)
T PF02290_consen 72 PDDLDKFWQSYANVLKA 88 (93)
T ss_dssp TTCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 35999999999999863
No 18
>PF15225 IL32: Interleukin 32
Probab=46.20 E-value=1.1e+02 Score=22.01 Aligned_cols=50 Identities=22% Similarity=0.337 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHHHhhh-cccCCCCCCCCCCch----------hhHHHHHHHHHHHHHHHhhhhH
Q 037135 41 VVARLAAARQEFESRQR-SSLNSRDSTNKDPEL----------DQFMEAYYDMLVKYREELTRPI 94 (124)
Q Consensus 41 ~~~~L~~~~~~~~~~~~-~~~~~~~~~~~dpEL----------DqFMeaYc~~L~kykeeL~~p~ 94 (124)
..+.|++.++++-.+-+ +++.. ..||++ |.-|+-+|.||+....-.++-+
T Consensus 2 l~PLLeeeRd~LR~RgnRspvp~----~EDp~te~~eP~Esf~dkvmR~FqamlqrLQ~ww~~vl 62 (104)
T PF15225_consen 2 LTPLLEEERDELRCRGNRSPVPD----VEDPATEVWEPGESFCDKVMRWFQAMLQRLQTWWQAVL 62 (104)
T ss_pred CccccHHHHHHHHhccCCCCCCC----CCCcccccCCcchhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567777777655433 22221 345554 6889999999999888777765
No 19
>KOG4460 consensus Nuclear pore complex, Nup88/rNup84 component [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=45.90 E-value=45 Score=31.12 Aligned_cols=37 Identities=27% Similarity=0.254 Sum_probs=30.6
Q ss_pred hhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhh
Q 037135 73 DQFMEAYYDMLVKYREELTRPIQEAMDFIRRIETQLNMLS 112 (124)
Q Consensus 73 DqFMeaYc~~L~kykeeL~~p~~EA~~f~~~iE~QL~~L~ 112 (124)
.-|-|.|..-=.+-|+|+++|+ -..|+.+++||+.|.
T Consensus 569 ~vfrEqYi~~~dlV~~e~qrH~---~~l~~~k~~QlQ~l~ 605 (741)
T KOG4460|consen 569 QVFREQYILKQDLVKEEIQRHV---KLLCDQKKKQLQDLS 605 (741)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHH
Confidence 4577888888888889999876 467899999999986
No 20
>KOG1338 consensus Uncharacterized conserved protein [Function unknown]
Probab=45.69 E-value=37 Score=30.37 Aligned_cols=64 Identities=20% Similarity=0.169 Sum_probs=37.4
Q ss_pred hhCCCcHHHHHHHHhhhhcCCchh-HHHHHHHHHHHHHHhh-hcccCCCCCCCCCCchhhHHHHHHHHH
Q 037135 17 ISHPQYSSLLEAYVDCQKVGAPPE-VVARLAAARQEFESRQ-RSSLNSRDSTNKDPELDQFMEAYYDML 83 (124)
Q Consensus 17 ~sHPlYp~LL~A~i~C~KVGaP~e-~~~~L~~~~~~~~~~~-~~~~~~~~~~~~dpELDqFMeaYc~~L 83 (124)
+.||.|=. .-=.+|++-||-.+ ......++.+.+...- .....+ ..+...|+|+.||-+|-.+|
T Consensus 122 m~spifWd--EnEl~~Ll~stvlee~~Kd~aeI~~~~i~~i~pf~~~~-p~vfs~~slEdF~y~~Al~l 187 (466)
T KOG1338|consen 122 MHSPIFWD--ENELSMLLCSTVLEETVKDKAEIEKDFIFVIQPFKQHC-PIVFSRPSLEDFMYAYALGL 187 (466)
T ss_pred cCCCccCC--chHHHHHhhcccchhhHhHHHHHHHHHHHHHHHHHHhC-cchhcccCHHHHHHHHHHHH
Confidence 34555522 22357888888555 6666677766654221 111111 12345699999999998776
No 21
>cd00669 Asp_Lys_Asn_RS_core Asp_Lys_Asn_tRNA synthetase class II core domain. This domain is the core catalytic domain of class II aminoacyl-tRNA synthetases of the subgroup containing aspartyl, lysyl, and asparaginyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. Nearly all class II tRNA synthetases are dimers and enzymes in this subgroup are homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA.
Probab=44.05 E-value=23 Score=28.74 Aligned_cols=36 Identities=14% Similarity=0.262 Sum_probs=30.5
Q ss_pred chhhHHHHHHHHhhCCCcHH----HHHHHHhhhhcCCchh
Q 037135 5 ESSETEAIKAKIISHPQYSS----LLEAYVDCQKVGAPPE 40 (124)
Q Consensus 5 ~~~e~~~iKa~I~sHPlYp~----LL~A~i~C~KVGaP~e 40 (124)
..++.+.+++++..|-.-+. ...-|++.+|-|.||-
T Consensus 199 r~~d~~~l~~~~~~~~~~~~~~~~~~~~yl~a~~~G~pp~ 238 (269)
T cd00669 199 RLHDPDIQAEVFQEQGINKEAGMEYFEFYLKALEYGLPPH 238 (269)
T ss_pred hcCCHHHHHHHHHHhCcChhhccccHHHHHHHHHcCCCCC
Confidence 45667889999999988887 8888999999999874
No 22
>PF08335 GlnD_UR_UTase: GlnD PII-uridylyltransferase; InterPro: IPR013546 This entry represents a region found in a family of nucleotide transferases that includes bifunctional uridylyl-removing enzymes/uridylyltransferases (UR/UTases, GlnD; 2.7.7.59 from EC) and glutamine-synthetase adenylyltransferases (GlnE; 2.7.7.42 from EC). The region described in this family is found in many of its members to be C-terminal to a nucleotidyltransferase domain, and N-terminal to an HD domain and two ACT domains []. Bifunctional uridylyl-removing enzymes/uridylyltransferases are responsible for the modification of the regulatory protein PII, or GlnB, thereby acting as the sensory component of the nitrogen regulation (ntr) system []. The ntr system modulates nitrogen metabolism in response to the prevailing nitrogen source and the requirements of the cell. During nitrogen fixation, ammonia and 2-oxoglutarate can be used to produce glutamate. In response to nitrogen limitation, these transferases catalyse the uridylylation of the PII protein, which in turn stimulates deadenylylation of glutamine synthetase (GlnA), leading to the activation of glutamate synthetase and to the stimulation of NtrC-dependent promoters []. Uridylylated PII can act together with NtrB and NtrC to increase transcription of genes in the sigma54 regulon, which include glnA and other nitrogen-level controlled genes []. Under high concentrations of fixed nitrogen, PII is de-uridylylated leading to the inactivation of the glutamate synthetase pathway and switching off NtrC-dependent promoters []. It has also been suggested that the product of the glnD gene is involved in other physiological functions such as control of iron metabolism in certain species []. Glutamine-synthetase adenylyltransferase is an adenylyl transferase comprised of an adenylylating domain and a deadenylylating domain which modulate glutamine synthetase (GS) activity, where GS plays an important role in nitrogen assimilation [].; GO: 0016779 nucleotidyltransferase activity; PDB: 3K7D_A 1V4A_A.
Probab=40.28 E-value=58 Score=23.46 Aligned_cols=47 Identities=23% Similarity=0.457 Sum_probs=28.8
Q ss_pred hHHHHHHHHHH----H------------HHHHhhhhHHHHHHHHHHHHHHHHHhhCCCcccCC
Q 037135 74 QFMEAYYDMLV----K------------YREELTRPIQEAMDFIRRIETQLNMLSNGPVRIFN 120 (124)
Q Consensus 74 qFMeaYc~~L~----k------------ykeeL~~p~~EA~~f~~~iE~QL~~L~~~~~~~~~ 120 (124)
+|+..|..+.. . .-++-.+-+.+|-.|++.|++.|+-+++......+
T Consensus 39 efi~q~~~l~~~~~~t~~~l~~l~~~g~l~~~~~~~L~~ay~fl~~l~~~L~l~~~~~~d~L~ 101 (142)
T PF08335_consen 39 EFIAQYLQLRHGARHTIDALEALAAAGLLSEEEAEALREAYRFLRRLRHALRLVSGRQTDRLP 101 (142)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHHCTTT----B--
T ss_pred HHHHHHHHHHHchhhhHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHHhCCccCCCC
Confidence 67777777555 1 11222344579999999999999998887655443
No 23
>PF10152 DUF2360: Predicted coiled-coil domain-containing protein (DUF2360); InterPro: IPR019309 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53.
Probab=37.58 E-value=1.2e+02 Score=22.53 Aligned_cols=42 Identities=12% Similarity=0.344 Sum_probs=29.9
Q ss_pred hhhHHHHHHHHHHHHHH-------HhhhhHHHHHHHHHHHHHHHHHhhC
Q 037135 72 LDQFMEAYYDMLVKYRE-------ELTRPIQEAMDFIRRIETQLNMLSN 113 (124)
Q Consensus 72 LDqFMeaYc~~L~kyke-------eL~~p~~EA~~f~~~iE~QL~~L~~ 113 (124)
+.+|+.+=+..|++|-- ++++-++.+-.-+.=+|..|.+|-|
T Consensus 1 vN~Fi~~tv~fLN~F~~~cE~kL~~~e~~Lq~~E~~l~iLEaKL~SIpg 49 (148)
T PF10152_consen 1 VNHFIVHTVQFLNRFASVCEEKLSDMEQRLQRLEATLNILEAKLSSIPG 49 (148)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 35788888999999853 3445556666666777888888754
No 24
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=36.38 E-value=93 Score=26.98 Aligned_cols=42 Identities=19% Similarity=0.226 Sum_probs=33.1
Q ss_pred chhhHHHHHHHH--HHHHHHHhhhhHHHHHHHHHHHHHHHHHhh
Q 037135 71 ELDQFMEAYYDM--LVKYREELTRPIQEAMDFIRRIETQLNMLS 112 (124)
Q Consensus 71 ELDqFMeaYc~~--L~kykeeL~~p~~EA~~f~~~iE~QL~~L~ 112 (124)
+-|+||-.||.. |+.....|.+-|++|-.-...+-.|...+|
T Consensus 135 ~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavc 178 (368)
T KOG4445|consen 135 ACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVC 178 (368)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhh
Confidence 679999999953 556666666667788888888888888887
No 25
>PF01563 Alpha_E3_glycop: Alphavirus E3 glycoprotein; InterPro: IPR002533 Alphaviruses are enveloped RNA viruses that use arthropods such as mosquitoes for transmission to their vertebrate hosts, and include Semliki Forest and Sindbis viruses []. Alphaviruses consist of three structural proteins: the core nucleocapsid protein C, and the envelope proteins P62 and E1 (IPR002548 from INTERPRO) that associate as a heterodimer. The viral membrane-anchored surface glycoproteins are responsible for receptor recognition and entry into target cells through membrane fusion. The proteolytic maturation of P62 into E2 (IPR000936 from INTERPRO) and E3 causes a change in the viral surface. Together the E1, E2, and sometimes E3 glycoprotein "spikes" form an E1/E2 dimer or an E1/E2/E3 trimer, where E2 extends from the centre to the vertices, E1 fills the space between the vertices, and E3, if present, is at the distal end of the spike [, ]. Upon exposure of the virus to the acidity of the endosome, E1 dissociates from E2 to form an E1 homotrimer, which is necessary for the fusion step to drive the cellular and viral membranes together []. This entry represents the alphaviral E3 glycoprotein. Most alphaviruses lose the peripheral protein E3, but in Semliki viruses it remains associated with the viral surface.; GO: 0004252 serine-type endopeptidase activity, 0019028 viral capsid, 0055036 virion membrane; PDB: 3J0C_H 3J0G_N 3N40_P 3N41_A 3N44_A 3N42_A 3N43_A.
Probab=34.94 E-value=20 Score=23.36 Aligned_cols=25 Identities=28% Similarity=0.543 Sum_probs=18.4
Q ss_pred HHHHHHHhhCCCcHHHHHHHHhhhh
Q 037135 10 EAIKAKIISHPQYSSLLEAYVDCQK 34 (124)
Q Consensus 10 ~~iKa~I~sHPlYp~LL~A~i~C~K 34 (124)
-+|=..=+.||-|-.||.|-+.|.-
T Consensus 26 L~mLe~Nvd~p~Y~~LL~a~l~C~~ 50 (56)
T PF01563_consen 26 LRMLEDNVDNPGYDDLLEAVLRCPS 50 (56)
T ss_dssp HHHHHCTSSSTTHHHHHHHHCC--S
T ss_pred HHHHHHhCCCccHHHHHHHHhhCCC
Confidence 3455556789999999999999953
No 26
>PF03401 TctC: Tripartite tricarboxylate transporter family receptor; InterPro: IPR005064 Bordetella pertussis, the causative agent of human whooping cough (pertussis), is an obligate human pathogen with diverse high-affinity transport systems for the assimilation of iron, a biometal that is essential for growth []. Periplasmic binding proteins of a new family, particularly well represented in this organism (and more generally in beta-proteobacteria), have been called Bug receptors []. They adopt a characteristic Venus flytrap fold with two globular domains bisected by a ligand-binding cleft. The family is specific for carboxylated solutes, with a characteristic mode of binding involving two highly conserved beta strand-beta turn-alpha helix motifs originating from each domain. These two motifs form hydrogen bonds with a carboxylate group of the ligand, both directly and via conserved water molecules, and have thus been termed the carboxylate pincers. Domain 1 recognises the ligand and the carboxylate group serves as an initial anchoring point. Domain 2 discriminates between productively and non-productively bound ligands as proper interactions with this domain is needed for the of the closed conformation []. BugE has a glutamate bound ligand. No charged residues are involved in glutamate binding by BugE, unlike what has been described for all glutamate receptors reported so far. The Bug architecture is highly conserved despite limited sequence identity [].; GO: 0030288 outer membrane-bounded periplasmic space; PDB: 2QPQ_C 2DVZ_A 2F5X_A.
Probab=34.88 E-value=63 Score=25.91 Aligned_cols=16 Identities=44% Similarity=0.677 Sum_probs=12.0
Q ss_pred cCCchhHHHHHHHHHH
Q 037135 35 VGAPPEVVARLAAARQ 50 (124)
Q Consensus 35 VGaP~e~~~~L~~~~~ 50 (124)
-|+|++++.+|.++-+
T Consensus 212 ~gtp~~~~~~l~~a~~ 227 (274)
T PF03401_consen 212 KGTPDEIVDKLADAIK 227 (274)
T ss_dssp TTS-HHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHH
Confidence 4899999999987643
No 27
>PF11014 DUF2852: Protein of unknown function (DUF2852); InterPro: IPR021273 This bacterial family of proteins has no known function.
Probab=34.40 E-value=28 Score=25.64 Aligned_cols=34 Identities=38% Similarity=0.584 Sum_probs=20.8
Q ss_pred hHHHHHHHHHHHHHHhhhcccCCCCCCCCC-CchhhHHHH
Q 037135 40 EVVARLAAARQEFESRQRSSLNSRDSTNKD-PELDQFMEA 78 (124)
Q Consensus 40 e~~~~L~~~~~~~~~~~~~~~~~~~~~~~d-pELDqFMea 78 (124)
+.+.+|++.++++...-... + -..| .|.|+||..
T Consensus 78 ~tL~RLEeEq~eF~~Fl~rL---R--~AKDk~EFD~FM~~ 112 (115)
T PF11014_consen 78 DTLRRLEEEQREFEDFLERL---R--RAKDKEEFDQFMAE 112 (115)
T ss_pred HHHHHHHHHHHHHHHHHHHH---H--HhhhHHHHHHHHHh
Confidence 56788888877766442211 0 0234 799999964
No 28
>PF13713 BRX_N: Transcription factor BRX N-terminal domain
Probab=33.96 E-value=57 Score=19.63 Aligned_cols=19 Identities=21% Similarity=0.429 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHHhhC
Q 037135 95 QEAMDFIRRIETQLNMLSN 113 (124)
Q Consensus 95 ~EA~~f~~~iE~QL~~L~~ 113 (124)
+-|.++++.|..||++++.
T Consensus 8 kaaKe~IKsLt~QlK~mae 26 (39)
T PF13713_consen 8 KAAKEVIKSLTAQLKDMAE 26 (39)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3678999999999999984
No 29
>COG5661 Predicted secreted Zn-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=33.12 E-value=1.3e+02 Score=24.26 Aligned_cols=43 Identities=23% Similarity=0.255 Sum_probs=35.8
Q ss_pred CCCCchhhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhh
Q 037135 67 NKDPELDQFMEAYYDMLVKYREELTRPIQEAMDFIRRIETQLNMLS 112 (124)
Q Consensus 67 ~~dpELDqFMeaYc~~L~kykeeL~~p~~EA~~f~~~iE~QL~~L~ 112 (124)
++||||--|-.+|-.-+.+-. ++|.+=|...-++||.+|.+|-
T Consensus 109 ~a~pElalvwdtlladikrHE---ErH~eiar~har~mEkaL~sl~ 151 (210)
T COG5661 109 KADPELALVWDTLLADIKRHE---ERHAEIARYHAREMEKALLSLR 151 (210)
T ss_pred CCCHhHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHhcC
Confidence 689999999999877766654 4788888888999999999873
No 30
>cd00776 AsxRS_core Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as a subgroup of AspRS. AsnRS and AspRS are homodimers, which attach either asparagine or aspartate to the 3'OH group of ribose of the appropriate tRNA. While archaea lack asnRS, they possess a non-discriminating aspRS, which can mischarge Asp-tRNA with Asn. Subsequently, a tRNA-dependent aspartate amidotransferase converts the bound aspartate to asparagine. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate.
Probab=32.57 E-value=53 Score=27.22 Aligned_cols=36 Identities=25% Similarity=0.456 Sum_probs=30.2
Q ss_pred chhhHHHHHHHHhhCCCcHHHHHHHHhhhhcCCchh
Q 037135 5 ESSETEAIKAKIISHPQYSSLLEAYVDCQKVGAPPE 40 (124)
Q Consensus 5 ~~~e~~~iKa~I~sHPlYp~LL~A~i~C~KVGaP~e 40 (124)
...+.+.++.++..|.+=+.-+.-|++.+|-|.||-
T Consensus 256 r~~d~~~l~~r~~~~g~~~~~~~~yl~a~~~G~pp~ 291 (322)
T cd00776 256 RIHDYDELEERIKEHGLDPESFEWYLDLRKYGMPPH 291 (322)
T ss_pred ecCCHHHHHHHHHHcCCChHHHHHHHHHHHCCCCCC
Confidence 456667899999999987777799999999999874
No 31
>KOG3489 consensus Mitochondrial import inner membrane translocase, subunit TIM8 [Intracellular trafficking, secretion, and vesicular transport]
Probab=32.46 E-value=77 Score=22.33 Aligned_cols=32 Identities=25% Similarity=0.500 Sum_probs=22.4
Q ss_pred CCCCchhhHHHHHHHHHHHHHHHhhhhHHHHHHHHHH
Q 037135 67 NKDPELDQFMEAYYDMLVKYREELTRPIQEAMDFIRR 103 (124)
Q Consensus 67 ~~dpELDqFMeaYc~~L~kykeeL~~p~~EA~~f~~~ 103 (124)
+.+|||-+|.++ .+=|..++.-+-..+.-||+
T Consensus 9 ~~~~el~~fl~~-----E~qk~k~~~~VHqft~~CWd 40 (86)
T KOG3489|consen 9 ANDPELQQFLEA-----ETQKQKFQEQVHQFTEICWD 40 (86)
T ss_pred cccHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHH
Confidence 578999999988 34455555555566666775
No 32
>PRK03826 5'-nucleotidase; Provisional
Probab=32.36 E-value=1.1e+02 Score=23.87 Aligned_cols=10 Identities=60% Similarity=1.235 Sum_probs=5.8
Q ss_pred CchhhHHHHH
Q 037135 70 PELDQFMEAY 79 (124)
Q Consensus 70 pELDqFMeaY 79 (124)
||.+-||+.+
T Consensus 172 pev~~f~~~f 181 (195)
T PRK03826 172 PEMDYFMEVF 181 (195)
T ss_pred hHHHHHHHHh
Confidence 6666666543
No 33
>PF01533 Tospo_nucleocap: Tospovirus nucleocapsid protein; InterPro: IPR002517 The tospovirus genome consists of three linear ssRNA segments, denoted L, M and S complexed with the nucleocapsid protein. The S RNA encodes the nucleocapsid protein and another non-structural protein [].; GO: 0019013 viral nucleocapsid
Probab=32.27 E-value=41 Score=27.87 Aligned_cols=37 Identities=27% Similarity=0.442 Sum_probs=23.8
Q ss_pred hhHHHHHHHHhhCCCcHHHHHHHHh---------h----hhcCCchhHHHHHHH
Q 037135 7 SETEAIKAKIISHPQYSSLLEAYVD---------C----QKVGAPPEVVARLAA 47 (124)
Q Consensus 7 ~e~~~iKa~I~sHPlYp~LL~A~i~---------C----~KVGaP~e~~~~L~~ 47 (124)
.+...|+.+|++|| ||+||== = .=+|-|--+++.++.
T Consensus 113 e~k~~~~~k~~~~P----LV~AYGL~~~~~~d~~s~rl~l~lGG~LpLLaS~~~ 162 (248)
T PF01533_consen 113 EAKQKMYSKIMSLP----LVQAYGLNVPAMFDAKSVRLMLCLGGPLPLLASVDS 162 (248)
T ss_pred HHHHHHHHHHhcCh----HHHHhCCCCCCcCChhheeeeeeeCCCcHHHhhcch
Confidence 34567999999999 4777731 0 015667666665553
No 34
>PRK13895 conjugal transfer protein TraM; Provisional
Probab=31.91 E-value=1.6e+02 Score=22.56 Aligned_cols=46 Identities=26% Similarity=0.476 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHhhhcccCCCCCCCCCCch------hhHH----HHHHHHHHHHHHHhhhhH
Q 037135 44 RLAAARQEFESRQRSSLNSRDSTNKDPEL------DQFM----EAYYDMLVKYREELTRPI 94 (124)
Q Consensus 44 ~L~~~~~~~~~~~~~~~~~~~~~~~dpEL------DqFM----eaYc~~L~kykeeL~~p~ 94 (124)
+++++-++...+++-..+ .+||=| |.+| .+=-.+|..|||||+.-.
T Consensus 4 ki~e~I~~IA~KHGIal~-----rDDPILilqTiNerLlees~kAQq~mL~~FkeelE~ia 59 (144)
T PRK13895 4 KIEELIKEIAAKHGIAVG-----RDDPILILQTINDRLMQDSAKAQQEMLDQFKEELESIA 59 (144)
T ss_pred HHHHHHHHHHHHcCcccC-----CCCCchhHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Confidence 456666666555543221 367866 5666 466789999999998776
No 35
>PF13865 FoP_duplication: C-terminal duplication domain of Friend of PRMT1
Probab=31.82 E-value=34 Score=22.79 Aligned_cols=7 Identities=57% Similarity=1.037 Sum_probs=3.2
Q ss_pred CchhhHH
Q 037135 70 PELDQFM 76 (124)
Q Consensus 70 pELDqFM 76 (124)
.|||.||
T Consensus 47 aELD~Ym 53 (74)
T PF13865_consen 47 AELDAYM 53 (74)
T ss_pred HHHHHHH
Confidence 4444444
No 36
>KOG4278 consensus Protein tyrosine kinase [Signal transduction mechanisms]
Probab=31.22 E-value=1.3e+02 Score=29.18 Aligned_cols=42 Identities=26% Similarity=0.557 Sum_probs=33.9
Q ss_pred CCCCCchhhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhh
Q 037135 66 TNKDPELDQFMEAYYDMLVKYREELTRPIQEAMDFIRRIETQLNMLS 112 (124)
Q Consensus 66 ~~~dpELDqFMeaYc~~L~kykeeL~~p~~EA~~f~~~iE~QL~~L~ 112 (124)
+...|-|-.|-..|++++..|+.-+ .|.||+. ++|+-|+.|-
T Consensus 1084 id~g~~l~d~cvsyvd~Iqq~rNkF--AfrEa~~---KLe~~L~eLq 1125 (1157)
T KOG4278|consen 1084 IDEGPVLKDMCVSYVDVIQQFRNKF--AFREATD---KLEQFLSELQ 1125 (1157)
T ss_pred cccCchHHHHHHHHHHHHHHHHHHH--HHHHHHH---HHHHHHHHhh
Confidence 4577999999999999998777766 5677765 8888888875
No 37
>COG1084 Predicted GTPase [General function prediction only]
Probab=29.31 E-value=2.3e+02 Score=24.64 Aligned_cols=83 Identities=19% Similarity=0.380 Sum_probs=41.8
Q ss_pred hCCCcHHHHHHHHhhhhcCCchhHHHHHHHHHH---HHHHhhhcccCCCCCCCCC-CchhhHHHHHHHHHHHHHHHhhhh
Q 037135 18 SHPQYSSLLEAYVDCQKVGAPPEVVARLAAARQ---EFESRQRSSLNSRDSTNKD-PELDQFMEAYYDMLVKYREELTRP 93 (124)
Q Consensus 18 sHPlYp~LL~A~i~C~KVGaP~e~~~~L~~~~~---~~~~~~~~~~~~~~~~~~d-pELDqFMeaYc~~L~kykeeL~~p 93 (124)
-||+|..|+.+-++--+.-- .++.++.+.. ++...+-.-. ..+.| -+..+-|++|..=+-+--+++.
T Consensus 75 LhpFY~eLidvl~d~d~~k~---sLs~v~~A~~~i~~l~~eYi~~l----k~a~~~~~~~~lrR~a~GR~aSiik~i~-- 145 (346)
T COG1084 75 LHPFYRELIDVLVDIDHLKI---SLSAVSWASKIIEKLAREYIRLL----KAAKDPKEANQLRRQAFGRVASIIKKID-- 145 (346)
T ss_pred cChHHHHHHHHHhCHHHHHH---HHHHHHHHHHHHHHHHHHHHHHH----hcCCChhHHHHHHHHHHHHHHHHHHHhh--
Confidence 49999999999886544211 1222222211 1111110000 01234 3788889888765555444444
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 037135 94 IQEAMDFIRRIETQLNML 111 (124)
Q Consensus 94 ~~EA~~f~~~iE~QL~~L 111 (124)
+...|+++.-.-|..|
T Consensus 146 --~~L~fL~~~r~~l~~L 161 (346)
T COG1084 146 --DDLEFLRKARDHLKKL 161 (346)
T ss_pred --HHHHHHHHHHHHHhcC
Confidence 3445555555555555
No 38
>PLN02372 violaxanthin de-epoxidase
Probab=29.03 E-value=3.4e+02 Score=24.44 Aligned_cols=65 Identities=23% Similarity=0.338 Sum_probs=36.6
Q ss_pred chhHHHHHHHHHHHHHHh-hh-cccCCCCCCCCCCchhhHHHHHHHHHHHHHHHhhhhH-HHHHHHHHHHHHHHHHh
Q 037135 38 PPEVVARLAAARQEFESR-QR-SSLNSRDSTNKDPELDQFMEAYYDMLVKYREELTRPI-QEAMDFIRRIETQLNML 111 (124)
Q Consensus 38 P~e~~~~L~~~~~~~~~~-~~-~~~~~~~~~~~dpELDqFMeaYc~~L~kykeeL~~p~-~EA~~f~~~iE~QL~~L 111 (124)
|.+.+++|..+.+..-.. .. ....+. + |..|+| .+-|.|=-|+.++-+ +|+...-.+||.+...|
T Consensus 328 P~~~~p~L~~Aa~kvG~df~~F~~tDNs-C-gpep~l-------~~~l~~~~e~~e~~i~~e~~~~~~e~~~~v~~~ 395 (455)
T PLN02372 328 PESIVPELEKAAKKVGRDFSDFVRTDNT-C-GPEPPL-------LERLEKDVEEGEKTIVKEARQIEEELEKEVEKL 395 (455)
T ss_pred ChhhhHHHHHHHHHcCCCHHHheeeCCC-C-CCCchH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 888889998876542211 01 111121 2 678888 556666666666655 45555555555555444
No 39
>PF12878 SICA_beta: SICA extracellular beta domain; InterPro: IPR024285 The schizont-infected cell agglutination (SICA) proteins of Plasmodium knowlesi, one of the variant antigen gene families, are associated with parasitic virulence. SICA proteins comprise multiple domains, with the extracellular cysteine-rich domains (CRDs) occurring at different frequencies. They contain a five-cysteine CRD (SICA-alpha) at the N terminus, which occurs once or twice, then between 1 and 10 SICA-beta CRDs with 7-10 cysteine residues, a transmembrane domain, and a conserved C-terminal domain []. This entry represents the extracellular SICA-beta domain.
Probab=28.77 E-value=63 Score=24.89 Aligned_cols=24 Identities=21% Similarity=0.436 Sum_probs=21.0
Q ss_pred CCCCchhhHHHHHHHHHHHHHHHhhh
Q 037135 67 NKDPELDQFMEAYYDMLVKYREELTR 92 (124)
Q Consensus 67 ~~dpELDqFMeaYc~~L~kykeeL~~ 92 (124)
..+|.++|.|. |.+|..|-++|..
T Consensus 95 ~~~~~f~qtm~--C~lLnaYAkkmke 118 (169)
T PF12878_consen 95 DDNPSFKQTMG--CFLLNAYAKKMKE 118 (169)
T ss_pred cCCccHHHHHH--HHHHHHHHHHHHH
Confidence 47899999995 9999999998865
No 40
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=27.51 E-value=1.7e+02 Score=18.53 Aligned_cols=36 Identities=25% Similarity=0.417 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHhhhhH------------HHHHHHHHHHHHHHHHhh
Q 037135 77 EAYYDMLVKYREELTRPI------------QEAMDFIRRIETQLNMLS 112 (124)
Q Consensus 77 eaYc~~L~kykeeL~~p~------------~EA~~f~~~iE~QL~~L~ 112 (124)
+.+...|.+++=+.-+++ ++|..+++++-.+++.+.
T Consensus 10 ~~~~~~lR~~RHD~~NhLqvI~gllqlg~~~~a~eYi~~~~~~~~~~s 57 (62)
T PF14689_consen 10 EELIDSLRAQRHDFLNHLQVIYGLLQLGKYEEAKEYIKELSKDLQQES 57 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 456677777777777776 588899988888887763
No 41
>PHA02698 hypothetical protein; Provisional
Probab=26.20 E-value=2.3e+02 Score=19.79 Aligned_cols=36 Identities=33% Similarity=0.596 Sum_probs=23.5
Q ss_pred chhhHHHHHHHHHHHHHHHhhhhHHHHH-HHHHHHHHHHHHh
Q 037135 71 ELDQFMEAYYDMLVKYREELTRPIQEAM-DFIRRIETQLNML 111 (124)
Q Consensus 71 ELDqFMeaYc~~L~kykeeL~~p~~EA~-~f~~~iE~QL~~L 111 (124)
-||+|.+. ..||.||+---+|-| +.+.++|.=..-|
T Consensus 49 mLD~FLed-----iq~ksElqLLsqEEMdELl~EledlarLL 85 (89)
T PHA02698 49 MLDNFLED-----IQYKSELQLLSQEEMDELLVELEDLARLL 85 (89)
T ss_pred HHHHHHHH-----HHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Confidence 38888886 467888776666554 5567776544433
No 42
>COG0365 Acs Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]
Probab=25.53 E-value=67 Score=28.95 Aligned_cols=21 Identities=19% Similarity=0.273 Sum_probs=18.6
Q ss_pred hCCCcHHHHHHHHhhhhcCCc
Q 037135 18 SHPQYSSLLEAYVDCQKVGAP 38 (124)
Q Consensus 18 sHPlYp~LL~A~i~C~KVGaP 38 (124)
-=|.-|.++.|++.|.|+||-
T Consensus 71 ymp~~pe~~~a~LA~~riGAI 91 (528)
T COG0365 71 YMPNSPEAVIALLATARIGAI 91 (528)
T ss_pred EcCCCHHHHHHHHHHHHcCCE
Confidence 348899999999999999983
No 43
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=25.19 E-value=1.8e+02 Score=22.14 Aligned_cols=43 Identities=28% Similarity=0.503 Sum_probs=29.2
Q ss_pred CchhhHHHHHH----HHHHHHHHHhhhhH--HHHHHHHHHHHHHHHHhh
Q 037135 70 PELDQFMEAYY----DMLVKYREELTRPI--QEAMDFIRRIETQLNMLS 112 (124)
Q Consensus 70 pELDqFMeaYc----~~L~kykeeL~~p~--~EA~~f~~~iE~QL~~L~ 112 (124)
+..+.||..|- .++.+|.+==.+|+ .++...+.+++.-|..|+
T Consensus 125 ~~a~~Fl~~yLp~~~~l~~kY~~l~~~~~~~~~~~~~l~e~~~~L~~l~ 173 (199)
T PF10112_consen 125 TQARKFLYYYLPTAVKLLEKYAELESQPVKSEEIKQSLEEIEETLDTLN 173 (199)
T ss_pred HHHHHHHHHHhhHHHHHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHH
Confidence 57899999995 56778877556666 355555666666665554
No 44
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=24.89 E-value=1.5e+02 Score=24.97 Aligned_cols=43 Identities=35% Similarity=0.576 Sum_probs=37.0
Q ss_pred CCCchhhHHHH-HHH--HHHHHH---HHhhhhHHHHHHHHHHHHHHHHH
Q 037135 68 KDPELDQFMEA-YYD--MLVKYR---EELTRPIQEAMDFIRRIETQLNM 110 (124)
Q Consensus 68 ~dpELDqFMea-Yc~--~L~kyk---eeL~~p~~EA~~f~~~iE~QL~~ 110 (124)
.++.|++|..| ||. +|.=|. .||.+-+.+-...+++||++...
T Consensus 47 ~~~sl~~~v~A~~~~iP~LElY~~sC~EL~~~I~egr~~~~~~E~et~~ 95 (312)
T smart00787 47 EDCSLDQYVVAGYCTVPLLELYQFSCKELKKYISEGRDLFKEIEEETLI 95 (312)
T ss_pred CCCCHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 57899999999 998 676665 79999999999999999998754
No 45
>PLN02850 aspartate-tRNA ligase
Probab=24.50 E-value=83 Score=28.32 Aligned_cols=36 Identities=19% Similarity=0.376 Sum_probs=30.1
Q ss_pred chhhHHHHHHHHhhCCCcHHHHHHHHhhhhcCCchh
Q 037135 5 ESSETEAIKAKIISHPQYSSLLEAYVDCQKVGAPPE 40 (124)
Q Consensus 5 ~~~e~~~iKa~I~sHPlYp~LL~A~i~C~KVGaP~e 40 (124)
.-.+.+.+++++..|-+=+.-+..||+.+|-|+||-
T Consensus 460 r~~d~~~l~~r~~~~g~d~~~~~~Yl~a~~~G~pPh 495 (530)
T PLN02850 460 RVHDPELLEKRAEECGIDVKTISTYIDSFRYGAPPH 495 (530)
T ss_pred ecCCHHHHHHHHHHcCCChHHHHHHHHHHHcCCCCC
Confidence 445567788899989887778899999999999985
No 46
>PF04711 ApoA-II: Apolipoprotein A-II (ApoA-II); InterPro: IPR006801 Apolipoprotein A-II (ApoA-II) is the second major apolipoprotein of high density lipoprotein in human plasma. Mature ApoA-II is present as a dimer of two 77-amino acid chains joined by a disulphide bridge []. ApoA-II regulates many steps in HDL metabolism, and its role in coronary heart disease is unclear []. In bovine serum, the ApoA-II homologue is present in almost free form. Bovine ApoA-II shows antimicrobial activity against Escherichia coli and yeasts in phosphate buffered saline (PBS) [].; GO: 0008289 lipid binding, 0006869 lipid transport, 0042157 lipoprotein metabolic process, 0005576 extracellular region; PDB: 1L6L_W 2OU1_E.
Probab=24.47 E-value=2.4e+02 Score=19.39 Aligned_cols=46 Identities=20% Similarity=0.571 Sum_probs=38.2
Q ss_pred CCCchhhHHHHHHHHHHHHHHHhhhhHH------HHHHHHHHHHHHHHHhhC
Q 037135 68 KDPELDQFMEAYYDMLVKYREELTRPIQ------EAMDFIRRIETQLNMLSN 113 (124)
Q Consensus 68 ~dpELDqFMeaYc~~L~kykeeL~~p~~------EA~~f~~~iE~QL~~L~~ 113 (124)
.+|.|-.+...|...+++|-.+|-..++ .|..++.+-..||--|.+
T Consensus 3 ee~~lq~lfsqY~qt~TdYgKDL~Ekvk~pElqsQakaYfektqeQltPlvk 54 (76)
T PF04711_consen 3 EEPDLQSLFSQYFQTVTDYGKDLVEKVKGPELQSQAKAYFEKTQEQLTPLVK 54 (76)
T ss_dssp BSSTTHHHHHHHHHHHHHHHHHHHHHHHSHHTSSTCHHHHHHHHHHHHHHHH
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHHhHHHH
Confidence 5688999999999999999999988874 577788887778776653
No 47
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=24.47 E-value=80 Score=27.35 Aligned_cols=36 Identities=19% Similarity=0.314 Sum_probs=30.5
Q ss_pred chhhHHHHHHHHhhCCCcHHHHHHHHhhhhcCCchh
Q 037135 5 ESSETEAIKAKIISHPQYSSLLEAYVDCQKVGAPPE 40 (124)
Q Consensus 5 ~~~e~~~iKa~I~sHPlYp~LL~A~i~C~KVGaP~e 40 (124)
..++.+.+++++..|-+-+.-..-|++.+|-|.||-
T Consensus 367 r~~d~~~~~~~~~~~g~~~~~~~~yl~a~~~G~pp~ 402 (437)
T PRK05159 367 RIHRYDMLVESIKEKGLNPESFEFYLEAFKYGMPPH 402 (437)
T ss_pred EcCCHHHHHHHHHHcCCCHHHHHHHHHHHHCCCCCC
Confidence 445667889999999888888899999999999985
No 48
>PF06238 Borrelia_lipo_2: Borrelia burgdorferi BBR25 lipoprotein; InterPro: IPR009358 This entry consists of a number of lipoproteins conserved in Borrelia species [].
Probab=23.03 E-value=2.7e+02 Score=20.44 Aligned_cols=38 Identities=16% Similarity=0.325 Sum_probs=28.2
Q ss_pred CCCchhhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHh
Q 037135 68 KDPELDQFMEAYYDMLVKYREELTRPIQEAMDFIRRIETQLNML 111 (124)
Q Consensus 68 ~dpELDqFMeaYc~~L~kykeeL~~p~~EA~~f~~~iE~QL~~L 111 (124)
.+.=.|-||-.|.+.|.+.+. .|+|..+.+||.=|+-.
T Consensus 34 F~kVvdffyk~Y~~TiksmE~------~EsiKIl~eIq~Ilk~n 71 (111)
T PF06238_consen 34 FNKVVDFFYKTYIETIKSMET------AESIKILEEIQDILKYN 71 (111)
T ss_pred HHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHH
Confidence 345679999999999988764 37777777777665543
No 49
>PF14591 AF0941-like: AF0941-like; PDB: 1YOZ_B.
Probab=22.92 E-value=59 Score=24.42 Aligned_cols=34 Identities=15% Similarity=0.286 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHh
Q 037135 78 AYYDMLVKYREELTRPIQEAMDFIRRIETQLNML 111 (124)
Q Consensus 78 aYc~~L~kykeeL~~p~~EA~~f~~~iE~QL~~L 111 (124)
.-...|..|.++|+.+|..+..++.++|-.....
T Consensus 65 ~ll~eL~~~asqL~~~~~~~~e~l~~le~k~~k~ 98 (127)
T PF14591_consen 65 QLLDELKSYASQLQEHYFRVRELLEDLERKIQKA 98 (127)
T ss_dssp HHHHHHHHHHHTHHHHHHHHHHHHHCTT------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3457899999999999999999997776554443
No 50
>PF07337 CagY_M: DC-EC Repeat; InterPro: IPR010853 This repeat is found in the CagY proteins - part of the CAG pathogenicity island - and involved in delivery of the protein CagA into host cells []. It forms part of a surface needle structure, and this repeat may form an alpha-helical rod structure []. The repeat contains a conserved -DC- and -EC-, which are regularly spaced in the alignment.
Probab=22.32 E-value=35 Score=20.02 Aligned_cols=16 Identities=38% Similarity=0.611 Sum_probs=11.4
Q ss_pred HHHHhhhhcC-CchhHH
Q 037135 27 EAYVDCQKVG-APPEVV 42 (124)
Q Consensus 27 ~A~i~C~KVG-aP~e~~ 42 (124)
.||+||+|-+ ++-|..
T Consensus 1 qA~lDCl~~Akte~Erk 17 (33)
T PF07337_consen 1 QAYLDCLKNAKTEEERK 17 (33)
T ss_pred CcHHHHHHhcCCHHHHH
Confidence 3899999976 555543
No 51
>KOG1733 consensus Mitochondrial import inner membrane translocase, subunit TIM13 [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.00 E-value=1.2e+02 Score=21.84 Aligned_cols=24 Identities=25% Similarity=0.422 Sum_probs=19.2
Q ss_pred CchhhHHHHHHHHHHHHHHHhhhh
Q 037135 70 PELDQFMEAYYDMLVKYREELTRP 93 (124)
Q Consensus 70 pELDqFMeaYc~~L~kykeeL~~p 93 (124)
.=+|.||++.-.+=..|-.-|++-
T Consensus 68 ~CmdRyMdawniVSrty~sRlQre 91 (97)
T KOG1733|consen 68 RCMDRYMDAWNIVSRTYISRLQRE 91 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 458899999988888888877763
No 52
>KOG1992 consensus Nuclear export receptor CSE1/CAS (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=21.77 E-value=1.6e+02 Score=28.84 Aligned_cols=34 Identities=21% Similarity=0.387 Sum_probs=25.3
Q ss_pred hhhHHHHHHHHHH--------------------------------HHHHHhhhhHHHHHHHHHHHH
Q 037135 72 LDQFMEAYYDMLV--------------------------------KYREELTRPIQEAMDFIRRIE 105 (124)
Q Consensus 72 LDqFMeaYc~~L~--------------------------------kykeeL~~p~~EA~~f~~~iE 105 (124)
++.||.++|..|. ||.|+.+.-+.+.+...|++=
T Consensus 232 m~~wM~~F~k~l~~~~p~le~~~ee~~~l~~lka~ICEi~~LY~~kYeEef~~fl~~fv~~~W~LL 297 (960)
T KOG1992|consen 232 MKTWMGAFHKLLTYDNPLLESDEEEATVLDKLKAQICEIFNLYATKYEEEFQPFLPDFVTATWNLL 297 (960)
T ss_pred HHHHHHHHHHHHhccCcccccCcccccHHHHHHHHHHHHHHHHHHhhHHHHHhhHHHHHHHHHHHH
Confidence 6788888887776 777777766677777777663
No 53
>TIGR00457 asnS asparaginyl-tRNA synthetase. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.
Probab=21.74 E-value=1e+02 Score=27.02 Aligned_cols=35 Identities=17% Similarity=0.349 Sum_probs=29.5
Q ss_pred hhhHHHHHHHHhhCCCcHHHHHHHHhhhhcCCchh
Q 037135 6 SSETEAIKAKIISHPQYSSLLEAYVDCQKVGAPPE 40 (124)
Q Consensus 6 ~~e~~~iKa~I~sHPlYp~LL~A~i~C~KVGaP~e 40 (124)
.++.+.+++++..|.+-+.-+.-|++-+|-|.||-
T Consensus 384 e~~~~~l~~~~~~~g~d~~~~~~Yl~~~~~G~pPh 418 (453)
T TIGR00457 384 EDDLDKLENRMKEMGLDTDALNWYLDLRKYGSVPH 418 (453)
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCC
Confidence 34456788899999999988888999999999985
No 54
>KOG2070 consensus Guanine nucleotide exchange factor [Nucleotide transport and metabolism]
Probab=21.67 E-value=57 Score=30.13 Aligned_cols=74 Identities=24% Similarity=0.352 Sum_probs=35.8
Q ss_pred HHhhCCCcHHHHHHHHhhhhcCCchhHHHHHHHHHHHHHHhhhcccCCCCCCCCCCchhhHHHHHH-------HHHHHHH
Q 037135 15 KIISHPQYSSLLEAYVDCQKVGAPPEVVARLAAARQEFESRQRSSLNSRDSTNKDPELDQFMEAYY-------DMLVKYR 87 (124)
Q Consensus 15 ~I~sHPlYp~LL~A~i~C~KVGaP~e~~~~L~~~~~~~~~~~~~~~~~~~~~~~dpELDqFMeaYc-------~~L~kyk 87 (124)
+|.+-|=|-.|+-.+...- -.-.|++.+|++-...-+.+++- ++..+..-|++-.-.-+|| .+|.||+
T Consensus 135 ~iLs~~ey~~LmgNfeeI~--t~~qdL~~qlEec~~~~~~q~RV---Gg~fln~ap~mkt~~~aYcanHP~AV~VL~k~~ 209 (661)
T KOG2070|consen 135 EILSSAEYSYLMGNFEEIC--TFQQDLVQQLEECTKLPEAQQRV---GGCFLNLAPQMKTLYLAYCANHPSAVNVLTKHS 209 (661)
T ss_pred cccchHHHHHHhcchHHhH--hHHHHHHHHHHHhhcCchhhhhh---hhHHHhhhHHHHHHHHHHHhcCchhhhHHHHhH
Confidence 5666677766665444321 11334444444432211111111 1122334566666666776 3677777
Q ss_pred HHhhhh
Q 037135 88 EELTRP 93 (124)
Q Consensus 88 eeL~~p 93 (124)
+||++-
T Consensus 210 dELek~ 215 (661)
T KOG2070|consen 210 DELEKF 215 (661)
T ss_pred HHHHHH
Confidence 776653
No 55
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=21.65 E-value=1.4e+02 Score=19.63 Aligned_cols=23 Identities=35% Similarity=0.466 Sum_probs=17.1
Q ss_pred CchhhHHH-HHHHHHHHHHHHhhh
Q 037135 70 PELDQFME-AYYDMLVKYREELTR 92 (124)
Q Consensus 70 pELDqFMe-aYc~~L~kykeeL~~ 92 (124)
++++..|. ++-.++.+|++.|++
T Consensus 48 ~~~~~~~~~~~~~~~~~y~~~l~~ 71 (74)
T TIGR02609 48 KELEKKMQMAVERAMSKYDEALKE 71 (74)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHH
Confidence 47877777 777788888877654
No 56
>PF07165 DUF1397: Protein of unknown function (DUF1397); InterPro: IPR009832 This entry consists of several insect specific 27 kDa Haemolymph glycoprotein precursors. The function of this family is unknown [].
Probab=21.40 E-value=1.4e+02 Score=23.64 Aligned_cols=58 Identities=16% Similarity=0.307 Sum_probs=32.0
Q ss_pred hhhhcCCchhHHHHHHHHHHHHHHhhhcccC----CCCCCCC--CCchhhHHHHHHHHHHHHHH
Q 037135 31 DCQKVGAPPEVVARLAAARQEFESRQRSSLN----SRDSTNK--DPELDQFMEAYYDMLVKYRE 88 (124)
Q Consensus 31 ~C~KVGaP~e~~~~L~~~~~~~~~~~~~~~~----~~~~~~~--dpELDqFMeaYc~~L~kyke 88 (124)
-|.|+|........|.+..+.+..=-...++ ..++... .-+||.|..-||.-+...++
T Consensus 19 kC~~~~g~~~~~~~i~~a~~~~~~C~~~~vd~~~l~~eie~~~p~g~ld~vF~KyC~k~~~~~~ 82 (213)
T PF07165_consen 19 KCKKNGGSDAAYEEIEEAAQQLPECLSGLVDLTQLQQEIEEAKPTGDLDEVFNKYCPKRPQAKE 82 (213)
T ss_pred HHHHhcCChHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHcCccccHHHHHHHHhHhhHHHHH
Confidence 4999999888555665543332210000000 0001112 34799999999997776443
No 57
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=20.77 E-value=2.2e+02 Score=28.81 Aligned_cols=80 Identities=23% Similarity=0.396 Sum_probs=46.4
Q ss_pred HHHHhhCCCcHHH----HHHHHhhhhcCC----c---------------hhHHHHHHHHHHHHHHhhhcccCCCCCCC-C
Q 037135 13 KAKIISHPQYSSL----LEAYVDCQKVGA----P---------------PEVVARLAAARQEFESRQRSSLNSRDSTN-K 68 (124)
Q Consensus 13 Ka~I~sHPlYp~L----L~A~i~C~KVGa----P---------------~e~~~~L~~~~~~~~~~~~~~~~~~~~~~-~ 68 (124)
++|+++||+|-.+ ..+|++=.-+|- | .++-..++-+ +....+..+.+...+++ .
T Consensus 1102 ~~RvI~HP~F~n~n~eQAe~yL~~~d~ge~iiRpSSrgddhLvvtwKVsD~iYqhidV~--E~eKEn~fslg~~l~i~~e 1179 (1299)
T KOG1856|consen 1102 VSRVIAHPLFKNLNAEQAEAYLSDMDQGELIIRPSSRGDDHLVVTWKVSDGIYQHIDVQ--ELEKENYFSLGKTLWIGGE 1179 (1299)
T ss_pred hhhhhcCccccCCCHHHHHHHHHhcccccEEeccccCCCCceEEEEEecCchhhhhhhh--hhhccccccccceEEECCc
Confidence 3899999999876 567776655553 1 1111222221 11111222222222233 2
Q ss_pred C-CchhhHHHHHHHHHHHHHHHhhhhH
Q 037135 69 D-PELDQFMEAYYDMLVKYREELTRPI 94 (124)
Q Consensus 69 d-pELDqFMeaYc~~L~kykeeL~~p~ 94 (124)
+ -.||+||.-|+.-+.+.-.+|..|=
T Consensus 1180 ~feDLDEiI~r~vqpm~~~~~em~nhk 1206 (1299)
T KOG1856|consen 1180 EFEDLDEIIARYVQPMATNLREMTNHK 1206 (1299)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHhhh
Confidence 2 6899999999998888888887663
No 58
>KOG4014 consensus Uncharacterized conserved protein (contains TPR repeat) [Function unknown]
Probab=20.74 E-value=1.4e+02 Score=24.59 Aligned_cols=24 Identities=21% Similarity=0.383 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHhhhhHHHHHHHHH
Q 037135 79 YYDMLVKYREELTRPIQEAMDFIR 102 (124)
Q Consensus 79 Yc~~L~kykeeL~~p~~EA~~f~~ 102 (124)
=|.+|..|-|-+++-|++|...++
T Consensus 36 ~C~lLgdYlEgi~knF~~A~kv~K 59 (248)
T KOG4014|consen 36 SCQLLGDYLEGIQKNFQAAVKVFK 59 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 499999999999999999987654
No 59
>PF06340 TcpF: Vibrio cholerae toxin co-regulated pilus biosynthesis protein F; InterPro: IPR009405 This family consists of several Vibrio cholerae toxin co-regulated pilus biosynthesis protein F (TcpF) sequences. TcpF is known to be a secreted virulence protein but its exact function is unknown [].; PDB: 3OC5_A 3OC8_A.
Probab=20.59 E-value=50 Score=27.95 Aligned_cols=21 Identities=24% Similarity=0.678 Sum_probs=13.7
Q ss_pred hhCCCcHHHHHHHHhhhhcCCchhHH
Q 037135 17 ISHPQYSSLLEAYVDCQKVGAPPEVV 42 (124)
Q Consensus 17 ~sHPlYp~LL~A~i~C~KVGaP~e~~ 42 (124)
..|=+|| |++|.|+|-|-|-+
T Consensus 24 se~lRYP-----yleCi~LGM~~~~L 44 (311)
T PF06340_consen 24 SENLRYP-----YLECIKLGMSRDYL 44 (311)
T ss_dssp ---TTTT-----HHHHHHTT--GGGG
T ss_pred ccccccc-----HHHHHhcCCchhhh
Confidence 4588898 78899999998864
No 60
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=20.57 E-value=95 Score=28.17 Aligned_cols=36 Identities=19% Similarity=0.262 Sum_probs=30.8
Q ss_pred chhhHHHHHHHHhhCCCcHHHHHHHHhhhhcCCchh
Q 037135 5 ESSETEAIKAKIISHPQYSSLLEAYVDCQKVGAPPE 40 (124)
Q Consensus 5 ~~~e~~~iKa~I~sHPlYp~LL~A~i~C~KVGaP~e 40 (124)
..++.+.+++++..|-+=+.-+.-|++.+|-|.||-
T Consensus 480 R~~d~~~l~~r~~~~G~d~~~~~~Yl~a~~~G~PPh 515 (550)
T PTZ00401 480 RIHDPDLLLARAKMLNVDLTPIKEYVDSFRLGAWPH 515 (550)
T ss_pred hcCCHHHHHHHHHHcCCCchhhHHHHHHHHcCCCCC
Confidence 456677899999999888888899999999999985
Done!