Query psy53
Match_columns 78
No_of_seqs 75 out of 77
Neff 4.0
Searched_HMMs 46136
Date Fri Aug 16 22:59:57 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy53.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/53hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1410|consensus 99.9 2.7E-28 5.8E-33 205.2 8.2 76 2-78 1007-1082(1082)
2 KOG4541|consensus 95.3 0.04 8.7E-07 47.2 5.5 60 3-62 684-745 (748)
3 PF08858 IDEAL: IDEAL domain; 80.4 1.3 2.9E-05 24.5 1.6 24 26-49 9-32 (37)
4 smart00394 RIIa RIIalpha, Regu 75.7 7.3 0.00016 21.1 3.7 32 2-33 4-35 (38)
5 PF02197 RIIa: Regulatory subu 75.1 6.3 0.00014 21.8 3.4 32 2-33 4-35 (38)
6 PF14829 GPAT_N: Glycerol-3-ph 70.0 12 0.00026 24.3 4.3 37 1-37 35-75 (77)
7 PRK02922 glycogen synthesis pr 69.7 5 0.00011 25.5 2.4 28 33-60 32-59 (67)
8 PF08971 GlgS: Glycogen synthe 55.8 19 0.00041 22.8 3.1 29 32-60 30-58 (66)
9 PRK03636 hypothetical protein; 48.4 12 0.00027 27.1 1.7 22 28-49 147-168 (179)
10 PF10350 DUF2428: Putative dea 48.2 26 0.00056 25.8 3.4 36 3-38 119-154 (255)
11 PRK03057 hypothetical protein; 47.1 14 0.0003 27.0 1.7 22 28-49 146-167 (180)
12 PF01297 TroA: Periplasmic sol 46.4 72 0.0016 22.7 5.4 41 18-62 98-138 (256)
13 PF08767 CRM1_C: CRM1 C termin 42.8 72 0.0016 24.4 5.1 45 18-62 260-311 (319)
14 PRK03573 transcriptional regul 41.6 71 0.0015 20.8 4.4 31 5-35 107-137 (144)
15 PLN02349 glycerol-3-phosphate 40.8 40 0.00087 28.0 3.7 36 1-36 108-147 (426)
16 PF11800 RP-C_C: Replication p 39.8 38 0.00082 24.2 3.1 43 2-44 7-49 (207)
17 COG0803 LraI ABC-type metal io 38.9 31 0.00066 26.0 2.6 25 38-62 155-179 (303)
18 PF14747 DUF4473: Domain of un 38.5 52 0.0011 20.6 3.2 23 8-30 59-81 (82)
19 cd01137 PsaA Metal binding pro 34.7 39 0.00084 25.2 2.5 41 18-62 123-163 (287)
20 PF00502 Phycobilisome: Phycob 34.6 68 0.0015 22.2 3.6 33 3-35 124-156 (157)
21 cd01145 TroA_c Periplasmic bin 34.0 43 0.00094 23.5 2.6 23 39-61 131-153 (203)
22 PF09088 MIF4G_like: MIF4G lik 31.8 1.4E+02 0.0031 21.9 5.0 46 3-49 90-135 (191)
23 COG2960 Uncharacterized protei 31.3 1.5E+02 0.0033 20.2 4.7 46 3-48 14-62 (103)
24 TIGR02464 ribofla_fusion conse 30.6 35 0.00075 23.6 1.6 53 8-65 48-105 (153)
25 cd01020 TroA_b Metal binding p 30.4 1.5E+02 0.0032 21.7 4.9 40 18-61 101-140 (264)
26 cd01017 AdcA Metal binding pro 30.0 1.5E+02 0.0032 21.7 4.9 24 38-61 135-158 (282)
27 KOG4001|consensus 29.1 81 0.0017 24.5 3.5 29 18-46 123-157 (259)
28 PF14846 DUF4485: Domain of un 28.7 1.5E+02 0.0032 18.7 4.2 60 4-65 9-68 (85)
29 CHL00089 apcF allophycocyanin 28.4 1.3E+02 0.0029 21.6 4.3 34 4-37 130-166 (169)
30 PF01152 Bac_globin: Bacterial 28.3 1.6E+02 0.0034 18.5 4.6 41 18-60 79-119 (120)
31 cd01018 ZntC Metal binding pro 27.8 1.7E+02 0.0038 21.2 5.0 40 18-61 118-157 (266)
32 PF11333 DUF3135: Protein of u 27.8 78 0.0017 20.3 2.8 24 3-26 18-45 (83)
33 PF03885 DUF327: Protein of un 27.7 1.2E+02 0.0025 20.8 3.8 39 25-63 42-80 (147)
34 PF08933 DUF1864: Domain of un 27.1 43 0.00093 27.5 1.8 55 2-56 252-308 (387)
35 cd01016 TroA Metal binding pro 26.5 66 0.0014 23.7 2.6 23 39-61 124-146 (276)
36 PF07159 DUF1394: Protein of u 26.4 1.8E+02 0.004 22.8 5.1 59 2-60 85-149 (303)
37 PF07208 DUF1414: Protein of u 26.2 1.5E+02 0.0032 17.4 3.7 27 6-32 13-40 (44)
38 cd00446 GrpE GrpE is the adeni 25.4 2.1E+02 0.0045 19.0 4.6 64 4-67 14-84 (137)
39 PF12884 TORC_N: Transducer of 25.2 77 0.0017 20.1 2.3 19 19-37 14-32 (67)
40 PF05757 PsbQ: Oxygen evolving 24.9 99 0.0022 22.9 3.2 27 11-37 144-170 (202)
41 PF06254 DUF1019: Protein of u 24.8 96 0.0021 20.4 2.8 35 4-38 27-63 (89)
42 PLN02999 photosystem II oxygen 24.5 94 0.002 23.3 3.0 34 11-45 132-165 (190)
43 cd02665 Peptidase_C19I A subfa 23.4 1.6E+02 0.0034 21.7 4.1 34 5-43 11-44 (228)
44 PRK11409 antitoxin YefM; Provi 22.9 1.8E+02 0.0039 18.2 3.8 32 3-34 43-74 (83)
45 PF14304 CSTF_C: Transcription 22.2 68 0.0015 18.9 1.6 26 9-34 18-43 (46)
46 cd01019 ZnuA Zinc binding prot 21.9 89 0.0019 23.2 2.5 24 39-62 144-167 (286)
47 COG2733 Predicted membrane pro 21.4 68 0.0015 26.6 1.9 20 38-57 74-93 (415)
48 PF02463 SMC_N: RecF/RecN/SMC 20.5 20 0.00042 24.7 -1.2 24 31-54 163-186 (220)
49 KOG4567|consensus 20.3 64 0.0014 26.4 1.5 37 27-63 224-270 (370)
50 PF14063 DUF4254: Protein of u 20.2 2E+02 0.0044 20.1 3.9 32 3-36 106-137 (145)
51 PF06371 Drf_GBD: Diaphanous G 20.2 83 0.0018 20.9 1.9 26 20-47 4-29 (187)
52 PF07350 DUF1479: Protein of u 20.1 1.6E+02 0.0034 24.3 3.8 34 1-36 3-36 (416)
No 1
>KOG1410|consensus
Probab=99.95 E-value=2.7e-28 Score=205.17 Aligned_cols=76 Identities=50% Similarity=0.774 Sum_probs=73.4
Q ss_pred hHHHHHHHHHHhhcCCchhHHHHHHHHHHHHHHhhhhcccchhhhhhhhHHHHHHHHHHhcCCCCCCCCCCcccccC
Q psy53 2 DIYFNQLRENIVRGQPPDKQASMVQWFENLMNSIERNLLTKNRDRFTQNLSMFRRDINDSLKGPNMNSSCTANDMMT 78 (78)
Q Consensus 2 e~~f~~lk~~li~sQp~ekq~~l~~~F~~LM~gIe~nL~~kNRDrFTQNLs~FRrdvr~~lk~~~~~~~~~~~~~m~ 78 (78)
|+||+.+|++|++|||+||||.+.+||++||+|||+||++||||||||||+.|||||+..|||...+++ +++|||+
T Consensus 1007 E~~fSdlk~~l~ssQp~dkqq~l~~cF~~LM~~ve~nL~~KNrD~FTQNLt~FRrdv~~~lk~~~~~~~-~s~d~~~ 1082 (1082)
T KOG1410|consen 1007 EKYFSDLKASLTSSQPYDKQQDLDMCFTNLMEGVERNLTVKNRDRFTQNLTRFRRDVALVLKGQALPSS-SSVDMMS 1082 (1082)
T ss_pred HHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHHHhccCCCCCC-ccccccC
Confidence 899999999999999999999999999999999999999999999999999999999999999977677 8899986
No 2
>KOG4541|consensus
Probab=95.30 E-value=0.04 Score=47.25 Aligned_cols=60 Identities=23% Similarity=0.327 Sum_probs=52.5
Q ss_pred HHHHHHHHHHhhcCC-chhHHHHHHHHHHHHHH-hhhhcccchhhhhhhhHHHHHHHHHHhc
Q psy53 3 IYFNQLRENIVRGQP-PDKQASMVQWFENLMNS-IERNLLTKNRDRFTQNLSMFRRDINDSL 62 (78)
Q Consensus 3 ~~f~~lk~~li~sQp-~ekq~~l~~~F~~LM~g-Ie~nL~~kNRDrFTQNLs~FRrdvr~~l 62 (78)
..|++|=..|+++|. |.-+|.++.+|.+||+- -+++|.-+||-+|-.||-.|-.+|-+.|
T Consensus 684 ~~y~elvneL~skq~np~~~qrLa~Af~~Lt~sn~~psldR~~~~~Frk~le~Fl~~V~Gll 745 (748)
T KOG4541|consen 684 NLYQELVNELISKQANPNFKQRLANAFQVLTTSNQLPSLDRLNYQRFRKNLENFLVEVLGLL 745 (748)
T ss_pred HHHHHHHHHHHhhccChHHHHHHHHHHHHHhccCCCCCccHHHHHHHHHHHHHHHHHhhccc
Confidence 478999999999888 88899999999999975 4556999999999999999988876644
No 3
>PF08858 IDEAL: IDEAL domain; InterPro: IPR014957 This entry represents the C-terminal domain of Bacteriophage SPP1, p90. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. his domain may also be referred to as the IDEAL domain, after the sequence of the most conserved region of the domain.; PDB: 3DO9_A.
Probab=80.38 E-value=1.3 Score=24.48 Aligned_cols=24 Identities=21% Similarity=0.352 Sum_probs=19.5
Q ss_pred HHHHHHHHHhhhhcccchhhhhhh
Q psy53 26 QWFENLMNSIERNLLTKNRDRFTQ 49 (78)
Q Consensus 26 ~~F~~LM~gIe~nL~~kNRDrFTQ 49 (78)
.-=+.|+.-|+.-|..++|++|-+
T Consensus 9 ~~~~~L~~~ID~ALd~~D~e~F~~ 32 (37)
T PF08858_consen 9 FRKEQLLELIDEALDNRDKEWFYE 32 (37)
T ss_dssp HHHHHHHHHHHHHHHTT-HHHHHH
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHH
Confidence 334689999999999999999964
No 4
>smart00394 RIIa RIIalpha, Regulatory subunit portion of type II PKA R-subunit. RIIalpha, Regulatory subunit portion of type II PKA R-subunit. Contains dimerisation interface and binding site for A-kinase-anchoring proteins (AKAPs).
Probab=75.72 E-value=7.3 Score=21.05 Aligned_cols=32 Identities=25% Similarity=0.462 Sum_probs=27.5
Q ss_pred hHHHHHHHHHHhhcCCchhHHHHHHHHHHHHH
Q psy53 2 DIYFNQLRENIVRGQPPDKQASMVQWFENLMN 33 (78)
Q Consensus 2 e~~f~~lk~~li~sQp~ekq~~l~~~F~~LM~ 33 (78)
+..+.++-..++..||++--+-.+.+|++|=.
T Consensus 4 ~~~L~~~~~~vl~~qP~d~~~f~~~yF~kL~~ 35 (38)
T smart00394 4 QALLEDLTVEVLRAQPSDLVQFAADYFEKLEE 35 (38)
T ss_pred HHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHH
Confidence 45677888899999999999999999988743
No 5
>PF02197 RIIa: Regulatory subunit of type II PKA R-subunit; InterPro: IPR003117 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. In the absence of cAMP, Protein Kinase A (PKA) exists as an equimolar tetramer of regulatory (R) and catalytic (C) subunits []. In addition to its role as an inhibitor of the C subunit, the R subunit anchors the holoenzyme to specific intracellular locations and prevents the C subunit from entering the nucleus. All R subunits have a conserved domain structure consisting of the N-terminal dimerization domain, inhibitory region, cAMP-binding domain A and cAMP-binding domain B. R subunits interact with C subunits primarily through the inhibitory site. The cAMP-binding domains show extensive sequence similarity and bind cAMP cooperatively. Two types of regulatory (R) subunits exist - types I and I - which differ in molecular weight, sequence, autophosphorylation cabaility, cellular location and tissue distribution. Types I and II were further sub-divided into alpha and beta subtypes, based mainly on sequence similarity. This entry represents types I-alpha, I-beta, II-alpha and II-beta regulatory subunits of PKA proteins. These subunits contain the dimerisation interface and binding site for A-kinase-anchoring proteins (AKAPs).; GO: 0008603 cAMP-dependent protein kinase regulator activity, 0007165 signal transduction; PDB: 2IZY_E 1R2A_A 1L6E_A 2IZX_B 2KYG_A 2EZW_B 3IM4_B 3IM3_A 4F9K_C 2HWN_B ....
Probab=75.07 E-value=6.3 Score=21.76 Aligned_cols=32 Identities=22% Similarity=0.426 Sum_probs=25.0
Q ss_pred hHHHHHHHHHHhhcCCchhHHHHHHHHHHHHH
Q psy53 2 DIYFNQLRENIVRGQPPDKQASMVQWFENLMN 33 (78)
Q Consensus 2 e~~f~~lk~~li~sQp~ekq~~l~~~F~~LM~ 33 (78)
++....+-..++..||.|=-+-.+.+|++|..
T Consensus 4 ~~lL~~~~~~vl~~qP~Di~~F~a~yF~~L~~ 35 (38)
T PF02197_consen 4 QELLKEFTREVLREQPDDILQFAADYFEKLEK 35 (38)
T ss_dssp HHHHHHHHHHHHHH--S-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHH
Confidence 35667888999999999999999999999865
No 6
>PF14829 GPAT_N: Glycerol-3-phosphate acyltransferase N-terminal; PDB: 1IUQ_A 1K30_A.
Probab=70.00 E-value=12 Score=24.34 Aligned_cols=37 Identities=11% Similarity=0.400 Sum_probs=28.8
Q ss_pred ChHHHHHHHHHHhhcCCchhH----HHHHHHHHHHHHHhhh
Q psy53 1 MDIYFNQLRENIVRGQPPDKQ----ASMVQWFENLMNSIER 37 (78)
Q Consensus 1 ~e~~f~~lk~~li~sQp~ekq----~~l~~~F~~LM~gIe~ 37 (78)
||+.|.++|.-.++|-.|--- ..|+..|+..+-+||.
T Consensus 35 meelY~NYk~AVl~Sg~p~A~eivlsnm~~~~Drvlldve~ 75 (77)
T PF14829_consen 35 MEELYQNYKNAVLQSGDPNADEIVLSNMAVALDRVLLDVED 75 (77)
T ss_dssp HHHHHHHHHHHHHHTT-TTHHHHHHHHHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHcccC
Confidence 689999999999988775332 5678889998888874
No 7
>PRK02922 glycogen synthesis protein GlgS; Provisional
Probab=69.69 E-value=5 Score=25.53 Aligned_cols=28 Identities=11% Similarity=0.299 Sum_probs=25.2
Q ss_pred HHhhhhcccchhhhhhhhHHHHHHHHHH
Q psy53 33 NSIERNLLTKNRDRFTQNLSMFRRDIND 60 (78)
Q Consensus 33 ~gIe~nL~~kNRDrFTQNLs~FRrdvr~ 60 (78)
+.|+.|++..-|+.|-.+|..+|+.+..
T Consensus 32 d~V~gnmsee~r~~F~eRla~Yr~~~~~ 59 (67)
T PRK02922 32 QAVTGNMDEEHRTWFCARYAWYCQQMMQ 59 (67)
T ss_pred HHHHhcCCHHHHHHHHHHHHHHHHHHHH
Confidence 5799999999999999999999988743
No 8
>PF08971 GlgS: Glycogen synthesis protein; InterPro: IPR015065 Members of this protein are involved in glycogen synthesis in Enterobacteria. The structure of the polypeptide chain comprises a bundle of two parallel amphipathic helices, alpha-1 and alpha-3, and a short hydrophobic helix alpha-2 sandwiched between them []. ; GO: 0005978 glycogen biosynthetic process; PDB: 1RRZ_A.
Probab=55.79 E-value=19 Score=22.84 Aligned_cols=29 Identities=17% Similarity=0.432 Sum_probs=23.2
Q ss_pred HHHhhhhcccchhhhhhhhHHHHHHHHHH
Q psy53 32 MNSIERNLLTKNRDRFTQNLSMFRRDIND 60 (78)
Q Consensus 32 M~gIe~nL~~kNRDrFTQNLs~FRrdvr~ 60 (78)
.+.|+.|++..-|..|-+.+..+|+....
T Consensus 30 ~~~I~gnM~ee~r~~F~~R~~~Yr~q~~~ 58 (66)
T PF08971_consen 30 VDAITGNMSEEQREWFCERYAHYRQQALQ 58 (66)
T ss_dssp HHHHHHH--TTHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhccCCHHHHHHHHHHHHHHHHHHHH
Confidence 35789999999999999999999986543
No 9
>PRK03636 hypothetical protein; Provisional
Probab=48.36 E-value=12 Score=27.13 Aligned_cols=22 Identities=23% Similarity=0.508 Sum_probs=20.0
Q ss_pred HHHHHHHhhhhcccchhhhhhh
Q psy53 28 FENLMNSIERNLLTKNRDRFTQ 49 (78)
Q Consensus 28 F~~LM~gIe~nL~~kNRDrFTQ 49 (78)
-++||..|+.-|..+++++|-+
T Consensus 147 ~~~L~~~ID~ALd~~D~e~F~~ 168 (179)
T PRK03636 147 REKLLKQIDEALDRRDKEAFHR 168 (179)
T ss_pred HHHHHHHHHHHHHcCCHHHHHH
Confidence 3689999999999999999976
No 10
>PF10350 DUF2428: Putative death-receptor fusion protein (DUF2428); InterPro: IPR019442 This domain is found in a family of proteins of unknown function that are conserved from plants to humans. Several of these proteins have been annotated as being HEAT repeat-containing proteins while others are designated as death-receptor interacting proteins, but neither of these has yet been confirmed. Aberrations in the genes encoding these proteins have been observed in benign thyroid adenomas [].
Probab=48.22 E-value=26 Score=25.83 Aligned_cols=36 Identities=19% Similarity=0.408 Sum_probs=33.3
Q ss_pred HHHHHHHHHHhhcCCchhHHHHHHHHHHHHHHhhhh
Q psy53 3 IYFNQLRENIVRGQPPDKQASMVQWFENLMNSIERN 38 (78)
Q Consensus 3 ~~f~~lk~~li~sQp~ekq~~l~~~F~~LM~gIe~n 38 (78)
..|..+...+..+..++=++...+|.+.+++.|+..
T Consensus 119 ~~f~~lc~~l~~~~~~~l~~LP~~WL~~~l~~i~~~ 154 (255)
T PF10350_consen 119 PGFTALCRRLWSSNNPELSELPEEWLDELLEAIESK 154 (255)
T ss_pred HHHHHHHHHHhcCCCchHHHhHHHHHHHHHHHHhcc
Confidence 468999999999999999999999999999999987
No 11
>PRK03057 hypothetical protein; Provisional
Probab=47.11 E-value=14 Score=26.97 Aligned_cols=22 Identities=23% Similarity=0.363 Sum_probs=20.1
Q ss_pred HHHHHHHhhhhcccchhhhhhh
Q psy53 28 FENLMNSIERNLLTKNRDRFTQ 49 (78)
Q Consensus 28 F~~LM~gIe~nL~~kNRDrFTQ 49 (78)
-+.||.-|+-.|+.+++++|.|
T Consensus 146 ~~~L~~~ID~ALd~~D~e~F~~ 167 (180)
T PRK03057 146 VSRLRMQIDQALDRKDMEEFQR 167 (180)
T ss_pred HHHHHHHHHHHHHCCCHHHHHH
Confidence 5679999999999999999976
No 12
>PF01297 TroA: Periplasmic solute binding protein family; InterPro: IPR006127 This is a family of ABC transporter metal-binding lipoproteins. An example is the periplasmic zinc-binding protein TroA P96116 from SWISSPROT that interacts with an ATP-binding cassette transport system in Treponema pallidum and plays a role in the transport of zinc across the cytoplasmic membrane. Related proteins are found in both Gram-positive and Gram-negative bacteria. ; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2PS9_A 2PS0_A 2OSV_A 2OGW_A 2PS3_A 2PRS_B 3MFQ_C 3GI1_B 2OV3_A 1PQ4_A ....
Probab=46.38 E-value=72 Score=22.75 Aligned_cols=41 Identities=15% Similarity=0.374 Sum_probs=27.1
Q ss_pred chhHHHHHHHHHHHHHHhhhhcccchhhhhhhhHHHHHHHHHHhc
Q psy53 18 PDKQASMVQWFENLMNSIERNLLTKNRDRFTQNLSMFRRDINDSL 62 (78)
Q Consensus 18 ~ekq~~l~~~F~~LM~gIe~nL~~kNRDrFTQNLs~FRrdvr~~l 62 (78)
|+.-..+.....+-+.. +.|.|++.|.+|+..|..++..+-
T Consensus 98 p~~~~~~~~~Ia~~L~~----~~P~~~~~y~~N~~~~~~~L~~l~ 138 (256)
T PF01297_consen 98 PENAKKMAEAIADALSE----LDPANKDYYEKNAEKYLKELDELD 138 (256)
T ss_dssp HHHHHHHHHHHHHHHHH----HTGGGHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHH----hCccchHHHHHHHHHHHHHHHHHH
Confidence 33334444444443333 588999999999999998876654
No 13
>PF08767 CRM1_C: CRM1 C terminal; InterPro: IPR014877 CRM1 (also known as Exportin1) mediates the nuclear export of proteins bearing a leucine-rich nuclear export signal (NES). CRM1 forms a complex with the NES containing protein and the small GTPase Ran. This region forms an alpha helical structure formed by six helical hairpin motifs that are structurally similar to the HEAT repeat, but share little sequence similarity to the HEAT repeat []. ; PDB: 3M1I_C 3GB8_A 1W9C_A 3NC1_A 3NBY_D 3NBZ_D 3NC0_A 3GJX_D.
Probab=42.80 E-value=72 Score=24.37 Aligned_cols=45 Identities=27% Similarity=0.404 Sum_probs=35.2
Q ss_pred chhHHHHHHHHHHHHHHhhhhcccchhhhhhhhH-------HHHHHHHHHhc
Q psy53 18 PDKQASMVQWFENLMNSIERNLLTKNRDRFTQNL-------SMFRRDINDSL 62 (78)
Q Consensus 18 ~ekq~~l~~~F~~LM~gIe~nL~~kNRDrFTQNL-------s~FRrdvr~~l 62 (78)
..++..+.+.+.+++...=+||.++.-..|.+.| ..||..+|+.|
T Consensus 260 ~~n~~~v~~~i~~~L~~~Fp~l~~~qi~~fv~~Lf~~~~d~~~Fk~~lrDFl 311 (319)
T PF08767_consen 260 MSNQEFVSEYIANLLSEAFPNLSPKQIENFVQGLFELNNDPEKFKTHLRDFL 311 (319)
T ss_dssp T-HHHHHHHHHHHHHHHH-TTS-HHHHHHHHHHHHHTTT-HHHHHHHHHHHH
T ss_pred CccHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHh
Confidence 4789999999999999999999999999988765 56777777654
No 14
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=41.57 E-value=71 Score=20.79 Aligned_cols=31 Identities=19% Similarity=0.424 Sum_probs=14.7
Q ss_pred HHHHHHHHhhcCCchhHHHHHHHHHHHHHHh
Q psy53 5 FNQLRENIVRGQPPDKQASMVQWFENLMNSI 35 (78)
Q Consensus 5 f~~lk~~li~sQp~ekq~~l~~~F~~LM~gI 35 (78)
+.++.+.+...-+++.++.+..++.+|...+
T Consensus 107 ~~~~~~~~~~~l~~ee~~~l~~~l~~l~~~l 137 (144)
T PRK03573 107 INKTRAEILHGISAEEIEQLITLIAKLEKNI 137 (144)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3344444444445555555555544444444
No 15
>PLN02349 glycerol-3-phosphate acyltransferase
Probab=40.77 E-value=40 Score=27.96 Aligned_cols=36 Identities=11% Similarity=0.420 Sum_probs=30.2
Q ss_pred ChHHHHHHHHHHhhcCCchhHH----HHHHHHHHHHHHhh
Q psy53 1 MDIYFNQLRENIVRGQPPDKQA----SMVQWFENLMNSIE 36 (78)
Q Consensus 1 ~e~~f~~lk~~li~sQp~ekq~----~l~~~F~~LM~gIe 36 (78)
||++|.++|...+.+..|...+ .|..+|+..+.||+
T Consensus 108 meely~nY~~Av~~sg~~~a~e~~~~~m~~~~d~v~~~~~ 147 (426)
T PLN02349 108 MEELYANYKNAVLSSGAPNADEIVVSNMASILDRVLLGVE 147 (426)
T ss_pred HHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhcc
Confidence 6899999999999988876664 34789999999886
No 16
>PF11800 RP-C_C: Replication protein C C-terminal region; InterPro: IPR021760 Replication protein C is involved in the early stages of viral DNA replication.
Probab=39.80 E-value=38 Score=24.17 Aligned_cols=43 Identities=19% Similarity=0.351 Sum_probs=35.4
Q ss_pred hHHHHHHHHHHhhcCCchhHHHHHHHHHHHHHHhhhhcccchh
Q psy53 2 DIYFNQLRENIVRGQPPDKQASMVQWFENLMNSIERNLLTKNR 44 (78)
Q Consensus 2 e~~f~~lk~~li~sQp~ekq~~l~~~F~~LM~gIe~nL~~kNR 44 (78)
++.|..|...|=..-+.+.-+.+...++.|.+.|+.-|+..-+
T Consensus 7 ~~~~~~l~~~L~R~~~~~~L~~l~~~L~~l~~~v~~~le~~~~ 49 (207)
T PF11800_consen 7 EDRFQALRRRLPRKASLADLEALLDELEALLEEVENALESQEK 49 (207)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 5677788877777677888899999999999999999987654
No 17
>COG0803 LraI ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]
Probab=38.86 E-value=31 Score=26.03 Aligned_cols=25 Identities=16% Similarity=0.360 Sum_probs=21.5
Q ss_pred hcccchhhhhhhhHHHHHHHHHHhc
Q psy53 38 NLLTKNRDRFTQNLSMFRRDINDSL 62 (78)
Q Consensus 38 nL~~kNRDrFTQNLs~FRrdvr~~l 62 (78)
-+.|+|++.|++|+..|...+..+-
T Consensus 155 ~~dP~~~~~y~~N~~~y~~kL~~l~ 179 (303)
T COG0803 155 ELDPENKETYEKNAEAYLKKLNKLD 179 (303)
T ss_pred HhCcccHHHHHHHHHHHHHHHHHHH
Confidence 4689999999999999998887654
No 18
>PF14747 DUF4473: Domain of unknown function (DUF4473)
Probab=38.54 E-value=52 Score=20.58 Aligned_cols=23 Identities=13% Similarity=0.277 Sum_probs=18.2
Q ss_pred HHHHHhhcCCchhHHHHHHHHHH
Q psy53 8 LRENIVRGQPPDKQASMVQWFEN 30 (78)
Q Consensus 8 lk~~li~sQp~ekq~~l~~~F~~ 30 (78)
--+.+|.+||++-|..+..||++
T Consensus 59 e~~~fikt~s~~DQ~~y~~~~eK 81 (82)
T PF14747_consen 59 EVDAFIKTQSEEDQTAYNAFVEK 81 (82)
T ss_pred HHHHHHHHCCHHHHHHHHHHHhc
Confidence 34578889998889998888864
No 19
>cd01137 PsaA Metal binding protein PsaA. These proteins have been shown to function as initial receptors in ABC transport of Mn2+ and as surface adhesins in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=34.73 E-value=39 Score=25.16 Aligned_cols=41 Identities=10% Similarity=0.216 Sum_probs=27.4
Q ss_pred chhHHHHHHHHHHHHHHhhhhcccchhhhhhhhHHHHHHHHHHhc
Q psy53 18 PDKQASMVQWFENLMNSIERNLLTKNRDRFTQNLSMFRRDINDSL 62 (78)
Q Consensus 18 ~ekq~~l~~~F~~LM~gIe~nL~~kNRDrFTQNLs~FRrdvr~~l 62 (78)
|..-..+.....+-+.. +.+.|++.|.+|+..|..++..+-
T Consensus 123 p~~~~~~a~~Ia~~L~~----~dP~~~~~y~~N~~~~~~~L~~l~ 163 (287)
T cd01137 123 PKNAIIYVKNIAKALSE----ADPANAETYQKNAAAYKAKLKALD 163 (287)
T ss_pred HHHHHHHHHHHHHHHHH----HCcccHHHHHHHHHHHHHHHHHHH
Confidence 44444455544444443 467999999999999988876543
No 20
>PF00502 Phycobilisome: Phycobilisome protein; InterPro: IPR012128 Cyanobacteria and red algae harvest light through water-soluble complexes, called phycobilisomes, which are attached to the outer face of the thylakoid membrane []. These complexes are capable of transferring the absorbed energy to the photosynthetic reaction centre with greater than 95% efficiency. Phycobilisomes contain various photosynthetic light harvesting proteins known as biliproteins, and linker proteins which help assemble the structure. The two main structural elements of the complex are a core located near the photosynthetic reaction centre, and rods attached to this core. Allophycocyanin is the major component of the core, while the rods contain phycocyanins, phycoerythrins and linker proteins. The rod biliproteins harvest photons, with the excitation energy being passed through the rods into the allophycocyanin in the core. Other core biliproteins subsequently pass this energy to chlorophyll within the thylakoid membrane. This entry represents the alpha and beta subunits found in biliproteins from cyanobacteria and red algae. Structural studies indicate that the basic structural unit of most biliproteins is a heterodimer composed of these alpha and beta subunits [, , , ]. The full protein is a ring-like trimer assembly of these heterodimers. Each subunit of the heterodimer has eight helices and binds chromophores through thioester bonds formed at particular cysteine residues. These chromophores, also known as bilins, are open-chain tetrapyrroles whose number and type vary with the particular biliprotein eg R-phyocerythrin binds five phycoerythrobilins per heterodimer, while allophycocyanin binds two phycocyanobilins per heterodimer.; GO: 0015979 photosynthesis, 0030089 phycobilisome; PDB: 2VML_I 2VJR_A 1KTP_B 3L0F_B 1JBO_B 3KVS_B 1PHN_B 3BRP_B 2C7K_B 2C7L_B ....
Probab=34.57 E-value=68 Score=22.16 Aligned_cols=33 Identities=21% Similarity=0.441 Sum_probs=28.5
Q ss_pred HHHHHHHHHHhhcCCchhHHHHHHHHHHHHHHh
Q psy53 3 IYFNQLRENIVRGQPPDKQASMVQWFENLMNSI 35 (78)
Q Consensus 3 ~~f~~lk~~li~sQp~ekq~~l~~~F~~LM~gI 35 (78)
..|..||+.+...-+++-++.+..+|+.|+..+
T Consensus 124 ~al~~lk~~~~~~l~~e~~~~~~~yfD~~i~~l 156 (157)
T PF00502_consen 124 EALQCLKEAALQLLSPEAAAEIAPYFDYLINAL 156 (157)
T ss_dssp HHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHC
Confidence 357888999888888999999999999998764
No 21
>cd01145 TroA_c Periplasmic binding protein TroA_c. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=34.04 E-value=43 Score=23.47 Aligned_cols=23 Identities=22% Similarity=0.457 Sum_probs=18.9
Q ss_pred cccchhhhhhhhHHHHHHHHHHh
Q psy53 39 LLTKNRDRFTQNLSMFRRDINDS 61 (78)
Q Consensus 39 L~~kNRDrFTQNLs~FRrdvr~~ 61 (78)
+.+.|++.|.+|+..|...+..+
T Consensus 131 ~dP~~~~~y~~N~~~~~~~l~~l 153 (203)
T cd01145 131 LDPSEQEEYKENLRVFLAKLNKL 153 (203)
T ss_pred hCcccHHHHHHHHHHHHHHHHHH
Confidence 46899999999999998877654
No 22
>PF09088 MIF4G_like: MIF4G like; InterPro: IPR015172 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 1", and is found in nuclear cap-binding proteins and eIF4G. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA.; GO: 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A.
Probab=31.82 E-value=1.4e+02 Score=21.93 Aligned_cols=46 Identities=20% Similarity=0.343 Sum_probs=39.3
Q ss_pred HHHHHHHHHHhhcCCchhHHHHHHHHHHHHHHhhhhcccchhhhhhh
Q psy53 3 IYFNQLRENIVRGQPPDKQASMVQWFENLMNSIERNLLTKNRDRFTQ 49 (78)
Q Consensus 3 ~~f~~lk~~li~sQp~ekq~~l~~~F~~LM~gIe~nL~~kNRDrFTQ 49 (78)
=||..+=-.++..+|..=-..++++++.|-..++. |...=+|||..
T Consensus 90 iyY~sllielCk~~P~~i~pv~~~air~ly~~l~~-md~e~~~Rf~d 135 (191)
T PF09088_consen 90 IYYHSLLIELCKLSPSAIPPVLGRAIRFLYRNLDS-MDFELRDRFVD 135 (191)
T ss_dssp HHHHHHHHHHHHHSTTTHHHHHHHHHHHHHHGGGG-B-HHHHHHHHH
T ss_pred hHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHhhhh-cCHHHHHHHHH
Confidence 37888888999999988889999999999999876 89999999965
No 23
>COG2960 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.25 E-value=1.5e+02 Score=20.21 Aligned_cols=46 Identities=13% Similarity=0.208 Sum_probs=39.3
Q ss_pred HHHHHHHHHHhhcCCc---hhHHHHHHHHHHHHHHhhhhcccchhhhhh
Q psy53 3 IYFNQLRENIVRGQPP---DKQASMVQWFENLMNSIERNLLTKNRDRFT 48 (78)
Q Consensus 3 ~~f~~lk~~li~sQp~---ekq~~l~~~F~~LM~gIe~nL~~kNRDrFT 48 (78)
+.|.++-.++...-|+ +=+.-++..|...|.+.=..|+...|.-|-
T Consensus 14 ~~~e~~~~ql~e~~a~~~~~~~~evE~~~r~~~q~~lnkLDlVsREEFd 62 (103)
T COG2960 14 NRFEDIAAQLSEDAAGAAQEVRAEVEKAFRAQLQRQLNKLDLVSREEFD 62 (103)
T ss_pred HHHHHHHHHHHHHccccchhhHHHHHHHHHHHHHHHHhhhhhhhHHHHH
Confidence 4577788888888886 677889999999999999999999999983
No 24
>TIGR02464 ribofla_fusion conserved hypothetical protein, ribA/ribD-fused. This model describes a sequence region that occurs in at least three different polypeptide contexts. It is found fused to GTP cyclohydrolase II, the RibA of riboflavin biosynthesis (TIGR00505), as in Vibrio vulnificus. It is found fused to riboflavin biosynthesis protein RibD (TIGR00326) in rice and Arabidopsis. It occurs as a standalone protein in a number of bacterial species in varied contexts, including single gene operons and bacteriophage genomes. The member from E. coli currently is named YbiA. The function(s) of members of this family is unknown.
Probab=30.56 E-value=35 Score=23.63 Aligned_cols=53 Identities=11% Similarity=0.258 Sum_probs=27.9
Q ss_pred HHHHHhhcCCchhHHHHHHHHHHHHHH-----hhhhcccchhhhhhhhHHHHHHHHHHhcCCC
Q psy53 8 LRENIVRGQPPDKQASMVQWFENLMNS-----IERNLLTKNRDRFTQNLSMFRRDINDSLKGP 65 (78)
Q Consensus 8 lk~~li~sQp~ekq~~l~~~F~~LM~g-----Ie~nL~~kNRDrFTQNLs~FRrdvr~~lk~~ 65 (78)
+++.|..+..|....++..-....-.. =..-+..-++.||+|| .+++..|-+.
T Consensus 48 ~~~~I~~~~sp~~ak~lgr~~~~~~~~~W~~~k~~vm~~~l~~KF~Qn-----~~Lr~~Ll~T 105 (153)
T TIGR02464 48 IAEEILEAKTPEEAKRLGRKVRGFLEKQWDQVKYEVMRRALLAKFSTH-----ADLREILLST 105 (153)
T ss_pred HHHHHHhCCCHHHHHHHhCcccCCChhhHHHHHHHHHHHHHHHHHHcC-----HHHHHHHHhc
Confidence 445566666666665554431110000 0112455688999999 4555555544
No 25
>cd01020 TroA_b Metal binding protein TroA_b. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=30.39 E-value=1.5e+02 Score=21.66 Aligned_cols=40 Identities=10% Similarity=0.215 Sum_probs=26.9
Q ss_pred chhHHHHHHHHHHHHHHhhhhcccchhhhhhhhHHHHHHHHHHh
Q psy53 18 PDKQASMVQWFENLMNSIERNLLTKNRDRFTQNLSMFRRDINDS 61 (78)
Q Consensus 18 ~ekq~~l~~~F~~LM~gIe~nL~~kNRDrFTQNLs~FRrdvr~~ 61 (78)
|..-..+.....+-+.. +.|+|++-|.+|+..|..++..+
T Consensus 101 p~n~~~~a~~I~~~L~~----~dP~~~~~y~~N~~~~~~~l~~l 140 (264)
T cd01020 101 PETMSKVANALADALVK----ADPDNKKYYQANAKKFVASLKPL 140 (264)
T ss_pred HhHHHHHHHHHHHHHHH----hCcccHHHHHHHHHHHHHHHHHH
Confidence 44444455444444443 35789999999999998887655
No 26
>cd01017 AdcA Metal binding protein AcdA. These proteins have been shown to function in the ABC uptake of Zn2+ and Mn2+ and in competence for genetic transformation and adhesion. The AcdA proteins belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and they bind their ligand in the cleft between these domains. In addition, many of these proteins have a low complexity region containing metal binding histidine-rich motif (repetitive HDH sequence).
Probab=29.97 E-value=1.5e+02 Score=21.71 Aligned_cols=24 Identities=13% Similarity=0.380 Sum_probs=19.5
Q ss_pred hcccchhhhhhhhHHHHHHHHHHh
Q psy53 38 NLLTKNRDRFTQNLSMFRRDINDS 61 (78)
Q Consensus 38 nL~~kNRDrFTQNLs~FRrdvr~~ 61 (78)
.+.+.|++.|.+|+..|...+..+
T Consensus 135 ~~dP~~~~~y~~N~~~~~~~L~~l 158 (282)
T cd01017 135 KLDPDNKEYYEKNAAAYAKKLEAL 158 (282)
T ss_pred HhCcccHHHHHHHHHHHHHHHHHH
Confidence 356899999999999998877544
No 27
>KOG4001|consensus
Probab=29.12 E-value=81 Score=24.48 Aligned_cols=29 Identities=28% Similarity=0.512 Sum_probs=22.2
Q ss_pred chhHHHHHHHHHHHHHHhhhh------cccchhhh
Q psy53 18 PDKQASMVQWFENLMNSIERN------LLTKNRDR 46 (78)
Q Consensus 18 ~ekq~~l~~~F~~LM~gIe~n------L~~kNRDr 46 (78)
|=+|..+++||+.|.-.|..| |...-||-
T Consensus 123 P~rreLYsQcFDElIRqvs~scveRGlll~rvRDE 157 (259)
T KOG4001|consen 123 PIRRELYSQCFDELIRQVSVSCVERGLLLVRVRDE 157 (259)
T ss_pred CCcHHHHHHHHHHHHHHcchhHHhcceeEEEehHH
Confidence 667899999999999886544 44566774
No 28
>PF14846 DUF4485: Domain of unknown function (DUF4485)
Probab=28.68 E-value=1.5e+02 Score=18.72 Aligned_cols=60 Identities=18% Similarity=0.349 Sum_probs=42.5
Q ss_pred HHHHHHHHHhhcCCchhHHHHHHHHHHHHHHhhhhcccchhhhhhhhHHHHHHHHHHhcCCC
Q psy53 4 YFNQLRENIVRGQPPDKQASMVQWFENLMNSIERNLLTKNRDRFTQNLSMFRRDINDSLKGP 65 (78)
Q Consensus 4 ~f~~lk~~li~sQp~ekq~~l~~~F~~LM~gIe~nL~~kNRDrFTQNLs~FRrdvr~~lk~~ 65 (78)
+...+|..+..-+....++....|..+|.+--..-..-+||-.+..-|...-+ +..|.|+
T Consensus 9 ~l~~~k~~~~~L~~~~~k~~a~~Wl~KL~~~~~~~~~~~~RN~Y~~~Ll~~l~--~~~L~~P 68 (85)
T PF14846_consen 9 YLEIIKPYILNLPDKSEKQRAALWLKKLCEPPHNVEEKKNRNEYASLLLHCLQ--QGRLEGP 68 (85)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHh--cCccCCC
Confidence 44455555554444888899999999999855455567888888888876655 4566666
No 29
>CHL00089 apcF allophycocyanin beta 18 subunit
Probab=28.39 E-value=1.3e+02 Score=21.59 Aligned_cols=34 Identities=15% Similarity=0.227 Sum_probs=25.5
Q ss_pred HHHHHHHHHhhcCCc---hhHHHHHHHHHHHHHHhhh
Q psy53 4 YFNQLRENIVRGQPP---DKQASMVQWFENLMNSIER 37 (78)
Q Consensus 4 ~f~~lk~~li~sQp~---ekq~~l~~~F~~LM~gIe~ 37 (78)
.+..+|+..+.--++ +-++.+..+|+.|..++..
T Consensus 130 al~~mk~~~~~~~~~~~~~~~~~~~~yFd~l~~~l~~ 166 (169)
T CHL00089 130 SIELLKEIIKEEIKSQNIDAHDYIDEPFQYMIKNLSE 166 (169)
T ss_pred HHHHHHHHHHHHhCccchHHHHHHHHHHHHHHHHHhh
Confidence 456677776665554 5579999999999998853
No 30
>PF01152 Bac_globin: Bacterial-like globin; InterPro: IPR001486 Globins are haem-containing proteins involved in binding and/or transporting oxygen. They belong to a very large and well studied family that is widely distributed in many organisms []. Globins have evolved from a common ancestor and can be divided into three groups: single-domain globins, and two types of chimeric globins, flavohaemoglobins and globin-coupled sensors. Bacteria have all three types of globins, while archaea lack flavohaemoglobins, and eukaryotes lack globin-coupled sensors []. Several functionally different haemoglobins can coexist in the same species. The major types of globins include: Haemoglobin (Hb): trimer of two alpha and two beta chains, although embryonic and foetal forms can substitute the alpha or beta chain for ones with higher oxygen affinity, such as gamma, delta, epsilon or zeta chains. Hb transports oxygen from lungs to other tissues in vertebrates []. Hb proteins are also present in unicellular organisms where they act as enzymes or sensors []. Myoglobin (Mb): monomeric protein responsible for oxygen storage in vertebrate muscle []. Neuroglobin: a myoglobin-like haemprotein expressed in vertebrate brain and retina, where it is involved in neuroprotection from damage due to hypoxia or ischemia []. Neuroglobin belongs to a branch of the globin family that diverged early in evolution. Cytoglobin: an oxygen sensor expressed in multiple tissues. Related to neuroglobin []. Erythrocruorin: highly cooperative extracellular respiratory proteins found in annelids and arthropods that are assembled from as many as 180 subunit into hexagonal bilayers []. Leghaemoglobin (legHb or symbiotic Hb): occurs in the root nodules of leguminous plants, where it facilitates the diffusion of oxygen to symbiotic bacteriods in order to promote nitrogen fixation. Non-symbiotic haemoglobin (NsHb): occurs in non-leguminous plants, and can be over-expressed in stressed plants []. Flavohaemoglobins (FHb): chimeric, with an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD/FAD-binding domain. FHb provides protection against nitric oxide via its C-terminal domain, which transfers electrons to haem in the globin []. Globin-coupled sensors: chimeric, with an N-terminal myoglobin-like domain and a C-terminal domain that resembles the cytoplasmic signalling domain of bacterial chemoreceptors. They bind oxygen, and act to initiate an aerotactic response or regulate gene expression [, ]. Protoglobin: a single domain globin found in archaea that is related to the N-terminal domain of globin-coupled sensors []. Truncated 2/2 globin: lack the first helix, giving them a 2-over-2 instead of the canonical 3-over-3 alpha-helical sandwich fold. Can be divided into three main groups (I, II and II) based on structural features []. This entry represents a group of haemoglobin-like proteins found in eubacteria, cyanobacteria, protozoa, algae and plants, but not in animals or yeast. These proteins have a truncated 2-over-2 rather than the canonical 3-over-3 alpha-helical sandwich fold []. This entry includes: HbN (or GlbN): a truncated haemoglobin-like protein that binds oxygen cooperatively with a very high affinity and a slow dissociation rate, which may exclude it from oxygen transport. It appears to be involved in bacterial nitric oxide detoxification and in nitrosative stress []. Cyanoglobin (or GlbN): a truncated haemoprotein found in cyanobacteria that has high oxygen affinity, and which appears to serve as part of a terminal oxidase, rather than as a respiratory pigment []. HbO (or GlbO): a truncated haemoglobin-like protein with a lower oxygen affinity than HbN. HbO associates with the bacterial cell membrane, where it significantly increases oxygen uptake over membranes lacking this protein. HbO appears to interact with a terminal oxidase, and could participate in an oxygen/electron-transfer process that facilitates oxygen transfer during aerobic metabolism []. Glb3: a nuclear-encoded truncated haemoglobin from plants that appears more closely related to HbO than HbN. Glb3 from Arabidopsis thaliana (Mouse-ear cress) exhibits an unusual concentration-independent binding of oxygen and carbon dioxide []. ; GO: 0019825 oxygen binding, 0015671 oxygen transport; PDB: 2BKM_B 1UVY_A 1DLW_A 2XYK_B 2IG3_A 2GKM_B 1S61_A 1S56_B 1RTE_B 2GLN_A ....
Probab=28.26 E-value=1.6e+02 Score=18.54 Aligned_cols=41 Identities=12% Similarity=0.259 Sum_probs=32.0
Q ss_pred chhHHHHHHHHHHHHHHhhhhcccchhhhhhhhHHHHHHHHHH
Q psy53 18 PDKQASMVQWFENLMNSIERNLLTKNRDRFTQNLSMFRRDIND 60 (78)
Q Consensus 18 ~ekq~~l~~~F~~LM~gIe~nL~~kNRDrFTQNLs~FRrdvr~ 60 (78)
++.....-+||..-|+.+ .+....++.+++-+..+|.+|.+
T Consensus 79 ~~~f~~~~~~~~~al~~~--~v~~~~~~~~~~~~~~~~~~i~n 119 (120)
T PF01152_consen 79 EEHFDRWLELLKQALDEL--GVPEELIDELLARLESLRDDIVN 119 (120)
T ss_dssp HHHHHHHHHHHHHHHHHT--TCTHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHh--CCCHHHHHHHHHHHHHHHHHhcC
Confidence 444566777777777754 66888999999999999999864
No 31
>cd01018 ZntC Metal binding protein ZntC. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and bind their specific ligands in the cleft between these domains. In addition, many of these proteins possess a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=27.81 E-value=1.7e+02 Score=21.22 Aligned_cols=40 Identities=15% Similarity=0.243 Sum_probs=25.6
Q ss_pred chhHHHHHHHHHHHHHHhhhhcccchhhhhhhhHHHHHHHHHHh
Q psy53 18 PDKQASMVQWFENLMNSIERNLLTKNRDRFTQNLSMFRRDINDS 61 (78)
Q Consensus 18 ~ekq~~l~~~F~~LM~gIe~nL~~kNRDrFTQNLs~FRrdvr~~ 61 (78)
|..-..+.....+-+.. +.|.|++.|.+|+..|...+..+
T Consensus 118 p~~~~~~a~~I~~~L~~----~dP~~~~~y~~N~~~~~~~L~~l 157 (266)
T cd01018 118 PANAKIMAENIYEALAE----LDPQNATYYQANLDALLAELDAL 157 (266)
T ss_pred HHHHHHHHHHHHHHHHH----hCcccHHHHHHHHHHHHHHHHHH
Confidence 33444444444444433 35789999999998888876654
No 32
>PF11333 DUF3135: Protein of unknown function (DUF3135); InterPro: IPR021482 This family of proteins with unkown function appears to be restricted to Proteobacteria.
Probab=27.78 E-value=78 Score=20.31 Aligned_cols=24 Identities=25% Similarity=0.487 Sum_probs=17.0
Q ss_pred HHHHHHHH----HHhhcCCchhHHHHHH
Q psy53 3 IYFNQLRE----NIVRGQPPDKQASMVQ 26 (78)
Q Consensus 3 ~~f~~lk~----~li~sQp~ekq~~l~~ 26 (78)
+.|.++|+ .+|.+-|++.|.+|..
T Consensus 18 e~fe~lr~~~~ee~I~~a~~~~q~rL~~ 45 (83)
T PF11333_consen 18 EAFEQLRQELIEEMIESAPEEMQPRLRA 45 (83)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence 44555554 5677889999988865
No 33
>PF03885 DUF327: Protein of unknown function (DUF327); InterPro: IPR005585 The proteins in this family are around 140-170 residues in length. The proteins contain many conserved residues, with the most conserved motifs found in the central and C-terminal region. The function of these proteins is unknown. ; PDB: 2P61_A 2QUP_A.
Probab=27.73 E-value=1.2e+02 Score=20.85 Aligned_cols=39 Identities=15% Similarity=0.216 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhhhhcccchhhhhhhhHHHHHHHHHHhcC
Q psy53 25 VQWFENLMNSIERNLLTKNRDRFTQNLSMFRRDINDSLK 63 (78)
Q Consensus 25 ~~~F~~LM~gIe~nL~~kNRDrFTQNLs~FRrdvr~~lk 63 (78)
.+-++.|+++|+.-=.-=-+..-..||..||+.|+..|+
T Consensus 42 ~e~L~~Ll~~I~~~G~~L~~~~t~~~l~~YK~~Vk~Fl~ 80 (147)
T PF03885_consen 42 EEELQELLDEIDEQGERLAESPTLENLKRYKELVKQFLK 80 (147)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHH
Confidence 366667777776544444556667899999999998886
No 34
>PF08933 DUF1864: Domain of unknown function (DUF1864); InterPro: IPR015029 This protein has no known function. It is found in various hypothetical and conserved domain proteins. ; PDB: 2NWB_A 1ZEE_B 2X66_A 2V7L_A 2V7M_A 2V7K_A 2X67_A 2X68_A 2V7J_A 2V7I_A.
Probab=27.15 E-value=43 Score=27.51 Aligned_cols=55 Identities=18% Similarity=0.232 Sum_probs=44.0
Q ss_pred hHHHHHHHHHHhhcCCchhHHHHHHHH--HHHHHHhhhhcccchhhhhhhhHHHHHH
Q psy53 2 DIYFNQLRENIVRGQPPDKQASMVQWF--ENLMNSIERNLLTKNRDRFTQNLSMFRR 56 (78)
Q Consensus 2 e~~f~~lk~~li~sQp~ekq~~l~~~F--~~LM~gIe~nL~~kNRDrFTQNLs~FRr 56 (78)
+.+|++++...+-=..|+-|+.++.|- .+||+.+=.-.....=+.|++|+..|-+
T Consensus 252 ~p~Ysq~lvdkf~Ym~P~dqailr~~mr~~SL~d~~l~~~~~~~~~~~~~~~~lfl~ 308 (387)
T PF08933_consen 252 DPAYSQFLVDKFLYMMPEDQAILRDCMRRPSLMDRFLAEAGAPGEPWYQENLRLFLE 308 (387)
T ss_dssp SHHHHHHHHCCGGGS-HHHHHHHHHHCTS--HHHHHHHCHHHCCTHHCCHHHHHHHH
T ss_pred ChHHHHHHHHHhcccCHHHHHHHHHHcCCchHHHHHHHhhccccCcchhhhHHHHHH
Confidence 457888888888888899999999996 4788887777777777999999999865
No 35
>cd01016 TroA Metal binding protein TroA. These proteins have been shown to function as initial receptors in ABC transport of Zn2+ and possibly Fe3+ in many eubacterial species. The TroA proteins belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=26.55 E-value=66 Score=23.74 Aligned_cols=23 Identities=17% Similarity=0.433 Sum_probs=18.9
Q ss_pred cccchhhhhhhhHHHHHHHHHHh
Q psy53 39 LLTKNRDRFTQNLSMFRRDINDS 61 (78)
Q Consensus 39 L~~kNRDrFTQNLs~FRrdvr~~ 61 (78)
+.+.|++.|.+|+..|..++..+
T Consensus 124 ~dP~~~~~y~~N~~~~~~~L~~l 146 (276)
T cd01016 124 KLPEHKDEFQANSEAYVEELDSL 146 (276)
T ss_pred HCcccHHHHHHHHHHHHHHHHHH
Confidence 57889999999999998876654
No 36
>PF07159 DUF1394: Protein of unknown function (DUF1394); InterPro: IPR009828 This family consists of several hypothetical eukaryotic proteins of around 320 residues in length. The function of this family is unknown.
Probab=26.42 E-value=1.8e+02 Score=22.80 Aligned_cols=59 Identities=17% Similarity=0.308 Sum_probs=46.0
Q ss_pred hHHHHHHHHHHhhcCC-----chhHHHHHHHHHHHHHHhhhhcccchhhhhhhh-HHHHHHHHHH
Q psy53 2 DIYFNQLRENIVRGQP-----PDKQASMVQWFENLMNSIERNLLTKNRDRFTQN-LSMFRRDIND 60 (78)
Q Consensus 2 e~~f~~lk~~li~sQp-----~ekq~~l~~~F~~LM~gIe~nL~~kNRDrFTQN-Ls~FRrdvr~ 60 (78)
|+.|-.+=..|++..- -+.+|++...|..+++-+-.==.-||+----|| .|.|||.+.-
T Consensus 85 e~~~~~ll~~L~~~~~~~~~~l~~~qAL~kq~a~iL~f~l~fD~LK~~npaIqNDFSyYRRa~sr 149 (303)
T PF07159_consen 85 EKVFPKLLKELCSGPLKPKEHLEQKQALAKQFAEILDFVLKFDELKMMNPAIQNDFSYYRRALSR 149 (303)
T ss_pred HHHHHHHHHHHhCCCCCchhhhHHhHHHHHHHHHHHHHHhhhhhhhccChhhhccHHHHHHHHHH
Confidence 5667777777775322 366789999999999888776678999899999 8999999863
No 37
>PF07208 DUF1414: Protein of unknown function (DUF1414); InterPro: IPR009857 This family consists of several hypothetical bacterial proteins of around 70 residues in length. Members of this family are often referred to as YejL. The function of this family is unknown.; PDB: 2JPQ_A 2JUZ_B 2JUW_B 2QTI_A 2OTA_A 2JR2_A 2JRX_A.
Probab=26.16 E-value=1.5e+02 Score=17.40 Aligned_cols=27 Identities=19% Similarity=0.489 Sum_probs=18.7
Q ss_pred HHHHHHHhh-cCCchhHHHHHHHHHHHH
Q psy53 6 NQLRENIVR-GQPPDKQASMVQWFENLM 32 (78)
Q Consensus 6 ~~lk~~li~-sQp~ekq~~l~~~F~~LM 32 (78)
.++=-.||+ +-|+++|+.+++-|.+-+
T Consensus 13 GN~vTniln~~V~~~qR~~iAe~Fa~AL 40 (44)
T PF07208_consen 13 GNMVTNILNTSVPPAQRQAIAEKFAQAL 40 (44)
T ss_dssp HHHHHHHHHHCS-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhhcCCHHHHHHHHHHHHHHH
Confidence 344456665 567899999999997643
No 38
>cd00446 GrpE GrpE is the adenine nucleotide exchange factor of DnaK (Hsp70)-type ATPases. The GrpE dimer binds to the ATPase domain of Hsp70 catalyzing the dissociation of ADP, which enables rebinding of ATP, one step in the Hsp70 reaction cycle in protein folding. In eukaryotes, only the mitochondrial Hsp70, not the cytosolic form, is GrpE dependent.
Probab=25.35 E-value=2.1e+02 Score=19.00 Aligned_cols=64 Identities=16% Similarity=0.356 Sum_probs=45.6
Q ss_pred HHHHHHHHHhhcCCchhHHHHHHHHHHHH---HHhhhhcccchh----hhhhhhHHHHHHHHHHhcCCCCC
Q psy53 4 YFNQLRENIVRGQPPDKQASMVQWFENLM---NSIERNLLTKNR----DRFTQNLSMFRRDINDSLKGPNM 67 (78)
Q Consensus 4 ~f~~lk~~li~sQp~ekq~~l~~~F~~LM---~gIe~nL~~kNR----DrFTQNLs~FRrdvr~~lk~~~~ 67 (78)
.|.++|...-......+....+..+.+|+ +.+|+-+..-.. ..|.+.+......+..+|...+.
T Consensus 14 e~~N~rkr~~~e~~~~~~~~~~~~~~~ll~v~D~le~a~~~~~~~~~~~~~~~g~~~i~~~l~~~L~~~Gv 84 (137)
T cd00446 14 EFENYRKRTEREREEARKYAIEKFAKDLLPVLDNLERALEAAKKEEELKNLVEGVEMTLKQLLDVLEKHGV 84 (137)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHHHHHHCCC
Confidence 46677777766666666667777776664 566777765444 37889999999999999986644
No 39
>PF12884 TORC_N: Transducer of regulated CREB activity, N terminus; InterPro: IPR024783 This entry represents the N-terminal domain of TORC proteins. TORC (transducer of regulated CREB activity) is a protein family of coactivators that enhances the activity of CRE-dependent transcription via a phosphorylation-independent interaction with the bZIP DNA binding/dimerisation domain of CREB (cAMP Response Element-Binding) []. The proteins display a highly conserved predicted N-terminal coiled-coil domain and an invariant sequence matching a protein kinase A (PKA) phosphorylation consensus sequence (RKXS) []. The coiled-coil structure interacts with the bZIP domain of CREB []. This interaction may occur via ionic bonds because it is disrupted under high-salt conditions []. In addition to CREB-binding, the N-terminal domain plays a role in the tetramer formation of TORCs [], but the physiological function of the multimeric complex has not been clarified yet.; GO: 0008140 cAMP response element binding protein binding, 0051289 protein homotetramerization
Probab=25.19 E-value=77 Score=20.09 Aligned_cols=19 Identities=32% Similarity=0.463 Sum_probs=16.2
Q ss_pred hhHHHHHHHHHHHHHHhhh
Q psy53 19 DKQASMVQWFENLMNSIER 37 (78)
Q Consensus 19 ekq~~l~~~F~~LM~gIe~ 37 (78)
.||+-=..+|+.+|.+|-.
T Consensus 14 QKQaEetaaFE~iM~ev~~ 32 (67)
T PF12884_consen 14 QKQAEETAAFEEIMKEVSS 32 (67)
T ss_pred HHHhHHHHHHHHHHHHHHH
Confidence 5788888999999999863
No 40
>PF05757 PsbQ: Oxygen evolving enhancer protein 3 (PsbQ); InterPro: IPR008797 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII OEC protein PsbQ. Both PsbQ and PsbP (IPR002683 from INTERPRO) are regulators that are necessary for the biogenesis of optically active PSII. The crystal structure of PsbQ from spinach revealed a 4-helical bundle polypeptide. The distribution of positive and negative charges on the protein surface might explain the ability of PsbQ to increase the binding of chloride and calcium ions and make them available to PSII [].; GO: 0005509 calcium ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 1VYK_A 1NZE_A 3LS1_A 3LS0_A.
Probab=24.86 E-value=99 Score=22.95 Aligned_cols=27 Identities=19% Similarity=0.523 Sum_probs=22.4
Q ss_pred HHhhcCCchhHHHHHHHHHHHHHHhhh
Q psy53 11 NIVRGQPPDKQASMVQWFENLMNSIER 37 (78)
Q Consensus 11 ~li~sQp~ekq~~l~~~F~~LM~gIe~ 37 (78)
.||++-|++.++.+..+-.+|.+.||+
T Consensus 144 ~liss~p~~~kk~l~~La~~lf~~ie~ 170 (202)
T PF05757_consen 144 TLISSKPKDEKKALTDLANKLFDNIEE 170 (202)
T ss_dssp HHHCCS-HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhCCHHHHHHHHHHHHHHHHHHHH
Confidence 578889999999999988999888874
No 41
>PF06254 DUF1019: Protein of unknown function (DUF1019); InterPro: IPR009364 This entry is represented by Bacteriophage phi-80, CII. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 3C4R_C.
Probab=24.81 E-value=96 Score=20.39 Aligned_cols=35 Identities=23% Similarity=0.345 Sum_probs=21.7
Q ss_pred HHHHHHHHHhhcCCchhHHHHH--HHHHHHHHHhhhh
Q psy53 4 YFNQLRENIVRGQPPDKQASMV--QWFENLMNSIERN 38 (78)
Q Consensus 4 ~f~~lk~~li~sQp~ekq~~l~--~~F~~LM~gIe~n 38 (78)
.+.+|---|+...|+|.++.|. .++..+++.+++-
T Consensus 27 ~~~~L~PAI~aAlP~E~rarl~~~~~~~~~la~~~kE 63 (89)
T PF06254_consen 27 KIMQLSPAILAALPPERRARLSSGDSTMYLLASAAKE 63 (89)
T ss_dssp HHHHHHHHHHHHS-HHHHHHHHCTT-HHH------HH
T ss_pred HHHHHHHHHHHhCCHHHHhhccCCCCchhhhhHhHHH
Confidence 4667777888899999999998 8888888777643
No 42
>PLN02999 photosystem II oxygen-evolving enhancer 3 protein (PsbQ)
Probab=24.52 E-value=94 Score=23.30 Aligned_cols=34 Identities=21% Similarity=0.218 Sum_probs=26.9
Q ss_pred HHhhcCCchhHHHHHHHHHHHHHHhhhhcccchhh
Q psy53 11 NIVRGQPPDKQASMVQWFENLMNSIERNLLTKNRD 45 (78)
Q Consensus 11 ~li~sQp~ekq~~l~~~F~~LM~gIe~nL~~kNRD 45 (78)
.+|++-|.+.++.+..+-.+|.+.|+ +|+-.-|+
T Consensus 132 tiIsskP~~eK~~L~~LankLFdnvt-~LDyAAR~ 165 (190)
T PLN02999 132 NAMNILPESRRNDYVQAANELVENMS-ELDYYVRT 165 (190)
T ss_pred HHHhcCCHhhhHHHHHHHHHHhhhHH-HHHHHHhc
Confidence 38999999999999999999999886 34444443
No 43
>cd02665 Peptidase_C19I A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=23.35 E-value=1.6e+02 Score=21.72 Aligned_cols=34 Identities=12% Similarity=0.294 Sum_probs=27.1
Q ss_pred HHHHHHHHhhcCCchhHHHHHHHHHHHHHHhhhhcccch
Q psy53 5 FNQLRENIVRGQPPDKQASMVQWFENLMNSIERNLLTKN 43 (78)
Q Consensus 5 f~~lk~~li~sQp~ekq~~l~~~F~~LM~gIe~nL~~kN 43 (78)
|+.+-+.+-+ .||-..++|..||+.+|..|...+
T Consensus 11 ~~~~~~~~~~-----~QQDa~Ef~~~Lld~Le~~l~~~~ 44 (228)
T cd02665 11 FSAVIQSLFS-----QQQDVSEFTHLLLDWLEDAFQAAA 44 (228)
T ss_pred HHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHhcccc
Confidence 5555555555 789999999999999999997554
No 44
>PRK11409 antitoxin YefM; Provisional
Probab=22.92 E-value=1.8e+02 Score=18.15 Aligned_cols=32 Identities=16% Similarity=0.243 Sum_probs=24.0
Q ss_pred HHHHHHHHHHhhcCCchhHHHHHHHHHHHHHH
Q psy53 3 IYFNQLRENIVRGQPPDKQASMVQWFENLMNS 34 (78)
Q Consensus 3 ~~f~~lk~~li~sQp~ekq~~l~~~F~~LM~g 34 (78)
+.|..|++.+---++|+..+.+.+..+.+-.|
T Consensus 43 ~~yesl~Etl~ll~~p~~~~~l~~~i~~~~~G 74 (83)
T PRK11409 43 EEYNSLEETAYLLRSPANARRLMDSIDSLKSG 74 (83)
T ss_pred HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHcC
Confidence 56888888876667888888877777777654
No 45
>PF14304 CSTF_C: Transcription termination and cleavage factor C-terminal; PDB: 2J8P_A.
Probab=22.24 E-value=68 Score=18.86 Aligned_cols=26 Identities=23% Similarity=0.488 Sum_probs=18.9
Q ss_pred HHHHhhcCCchhHHHHHHHHHHHHHH
Q psy53 9 RENIVRGQPPDKQASMVQWFENLMNS 34 (78)
Q Consensus 9 k~~li~sQp~ekq~~l~~~F~~LM~g 34 (78)
-..-|+.-||+.|+.+-.+=..||.|
T Consensus 18 t~eQI~~LPp~qR~~I~~Lr~ql~~~ 43 (46)
T PF14304_consen 18 TPEQINALPPDQRQQILQLRQQLMRG 43 (46)
T ss_dssp -HHHHHTS-HHHHTHHHHHHHHHH--
T ss_pred CHHHHHhCCHHHHHHHHHHHHHHHhc
Confidence 35568899999999999888888876
No 46
>cd01019 ZnuA Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a single helix and bind their specific ligands in the cleft between these domains. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=21.86 E-value=89 Score=23.18 Aligned_cols=24 Identities=21% Similarity=0.302 Sum_probs=20.5
Q ss_pred cccchhhhhhhhHHHHHHHHHHhc
Q psy53 39 LLTKNRDRFTQNLSMFRRDINDSL 62 (78)
Q Consensus 39 L~~kNRDrFTQNLs~FRrdvr~~l 62 (78)
+.|.|++.|.+|...|...+..+-
T Consensus 144 ~dP~~~~~y~~N~~~~~~~L~~l~ 167 (286)
T cd01019 144 LDPDNAATYAANLEAFNARLAELD 167 (286)
T ss_pred HCchhHHHHHHHHHHHHHHHHHHH
Confidence 578999999999999999887554
No 47
>COG2733 Predicted membrane protein [Function unknown]
Probab=21.41 E-value=68 Score=26.61 Aligned_cols=20 Identities=30% Similarity=0.692 Sum_probs=17.0
Q ss_pred hcccchhhhhhhhHHHHHHH
Q psy53 38 NLLTKNRDRFTQNLSMFRRD 57 (78)
Q Consensus 38 nL~~kNRDrFTQNLs~FRrd 57 (78)
-+-++||||+-.||..|-++
T Consensus 74 AIIprNKdri~e~l~~FV~~ 93 (415)
T COG2733 74 AIIPRNKDRIGENLGQFVQN 93 (415)
T ss_pred hhccccHHHHHHHHHHHHHH
Confidence 35689999999999999664
No 48
>PF02463 SMC_N: RecF/RecN/SMC N terminal domain; InterPro: IPR003395 This domain is found at the N terminus of structural maintenance of chromosomes (SMC) proteins, which function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression []. The domain is also found in RecF and RecN proteins, which are involved in DNA metabolism and recombination.; PDB: 3HTK_A 1W1W_C 2WD5_A 3L51_A 1XEW_Y 3KTA_B 3NWC_B 1XEX_A 1GXL_C 1GXK_A ....
Probab=20.47 E-value=20 Score=24.74 Aligned_cols=24 Identities=21% Similarity=0.454 Sum_probs=19.1
Q ss_pred HHHHhhhhcccchhhhhhhhHHHH
Q psy53 31 LMNSIERNLLTKNRDRFTQNLSMF 54 (78)
Q Consensus 31 LM~gIe~nL~~kNRDrFTQNLs~F 54 (78)
++|+|+.+|+..||.++.+=|..+
T Consensus 163 ilDEvd~~LD~~~~~~l~~~l~~~ 186 (220)
T PF02463_consen 163 ILDEVDAALDEQNRKRLADLLKEL 186 (220)
T ss_dssp EEESTTTTS-HHHHHHHHHHHHHH
T ss_pred cccccccccccccccccccccccc
Confidence 678999999999999988766543
No 49
>KOG4567|consensus
Probab=20.30 E-value=64 Score=26.36 Aligned_cols=37 Identities=22% Similarity=0.370 Sum_probs=21.7
Q ss_pred HHHHHHHHhhhhcccch----------hhhhhhhHHHHHHHHHHhcC
Q psy53 27 WFENLMNSIERNLLTKN----------RDRFTQNLSMFRRDINDSLK 63 (78)
Q Consensus 27 ~F~~LM~gIe~nL~~kN----------RDrFTQNLs~FRrdvr~~lk 63 (78)
||..||.+|-.|.--.= =-||++=|..+=.++-..|+
T Consensus 224 CF~~LMseirDnf~k~LDdS~~GI~~~Msr~~~~lk~~D~EL~~~L~ 270 (370)
T KOG4567|consen 224 CFTQLMSEIRDNFIKTLDDSVGGIHFLMSRLSELLKKHDEELWRHLE 270 (370)
T ss_pred HHHHHHHHHHHHHHHhccccccchHHHHHHHHHHHHHhhHHHHHHHH
Confidence 89999999965532111 12455555555555555554
No 50
>PF14063 DUF4254: Protein of unknown function (DUF4254)
Probab=20.24 E-value=2e+02 Score=20.08 Aligned_cols=32 Identities=13% Similarity=0.182 Sum_probs=24.1
Q ss_pred HHHHHHHHHHhhcCCchhHHHHHHHHHHHHHHhh
Q psy53 3 IYFNQLRENIVRGQPPDKQASMVQWFENLMNSIE 36 (78)
Q Consensus 3 ~~f~~lk~~li~sQp~ekq~~l~~~F~~LM~gIe 36 (78)
++|..++..+-- --++++.|+.|++.|+.+|.
T Consensus 106 ~h~~~~~~kl~v--l~~qradL~~~i~~Ll~d~~ 137 (145)
T PF14063_consen 106 EHFIRCARKLYV--LNEQRADLKRAIDQLLGDIL 137 (145)
T ss_pred HHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHH
Confidence 455666655544 46889999999999999885
No 51
>PF06371 Drf_GBD: Diaphanous GTPase-binding Domain; InterPro: IPR010473 Diaphanous-related formins (Drfs) are a family of formin homology (FH) proteins that act as effectors of Rho small GTPases during growth factor-induced cytoskeletal remodelling, stress fibre formation, and cell division []. Drf proteins are characterised by a variety of shared domains: an N-terminal GTPase-binding domain (GBD), formin-homology domains FH1, FH2 (IPR003104 from INTERPRO) and FH3 (IPR010472 from INTERPRO), and a C-terminal conserved Dia-autoregulatory domain (DAD) that binds the GBD. This entry represents the GBD, which is a bifunctional autoinhibitory domain that interacts with and is regulated by activated Rho family members. Mammalian Drf3 contains a CRIB-like motif within its GBD for binding to Cdc42, which is required for Cdc42 to activate and guide Drf3 towards the cell cortex where it remodels the actin skeleton [].; GO: 0003779 actin binding, 0017048 Rho GTPase binding, 0030036 actin cytoskeleton organization; PDB: 3OBV_A 2BNX_A 3EG5_D 2BAP_B 3O4X_B 1Z2C_B 2F31_A.
Probab=20.19 E-value=83 Score=20.95 Aligned_cols=26 Identities=23% Similarity=0.496 Sum_probs=15.2
Q ss_pred hHHHHHHHHHHHHHHhhhhcccchhhhh
Q psy53 20 KQASMVQWFENLMNSIERNLLTKNRDRF 47 (78)
Q Consensus 20 kq~~l~~~F~~LM~gIe~nL~~kNRDrF 47 (78)
..+.+.+.|++||++. |+...-|+..
T Consensus 4 ~~~~v~~~F~~ll~~~--~~~~~~r~~l 29 (187)
T PF06371_consen 4 SEEEVDEMFEELLEEL--NLPEEKRKEL 29 (187)
T ss_dssp -----HHHHHHHHHHT--T--HHHHHHH
T ss_pred CHHHHHHHHHHHHHhc--CCCHHHHHHH
Confidence 5677889999999977 7777766654
No 52
>PF07350 DUF1479: Protein of unknown function (DUF1479); InterPro: IPR010856 This family consists of several hypothetical Enterobacterial proteins, of around 420 residues in length. Members of this family are often known as YbiU. The function of this family is unknown.; PDB: 2CSG_A 2DBI_A 2DBN_A.
Probab=20.11 E-value=1.6e+02 Score=24.26 Aligned_cols=34 Identities=15% Similarity=0.437 Sum_probs=20.4
Q ss_pred ChHHHHHHHHHHhhcCCchhHHHHHHHHHHHHHHhh
Q psy53 1 MDIYFNQLRENIVRGQPPDKQASMVQWFENLMNSIE 36 (78)
Q Consensus 1 ~e~~f~~lk~~li~sQp~ekq~~l~~~F~~LM~gIe 36 (78)
|.+-|.+||++|++.- .+.+.+.+..+.|+...+
T Consensus 3 Lp~rf~~lK~~L~~~~--~~~~~v~~sw~rll~~l~ 36 (416)
T PF07350_consen 3 LPARFAELKRSLIAKP--GNEEAVFASWERLLEALE 36 (416)
T ss_dssp --HHHHHHHHHHHHHH--S-HHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHhhc--CCHHHHHHHHHHHHHHHH
Confidence 4567999999999632 345555555555555443
Done!