Query psy5991
Match_columns 223
No_of_seqs 87 out of 106
Neff 3.8
Searched_HMMs 46136
Date Fri Aug 16 23:47:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5991.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5991hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4345|consensus 99.9 1.1E-26 2.4E-31 228.2 5.4 178 22-223 419-607 (774)
2 KOG4345|consensus 99.9 4.1E-27 8.9E-32 231.1 2.1 160 37-222 74-258 (774)
3 PF02338 OTU: OTU-like cystein 99.5 5.4E-14 1.2E-18 107.7 7.2 77 104-206 1-82 (121)
4 KOG2606|consensus 97.6 0.00037 8.1E-09 64.5 8.8 100 97-206 158-260 (302)
5 PF10275 Peptidase_C65: Peptid 88.8 2.1 4.4E-05 37.4 7.5 26 180-205 179-204 (244)
6 KOG2605|consensus 79.0 1.3 2.7E-05 42.5 2.0 40 99-138 219-258 (371)
7 KOG3991|consensus 72.8 1.9 4.2E-05 39.5 1.4 22 184-205 198-219 (256)
8 cd03036 ArsC_like Arsenate Red 65.8 2.8 6.2E-05 32.5 0.9 20 194-213 88-107 (111)
9 PF03960 ArsC: ArsC family; I 64.9 4.3 9.3E-05 31.2 1.7 22 194-215 84-105 (110)
10 TIGR00014 arsC arsenate reduct 63.3 4 8.7E-05 32.0 1.3 19 195-213 88-106 (114)
11 cd03035 ArsC_Yffb Arsenate Red 62.6 3.6 7.8E-05 32.0 0.9 18 195-212 86-103 (105)
12 TIGR01617 arsC_related transcr 61.9 4 8.6E-05 31.8 1.0 19 195-213 89-108 (117)
13 COG1393 ArsC Arsenate reductas 59.3 8.9 0.00019 30.8 2.7 30 184-213 76-107 (117)
14 cd03032 ArsC_Spx Arsenate Redu 56.7 6.4 0.00014 30.6 1.4 19 195-213 88-106 (115)
15 cd03034 ArsC_ArsC Arsenate Red 56.4 4.7 0.0001 31.5 0.6 19 195-213 87-105 (112)
16 TIGR01616 nitro_assoc nitrogen 55.0 6.3 0.00014 32.0 1.1 19 195-213 87-105 (126)
17 cd02977 ArsC_family Arsenate R 54.2 6.4 0.00014 29.8 1.0 15 194-208 87-101 (105)
18 COG5539 Predicted cysteine pro 53.1 18 0.00039 34.2 3.9 94 97-205 170-270 (306)
19 PRK13344 spxA transcriptional 51.8 7.8 0.00017 31.4 1.2 20 195-214 88-107 (132)
20 PRK12559 transcriptional regul 51.3 7.5 0.00016 31.5 1.0 19 195-213 88-106 (131)
21 PRK01655 spxA transcriptional 49.1 9 0.0002 30.8 1.2 19 195-213 88-106 (131)
22 PRK10026 arsenate reductase; P 47.8 8.5 0.00018 32.1 0.9 13 195-207 90-102 (141)
23 COG1435 Tdk Thymidine kinase [ 43.5 18 0.00039 32.3 2.3 36 183-220 92-130 (201)
24 cd03033 ArsC_15kD Arsenate Red 42.7 13 0.00028 29.4 1.2 20 194-213 85-104 (113)
25 PRK10853 putative reductase; P 42.6 12 0.00027 29.8 1.0 18 196-213 89-107 (118)
26 PF02542 YgbB: YgbB family; I 38.6 20 0.00044 30.7 1.8 21 100-120 30-50 (157)
27 PF08671 SinI: Anti-repressor 36.7 26 0.00057 22.4 1.7 25 168-192 2-26 (30)
28 PF00469 F-protein: Negative f 32.9 15 0.00032 33.2 0.1 71 40-118 93-187 (220)
29 PF11985 DUF3486: Protein of u 29.9 28 0.0006 29.3 1.2 23 30-52 4-26 (180)
30 PF05412 Peptidase_C33: Equine 26.3 36 0.00078 27.9 1.2 17 104-120 5-21 (108)
31 KOG1092|consensus 26.0 1.4E+02 0.0029 30.1 5.3 106 64-198 312-431 (484)
32 PF15315 FRG2: Facioscapulohum 25.7 1.2E+02 0.0026 26.9 4.3 43 122-167 105-147 (181)
33 KOG2426|consensus 22.5 56 0.0012 33.3 2.0 48 53-111 365-416 (582)
No 1
>KOG4345|consensus
Probab=99.93 E-value=1.1e-26 Score=228.17 Aligned_cols=178 Identities=34% Similarity=0.361 Sum_probs=165.6
Q ss_pred ccceEEEeccccccCCHHHHHHHHHhhcCHHHHHHHhcCCCCCCcchhhhhhHHHHhhhhcCCCCcccccccccc----e
Q psy5991 22 TSKYFVCFFSEIENLPPSIQEQLFDELLDKEAQQQLEAEPHPVINWSHELLDKEAQQQLEAEPHPVINWSHEVTA----H 97 (223)
Q Consensus 22 ~~~~t~~lP~~i~~~p~~~re~l~~~LlD~~~q~~LE~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LNW~~~~~~----r 97 (223)
+.+-||.+++++...|+.++++++++.+|+++|+.||+.. +.+||..+... +
T Consensus 419 qk~~t~a~s~~~~eg~~~~~lg~~~~~~~~~l~~~~e~~~------------------------g~~nsal~~a~~~~sr 474 (774)
T KOG4345|consen 419 QKDKTRADSVANKEGSPGKTLGLKLKKNMGGLQKNLEEKP------------------------GGPNSALGTAPRLFSR 474 (774)
T ss_pred hhccccccccccccCCcchhhhhhhhhhhhhhhhCcCCCC------------------------CCCCCCCCCCCCHHHH
Confidence 5678999999999999999999999999999999999976 67888887643 7
Q ss_pred eeeeeeCCCCcchhHHhhhhhhccccCchHHH-HHHHHHHHhhh--hhHHHHHHHHH--HHhhcccccccChhHHHHHHH
Q psy5991 98 LYALWNRSAGDCLLDSLMQATWGVFDRENVLR-RALADSLAQAS--HLFYPRWKEYE--DMHASLLHFSLDESQWEEDWA 172 (223)
Q Consensus 98 L~pL~t~GDGNCLlHA~S~~mWGv~Drdl~LR-kaL~~~L~~~~--~~f~rRW~~~e--~~~s~~~~~~~~e~eW~~EW~ 172 (223)
++.+|++..|.|++++..|+.|||.|+++.+| +++++.+.++. +.|+.||+.++ ..++..+++++...||++||.
T Consensus 475 ~~~~~nk~r~~c~~~s~~qat~~v~~k~n~~~~~~~~~~~~~~~~~~~~~tr~k~~~~~~~~s~gl~~~~~~hQ~~Ee~~ 554 (774)
T KOG4345|consen 475 SKTKKNKSRSGCLLDSNAQATGGVSEKDNALRKRALADKYSTCVFNSLFITRWKMQGEEKSISLGLLLTLHRHQFQEEMI 554 (774)
T ss_pred HHHHHhhhccCCccchhccccCCcccCCccccccccchhhhhhhhhhhhhhhHhhhhhhHHHhhhcccCchHhhhhHHHH
Confidence 88899999999999999999999999999999 99999999886 88999999876 444556899999999999999
Q ss_pred HHHHhhCCCcchhhHHHHHHHhhhhcCceEEecccccc--ccCCCcccccCCC
Q psy5991 173 SLVSLASQPGAALEQLHVFALAHILRRPIIVYGVKYVK--SFRGEDIGYARFE 223 (223)
Q Consensus 173 ~iv~~As~pg~sLEeiHIFvLAnILRRPIIVy~~~~lr--~~rGe~l~~~rf~ 223 (223)
..+..+++|+.++||-|+|+||||++|||||++.++.+ +++||+.|+++||
T Consensus 555 ~rll~saqp~~s~EQ~q~~~~a~ia~rai~~ggv~g~k~p~krgE~~g~~k~q 607 (774)
T KOG4345|consen 555 QRLLLSAQPRFSAEQKQIFPLAHIARRAIIVGGVKGGKPPSKRGETDGYNKEQ 607 (774)
T ss_pred HHHhcCCCcchhhhhhcchhhhhhhhcccccccccCCCCCccCCCcccccccC
Confidence 99999999999999999999999999999999999999 9999999999986
No 2
>KOG4345|consensus
Probab=99.93 E-value=4.1e-27 Score=231.14 Aligned_cols=160 Identities=24% Similarity=0.332 Sum_probs=140.8
Q ss_pred CHHHHHHHHHhhcCHHHHHHHhcCCCCCCcchhhhhhHHHHhhhhcCCCCcccccccccceeeeeeeCCCCcchhHHhhh
Q psy5991 37 PPSIQEQLFDELLDKEAQQQLEAEPHPVINWSHELLDKEAQQQLEAEPHPVINWSHEVTAHLYALWNRSAGDCLLDSLMQ 116 (223)
Q Consensus 37 p~~~re~l~~~LlD~~~q~~LE~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LNW~~~~~~rL~pL~t~GDGNCLlHA~S~ 116 (223)
+..+|++..+.++|+.++-.++.+. +|||++++. .+..|.++||++|+.|+++|
T Consensus 74 s~~~r~~~~~s~~~~~~k~~~~~~~-------------------------~lnw~re~R-~~~~ls~~gd~~~~~~q~pq 127 (774)
T KOG4345|consen 74 SGQPREIIHKSLIDRNIKWPRPSLQ-------------------------RLNWPREKR-LSRGLSHAGDMPILAFQLPQ 127 (774)
T ss_pred cCCcccccccccccccccCCchHhh-------------------------hhhHHHHHH-HHHHhhccCCCccchhccch
Confidence 4588999999999999999999998 999999984 78899999999999999999
Q ss_pred hhhccccCchHHHHHHHHHHHhhh-hhHHHH-HHHHHH-Hhhc-ccccccChhHHHHHHHHHHHhhCC------------
Q psy5991 117 ATWGVFDRENVLRRALADSLAQAS-HLFYPR-WKEYED-MHAS-LLHFSLDESQWEEDWASLVSLASQ------------ 180 (223)
Q Consensus 117 ~mWGv~Drdl~LRkaL~~~L~~~~-~~f~rR-W~~~e~-~~s~-~~~~~~~e~eW~~EW~~iv~~As~------------ 180 (223)
+||+++|+...|++++..+|...+ +.+.-+ |..+.. .+.+ .+++.+..+.|++||+.++++||.
T Consensus 128 ~s~~~qs~~VaL~~~l~~~l~~~dt~~~N~l~w~~h~lvlqk~l~t~l~~~~~rw~~eW~~lik~ass~pr~~r~~~~~~ 207 (774)
T KOG4345|consen 128 LSVYEQSTPVALEKALFRLLPLADTGDGNCLMWGFHDLVLQKALYTGLCYGTERWNDEWTELIKLASSEPRMHRSGNGGT 207 (774)
T ss_pred hhccccccchhhhhhhhhcccccccCCccchhhhhhhHHHHHHHHHhhchhhHHHHHHHHHHHHhhcccchhhhcccCCC
Confidence 999999999999999999998654 456555 764322 1222 377888999999999999999996
Q ss_pred ---------CcchhhHHHHHHHhhhhcCceEEeccccccccCCCcccccCC
Q psy5991 181 ---------PGAALEQLHVFALAHILRRPIIVYGVKYVKSFRGEDIGYARF 222 (223)
Q Consensus 181 ---------pg~sLEeiHIFvLAnILRRPIIVy~~~~lr~~rGe~l~~~rf 222 (223)
||++||+||||||||||||||||++|+++||..|++++++.|
T Consensus 208 ~~~~e~s~~~yesLEe~hifvl~~ilRrpivvvsd~mlR~s~~~sfap~~~ 258 (774)
T KOG4345|consen 208 GGGVEISEDPYESLEEFHIFVLAHILRRPIVVVSDTMLRDSGGESFAPIPV 258 (774)
T ss_pred CCCcccccccchhHHHHHHHHHHHHhhCCeeEecccccccCCCcccccCcc
Confidence 258999999999999999999999999999999999999877
No 3
>PF02338 OTU: OTU-like cysteine protease; InterPro: IPR003323 This is a group of proteins found primarily in viruses, eukaryotes and in the pathogenic bacterium Chlamydia pneumoniae. In viruses they are annotated as replicase or RNA-dependent RNA polymerase. The eukaryotic sequences are related to the Ovarian Tumour (OTU) gene in Drosophila, cezanne deubiquitinating peptidase and tumor necrosis factor, alpha-induced protein 3 (MEROPS peptidase family C64) and otubain 1 and otubain 2 (MEROPS peptidase family C65). None of these proteins has a known biochemical function but low sequence similarity with the polyprotein regions of arteriviruses, and conserved cysteine and histidine, and possibly the aspartate, residues suggests that those not yet recognised as peptidases could possess cysteine protease activity [].; PDB: 2VFJ_C 3DKB_F 3PHW_A 3PHU_B 3PHX_A 3BY4_A 3C0R_C 3PRM_C 3PRP_C 3ZRH_A ....
Probab=99.50 E-value=5.4e-14 Score=107.70 Aligned_cols=77 Identities=31% Similarity=0.495 Sum_probs=61.5
Q ss_pred CCCCcchhHHhhhhhh----ccccCchHHHHHHHHHHH-hhhhhHHHHHHHHHHHhhcccccccChhHHHHHHHHHHHhh
Q psy5991 104 RSAGDCLLDSLMQATW----GVFDRENVLRRALADSLA-QASHLFYPRWKEYEDMHASLLHFSLDESQWEEDWASLVSLA 178 (223)
Q Consensus 104 ~GDGNCLlHA~S~~mW----Gv~Drdl~LRkaL~~~L~-~~~~~f~rRW~~~e~~~s~~~~~~~~e~eW~~EW~~iv~~A 178 (223)
+||||||+||+|.+|+ |..|....||+.+.+.|+ .....|..-.... ..
T Consensus 1 pgDGnClF~Avs~~l~~~~~~~~~~~~~lR~~~~~~l~~~~~~~~~~~~~~~--------------------------~~ 54 (121)
T PF02338_consen 1 PGDGNCLFRAVSDQLYGDGGGSEDNHQELRKAVVDYLRDKNRDKFEEFLEGD--------------------------KM 54 (121)
T ss_dssp -SSTTHHHHHHHHHHCTT-SSSTTTHHHHHHHHHHHHHTHTTTHHHHHHHHH--------------------------HH
T ss_pred CCCccHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhccchhhhhhhhh--------------------------hh
Confidence 5999999999999999 999999999999999998 5544444444311 23
Q ss_pred CCCcchhhHHHHHHHhhhhcCceEEecc
Q psy5991 179 SQPGAALEQLHVFALAHILRRPIIVYGV 206 (223)
Q Consensus 179 s~pg~sLEeiHIFvLAnILRRPIIVy~~ 206 (223)
+.+|.-..+++|++||++++|||+||..
T Consensus 55 ~~~~~Wg~~~el~a~a~~~~~~I~v~~~ 82 (121)
T PF02338_consen 55 SKPGTWGGEIELQALANVLNRPIIVYSS 82 (121)
T ss_dssp TSTTSHEEHHHHHHHHHHHTSEEEEECE
T ss_pred ccccccCcHHHHHHHHHHhCCeEEEEEc
Confidence 4455555689999999999999999865
No 4
>KOG2606|consensus
Probab=97.57 E-value=0.00037 Score=64.55 Aligned_cols=100 Identities=22% Similarity=0.244 Sum_probs=68.0
Q ss_pred eeeeeeeCCCCcchhHHhhhhhhccccC---chHHHHHHHHHHHhhhhhHHHHHHHHHHHhhcccccccChhHHHHHHHH
Q psy5991 97 HLYALWNRSAGDCLLDSLMQATWGVFDR---ENVLRRALADSLAQASHLFYPRWKEYEDMHASLLHFSLDESQWEEDWAS 173 (223)
Q Consensus 97 rL~pL~t~GDGNCLlHA~S~~mWGv~Dr---dl~LRkaL~~~L~~~~~~f~rRW~~~e~~~s~~~~~~~~e~eW~~EW~~ 173 (223)
.|.......|||||+-|++.++==-++. -..||+...+-|++....|..-.. ....+.++++++.+.-=.+
T Consensus 158 ~l~~~~Ip~DG~ClY~aI~hQL~~~~~~~~~v~kLR~~~a~Ymr~H~~df~pf~~------~eet~d~~~~~~f~~Yc~e 231 (302)
T KOG2606|consen 158 GLKMFDIPADGHCLYAAISHQLKLRSGKLLSVQKLREETADYMREHVEDFLPFLL------DEETGDSLGPEDFDKYCRE 231 (302)
T ss_pred cCccccCCCCchhhHHHHHHHHHhccCCCCcHHHHHHHHHHHHHHHHHHhhhHhc------CccccccCCHHHHHHHHHH
Confidence 6888899999999999999887433332 356888888888876555554433 2234555564444444334
Q ss_pred HHHhhCCCcchhhHHHHHHHhhhhcCceEEecc
Q psy5991 174 LVSLASQPGAALEQLHVFALAHILRRPIIVYGV 206 (223)
Q Consensus 174 iv~~As~pg~sLEeiHIFvLAnILRRPIIVy~~ 206 (223)
|..- +..|+ +|-+|+|+|||+-||-||.-
T Consensus 232 I~~t-~~WGg---elEL~AlShvL~~PI~Vy~~ 260 (302)
T KOG2606|consen 232 IRNT-AAWGG---ELELKALSHVLQVPIEVYQA 260 (302)
T ss_pred hhhh-ccccc---hHHHHHHHHhhccCeEEeec
Confidence 4442 44554 57799999999999999974
No 5
>PF10275 Peptidase_C65: Peptidase C65 Otubain; InterPro: IPR019400 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This family of proteins is a highly specific ubiquitin iso-peptidase that removes ubiquitin from proteins. The modification of cellular proteins by ubiquitin (Ub) is an important event that underlies protein stability and function in eukaryotes, as it is a dynamic and reversible process. Otubain carries several key conserved domains: (i) the OTU (ovarian tumour domain) in which there is an active cysteine protease triad (ii) a nuclear localisation signal, (iii) a Ub interaction motif (UIM)-like motif phi-xx-A-xxxs-xx-Ac (where phi indicates an aromatic amino acid, x indicates any amino acid and Ac indicates an acidic amino acid), (iv) a Ub-associated (UBA)-like domain and (v) the LxxLL motif. ; PDB: 4DDG_C 3VON_O 2ZFY_A 4DHZ_A 4DDI_C 1TFF_A 4DHJ_I 4DHI_B.
Probab=88.80 E-value=2.1 Score=37.45 Aligned_cols=26 Identities=31% Similarity=0.379 Sum_probs=18.0
Q ss_pred CCcchhhHHHHHHHhhhhcCceEEec
Q psy5991 180 QPGAALEQLHVFALAHILRRPIIVYG 205 (223)
Q Consensus 180 ~pg~sLEeiHIFvLAnILRRPIIVy~ 205 (223)
|++.--.+++|-+||+.|+=||.|+-
T Consensus 179 p~~~Ead~v~i~ALa~aL~v~i~v~y 204 (244)
T PF10275_consen 179 PMGKEADHVQIIALAQALGVPIRVEY 204 (244)
T ss_dssp STT--B-HHHHHHHHHHHT--EEEEE
T ss_pred cccccchhHHHHHHHHHhCCeEEEEE
Confidence 44444479999999999999999985
No 6
>KOG2605|consensus
Probab=78.96 E-value=1.3 Score=42.52 Aligned_cols=40 Identities=23% Similarity=0.316 Sum_probs=33.7
Q ss_pred eeeeeCCCCcchhHHhhhhhhccccCchHHHHHHHHHHHh
Q psy5991 99 YALWNRSAGDCLLDSLMQATWGVFDRENVLRRALADSLAQ 138 (223)
Q Consensus 99 ~pL~t~GDGNCLlHA~S~~mWGv~Drdl~LRkaL~~~L~~ 138 (223)
.-.+..+||||+++|.+...||-.|....-|+...+-|+.
T Consensus 219 e~~Kv~edGsC~fra~aDQvy~d~e~~~~~~~~~~dq~~~ 258 (371)
T KOG2605|consen 219 EYKKVVEDGSCLFRALADQVYGDDEQHDHNRRECVDQLKK 258 (371)
T ss_pred hhhhcccCCchhhhccHHHhhcCHHHHHHHHHHHHHHHhh
Confidence 3456789999999999999999888888888888888743
No 7
>KOG3991|consensus
Probab=72.75 E-value=1.9 Score=39.53 Aligned_cols=22 Identities=27% Similarity=0.265 Sum_probs=17.8
Q ss_pred hhhHHHHHHHhhhhcCceEEec
Q psy5991 184 ALEQLHVFALAHILRRPIIVYG 205 (223)
Q Consensus 184 sLEeiHIFvLAnILRRPIIVy~ 205 (223)
--.-|||-+|++-|---|-|.-
T Consensus 198 esdhi~I~ALs~Al~i~irVey 219 (256)
T KOG3991|consen 198 ESDHIHITALSQALGIRIRVEY 219 (256)
T ss_pred ccCceeHHHHHhhhCceEEEEE
Confidence 3357999999999988887764
No 8
>cd03036 ArsC_like Arsenate Reductase (ArsC) family, unknown subfamily; uncharacterized proteins containing a CXXC motif with similarity to thioredoxin (TRX)-fold arsenic reductases, ArsC. Proteins containing a redox active CXXC motif like TRX and glutaredoxin (GRX) function as protein disulfide oxidoreductases, altering the redox state of target proteins via the reversible oxidation of the active site dithiol. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione via GRX, through a single catalytic cysteine.
Probab=65.78 E-value=2.8 Score=32.55 Aligned_cols=20 Identities=25% Similarity=0.567 Sum_probs=15.8
Q ss_pred hhhhcCceEEeccccccccC
Q psy5991 194 AHILRRPIIVYGVKYVKSFR 213 (223)
Q Consensus 194 AnILRRPIIVy~~~~lr~~r 213 (223)
-.+||||||+.+++.+-.|+
T Consensus 88 p~LikRPIi~~~~~~~vGf~ 107 (111)
T cd03036 88 GMLIKRPFVVDDDKVLVGFK 107 (111)
T ss_pred cCeeeCCEEEeCCEEEEccC
Confidence 35899999999887766655
No 9
>PF03960 ArsC: ArsC family; InterPro: IPR006660 Several bacterial taxon have a chromosomal resistance system, encoded by the ars operon, for the detoxification of arsenate, arsenite, and antimonite []. This system transports arsenite and antimonite out of the cell. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. Arsenate, however, must first be reduced to arsenite before it is extruded. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance. ArsC is an approximately 150-residue arsenate reductase that uses reduced glutathione (GSH) to convert arsenate to arsenite with a redox active cysteine residue in the active site. ArsC forms an active quaternary complex with GSH, arsenate, and glutaredoxin 1 (Grx1). The three ligands must be present simultaneously for reduction to occur []. The arsC family also comprises the Spx proteins which are GRAM-positive bacterial transcription factors that regulate the transcription of multiple genes in response to disulphide stress []. The arsC protein structure has been solved []. It belongs to the thioredoxin superfamily fold which is defined by a beta-sheet core surrounded by alpha-helices. The active cysteine residue of ArsC is located in the loop between the first beta-strand and the first helix, which is also conserved in the Spx protein and its homologues.; PDB: 2KOK_A 1SK1_A 1SK2_A 1JZW_A 1J9B_A 1S3C_A 1SD8_A 1SD9_A 1I9D_A 1SK0_A ....
Probab=64.89 E-value=4.3 Score=31.21 Aligned_cols=22 Identities=45% Similarity=0.724 Sum_probs=16.0
Q ss_pred hhhhcCceEEeccccccccCCC
Q psy5991 194 AHILRRPIIVYGVKYVKSFRGE 215 (223)
Q Consensus 194 AnILRRPIIVy~~~~lr~~rGe 215 (223)
-.+|||||||.+.+++-.|.=+
T Consensus 84 p~LikRPIi~~~~~~~iG~~~~ 105 (110)
T PF03960_consen 84 PKLIKRPIIVDGKKAVIGFNEE 105 (110)
T ss_dssp GGGB-SSEEEETTEEEESSSGG
T ss_pred hhheeCCEEEECCEEEEeCCHH
Confidence 4589999999998877666543
No 10
>TIGR00014 arsC arsenate reductase (glutaredoxin). composed of two polypeptides, the products of the arsA and arsB genes. The pump alone produces resistance to arsenite and antimonite. This protein, ArsC, catalyzes the reduction of arsenate to arsenite, and thus extends resistance to include arsenate.
Probab=63.29 E-value=4 Score=32.01 Aligned_cols=19 Identities=32% Similarity=0.321 Sum_probs=14.7
Q ss_pred hhhcCceEEeccccccccC
Q psy5991 195 HILRRPIIVYGVKYVKSFR 213 (223)
Q Consensus 195 nILRRPIIVy~~~~lr~~r 213 (223)
.+|||||||.+++.+-.|.
T Consensus 88 ~LikRPIi~~~~~~~vG~~ 106 (114)
T TIGR00014 88 ILLERPIVVAGDGARIGRP 106 (114)
T ss_pred CcccCCeEEECCEEEEcCC
Confidence 3899999999887655444
No 11
>cd03035 ArsC_Yffb Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine suggest that it is likely to function as a glutathione (GSH)-dependent thiol reductase. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from GSH via glutaredoxin, through a single catalytic cysteine.
Probab=62.61 E-value=3.6 Score=32.03 Aligned_cols=18 Identities=28% Similarity=0.656 Sum_probs=13.6
Q ss_pred hhhcCceEEecccccccc
Q psy5991 195 HILRRPIIVYGVKYVKSF 212 (223)
Q Consensus 195 nILRRPIIVy~~~~lr~~ 212 (223)
.+|||||||.+++.+-.|
T Consensus 86 ~LikRPIi~~~~~~~iGf 103 (105)
T cd03035 86 SLIKRPVLETGGKVLVGF 103 (105)
T ss_pred CeeecceEEeCCEEEEee
Confidence 589999999887655433
No 12
>TIGR01617 arsC_related transcriptional regulator, Spx/MgsR family. This model represents a portion of the proteins within the larger set covered by Pfam model pfam03960. That larger family includes a glutaredoxin-dependent arsenate reductase (TIGR00014). Characterized members of this family include Spx and MgsR from Bacillus subtili. Spx is a global regulator for response to thiol-specific oxidative stress. It interacts with RNA polymerase. MgsR (modulator of the general stress response, also called YqgZ) provides a second level of regulation for more than a third of the proteins in the B. subtilis general stress regulon controlled by Sigma-B.
Probab=61.91 E-value=4 Score=31.80 Aligned_cols=19 Identities=37% Similarity=0.704 Sum_probs=14.0
Q ss_pred hhhcCceEEecc-ccccccC
Q psy5991 195 HILRRPIIVYGV-KYVKSFR 213 (223)
Q Consensus 195 nILRRPIIVy~~-~~lr~~r 213 (223)
.+|||||||.++ +++-.|+
T Consensus 89 ~LikRPIi~~~~~~~~vG~~ 108 (117)
T TIGR01617 89 ALLRRPLIVDTKNRLLIGFK 108 (117)
T ss_pred ceEecCEEEeCCceEEecCC
Confidence 489999999987 5444443
No 13
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=59.33 E-value=8.9 Score=30.82 Aligned_cols=30 Identities=30% Similarity=0.426 Sum_probs=19.9
Q ss_pred hhhHHHHHHHhh--hhcCceEEeccccccccC
Q psy5991 184 ALEQLHVFALAH--ILRRPIIVYGVKYVKSFR 213 (223)
Q Consensus 184 sLEeiHIFvLAn--ILRRPIIVy~~~~lr~~r 213 (223)
+.++.....++| ++||||||-+.++.-.|+
T Consensus 76 ~~~~~~~~i~~~~~LikRPivv~~~~~~iG~~ 107 (117)
T COG1393 76 SDEELIEALLENPSLIKRPIVVDNKKLRVGFN 107 (117)
T ss_pred ChHHHHHHHHhChhhccCCeEEeCCceEecCC
Confidence 444555555554 799999998876555554
No 14
>cd03032 ArsC_Spx Arsenate Reductase (ArsC) family, Spx subfamily; Spx is a unique RNA polymerase (RNAP)-binding protein present in bacilli and some mollicutes. It inhibits transcription by binding to the C-terminal domain of the alpha subunit of RNAP, disrupting complex formation between RNAP and certain transcriptional activator proteins like ResD and ComA. In response to oxidative stress, Spx can also activate transcription, making it a general regulator that exerts both positive and negative control over transcription initiation. Spx has been shown to exert redox-sensitive transcriptional control over genes like trxA (TRX) and trxB (TRX reductase), genes that function in thiol homeostasis. This redox-sensitive activity is dependent on the presence of a CXXC motif, present in some members of the Spx subfamily, that acts as a thiol/disulfide switch. Spx has also been shown to repress genes in a sulfate-dependent manner independent of the presence of the CXXC motif.
Probab=56.71 E-value=6.4 Score=30.63 Aligned_cols=19 Identities=32% Similarity=0.602 Sum_probs=14.7
Q ss_pred hhhcCceEEeccccccccC
Q psy5991 195 HILRRPIIVYGVKYVKSFR 213 (223)
Q Consensus 195 nILRRPIIVy~~~~lr~~r 213 (223)
.++|||||+.+++++-.|.
T Consensus 88 ~LikRPii~~~~~~~vG~~ 106 (115)
T cd03032 88 SLLRRPIIIDEKRLQIGYN 106 (115)
T ss_pred hheeCCEEEeCCEEEeCCC
Confidence 4899999998877665554
No 15
>cd03034 ArsC_ArsC Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the detoxification of arsenic, using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX). ArsC contains a single catalytic cysteine, within a thioredoxin fold, that forms a covalent thiolate-As(V) intermediate, which is reduced by GRX through a mixed GSH-arsenate intermediate. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases.
Probab=56.43 E-value=4.7 Score=31.46 Aligned_cols=19 Identities=32% Similarity=0.399 Sum_probs=14.4
Q ss_pred hhhcCceEEeccccccccC
Q psy5991 195 HILRRPIIVYGVKYVKSFR 213 (223)
Q Consensus 195 nILRRPIIVy~~~~lr~~r 213 (223)
.++||||||.+++.+-.|.
T Consensus 87 ~LikRPIi~~~~~~~vG~~ 105 (112)
T cd03034 87 ILIERPIVVTGDGAVLGRP 105 (112)
T ss_pred CcccCCEEEECCEEEEcCC
Confidence 3899999998877655443
No 16
>TIGR01616 nitro_assoc nitrogenase-associated protein. This model describes a small family of uncharacterized proteins found so far in alpha and gamma proteobacteria and in Nostoc sp. PCC 7120, a cyanobacterium. The gene for this protein is associated with nitrogenase genes. This family shows sequence similarity to TIGR00014, a glutaredoxin-dependent arsenate reductase that converts arsentate to arsenite for disposal. This family is one of several included in Pfam model pfam03960.
Probab=55.03 E-value=6.3 Score=31.96 Aligned_cols=19 Identities=26% Similarity=0.513 Sum_probs=15.0
Q ss_pred hhhcCceEEeccccccccC
Q psy5991 195 HILRRPIIVYGVKYVKSFR 213 (223)
Q Consensus 195 nILRRPIIVy~~~~lr~~r 213 (223)
.++||||||.+++++-.|.
T Consensus 87 ~LIKRPIi~~~~~~~iGf~ 105 (126)
T TIGR01616 87 LLIRRPLMDLGGIRCAGFD 105 (126)
T ss_pred CeEeCCEEEECCEEEEcCC
Confidence 4899999999877665554
No 17
>cd02977 ArsC_family Arsenate Reductase (ArsC) family; composed of TRX-fold arsenic reductases and similar proteins including the transcriptional regulator, Spx. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX), through a single catalytic cysteine. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases. Spx is a general regulator that exerts negative and positive control over transcription initiation by binding to the C-terminal domain of the alpha subunit of RNA polymerase.
Probab=54.19 E-value=6.4 Score=29.76 Aligned_cols=15 Identities=33% Similarity=0.791 Sum_probs=12.1
Q ss_pred hhhhcCceEEecccc
Q psy5991 194 AHILRRPIIVYGVKY 208 (223)
Q Consensus 194 AnILRRPIIVy~~~~ 208 (223)
-++|||||||-+++.
T Consensus 87 p~LikRPii~~~~~~ 101 (105)
T cd02977 87 PKLIKRPIVVDGDRL 101 (105)
T ss_pred cCeeeCCEEEECCEE
Confidence 358999999987754
No 18
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=53.10 E-value=18 Score=34.21 Aligned_cols=94 Identities=12% Similarity=0.095 Sum_probs=54.0
Q ss_pred eeeeeeeCCCCcchhHHhhhhhhc-cc--cCchHHHHHHHHHHHhhhhhHHHHHHHH---HHHhhcccccccChhHH-HH
Q psy5991 97 HLYALWNRSAGDCLLDSLMQATWG-VF--DRENVLRRALADSLAQASHLFYPRWKEY---EDMHASLLHFSLDESQW-EE 169 (223)
Q Consensus 97 rL~pL~t~GDGNCLlHA~S~~mWG-v~--Drdl~LRkaL~~~L~~~~~~f~rRW~~~---e~~~s~~~~~~~~e~eW-~~ 169 (223)
+++...--|||+|++-++|..+== ++ |-+.. -..||... +...-...|+-|+++-- -.
T Consensus 170 ~i~k~d~~~dG~ieia~iS~~l~v~i~~Vdv~~~---------------~~dr~~~~~~~q~~~i~f~g~hfD~~t~~m~ 234 (306)
T COG5539 170 WIVKPDSQGDGCIEIAIISDQLPVRIHVVDVDKD---------------SEDRYNSHPYVQRISILFTGIHFDEETLAMV 234 (306)
T ss_pred hhhccccCCCceEEEeEeccccceeeeeeecchh---------------HHhhccCChhhhhhhhhhcccccchhhhhcc
Confidence 777788899999999999987611 11 11110 12333311 11112234555666432 34
Q ss_pred HHHHHHHhhCCCcchhhHHHHHHHhhhhcCceEEec
Q psy5991 170 DWASLVSLASQPGAALEQLHVFALAHILRRPIIVYG 205 (223)
Q Consensus 170 EW~~iv~~As~pg~sLEeiHIFvLAnILRRPIIVy~ 205 (223)
+|+..+..--+...-.-.|.|-+|||+|+-|+-++.
T Consensus 235 ~~dt~~ne~~~~a~~g~~~ei~qLas~lk~~~~~~n 270 (306)
T COG5539 235 LWDTYVNEVLFDASDGITIEIQQLASLLKNPHYYTN 270 (306)
T ss_pred hHHHHHhhhcccccccchHHHHHHHHHhcCceEEee
Confidence 566555544332221257899999999998887775
No 19
>PRK13344 spxA transcriptional regulator Spx; Reviewed
Probab=51.80 E-value=7.8 Score=31.42 Aligned_cols=20 Identities=20% Similarity=0.519 Sum_probs=15.2
Q ss_pred hhhcCceEEeccccccccCC
Q psy5991 195 HILRRPIIVYGVKYVKSFRG 214 (223)
Q Consensus 195 nILRRPIIVy~~~~lr~~rG 214 (223)
.++|||||+.+.+++=.|.=
T Consensus 88 ~LikRPIv~~~~~~~iG~~~ 107 (132)
T PRK13344 88 RILKSPILIDDKRLQVGYKE 107 (132)
T ss_pred cceeCcEEEeCCEEEeCCCH
Confidence 38999999988776655543
No 20
>PRK12559 transcriptional regulator Spx; Provisional
Probab=51.28 E-value=7.5 Score=31.50 Aligned_cols=19 Identities=32% Similarity=0.551 Sum_probs=14.8
Q ss_pred hhhcCceEEeccccccccC
Q psy5991 195 HILRRPIIVYGVKYVKSFR 213 (223)
Q Consensus 195 nILRRPIIVy~~~~lr~~r 213 (223)
.++|||||+.+++.+-.|.
T Consensus 88 ~LikRPIi~~~~~~~iGf~ 106 (131)
T PRK12559 88 LMLRRPIMLDEKRLQIGFN 106 (131)
T ss_pred ceEeCCEEEeCCEEEEcCC
Confidence 4899999998877665554
No 21
>PRK01655 spxA transcriptional regulator Spx; Reviewed
Probab=49.11 E-value=9 Score=30.84 Aligned_cols=19 Identities=32% Similarity=0.588 Sum_probs=14.7
Q ss_pred hhhcCceEEeccccccccC
Q psy5991 195 HILRRPIIVYGVKYVKSFR 213 (223)
Q Consensus 195 nILRRPIIVy~~~~lr~~r 213 (223)
.++||||||.+++.+-.|.
T Consensus 88 ~LikRPIi~~~~~~~vG~~ 106 (131)
T PRK01655 88 GLLRRPIIIDEKRLQVGYN 106 (131)
T ss_pred ceEeCCEEEECCEEEecCC
Confidence 4899999999887665554
No 22
>PRK10026 arsenate reductase; Provisional
Probab=47.85 E-value=8.5 Score=32.08 Aligned_cols=13 Identities=31% Similarity=0.608 Sum_probs=11.2
Q ss_pred hhhcCceEEeccc
Q psy5991 195 HILRRPIIVYGVK 207 (223)
Q Consensus 195 nILRRPIIVy~~~ 207 (223)
.++||||||.+++
T Consensus 90 ~LIKRPIi~~~~~ 102 (141)
T PRK10026 90 ILINRPIVVTPLG 102 (141)
T ss_pred cceeCcEEEcCCC
Confidence 4899999999765
No 23
>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]
Probab=43.54 E-value=18 Score=32.33 Aligned_cols=36 Identities=28% Similarity=0.530 Sum_probs=26.1
Q ss_pred chhhHHHHHHHhhhh---cCceEEeccccccccCCCccccc
Q psy5991 183 AALEQLHVFALAHIL---RRPIIVYGVKYVKSFRGEDIGYA 220 (223)
Q Consensus 183 ~sLEeiHIFvLAnIL---RRPIIVy~~~~lr~~rGe~l~~~ 220 (223)
.-+.+=||++|+.|- .+|+|+|+= -.||+||+|..+
T Consensus 92 QF~~~~~v~~l~~lad~lgi~Vi~~GL--~~DFrgepFe~s 130 (201)
T COG1435 92 QFFDEELVYVLNELADRLGIPVICYGL--DTDFRGEPFEGS 130 (201)
T ss_pred HhCCHHHHHHHHHHHhhcCCEEEEecc--ccccccCCCccH
Confidence 456667788876665 557777773 359999999864
No 24
>cd03033 ArsC_15kD Arsenate Reductase (ArsC) family, 15kD protein subfamily; composed of proteins of unknown function with similarity to thioredoxin-fold arsenic reductases, ArsC. It is encoded by an ORF present in a gene cluster associated with nitrogen fixation that also encodes dinitrogenase reductase ADP-ribosyltransferase (DRAT) and dinitrogenase reductase activating glycohydrolase (DRAG). ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione via glutaredoxin, through a single catalytic cysteine.
Probab=42.73 E-value=13 Score=29.43 Aligned_cols=20 Identities=25% Similarity=0.589 Sum_probs=14.5
Q ss_pred hhhhcCceEEeccccccccC
Q psy5991 194 AHILRRPIIVYGVKYVKSFR 213 (223)
Q Consensus 194 AnILRRPIIVy~~~~lr~~r 213 (223)
-.+++||||+.+++.+=.|.
T Consensus 85 P~LikRPIv~~~~~~~vG~~ 104 (113)
T cd03033 85 PLLIRRPLMQVGDRRMVGFD 104 (113)
T ss_pred cceeeCCeEEECCEEEecCC
Confidence 35899999998776554444
No 25
>PRK10853 putative reductase; Provisional
Probab=42.65 E-value=12 Score=29.76 Aligned_cols=18 Identities=22% Similarity=0.490 Sum_probs=13.1
Q ss_pred hhcCceEEecc-ccccccC
Q psy5991 196 ILRRPIIVYGV-KYVKSFR 213 (223)
Q Consensus 196 ILRRPIIVy~~-~~lr~~r 213 (223)
++||||||.++ +.+-.|+
T Consensus 89 LikRPIv~~~~~~~~vGf~ 107 (118)
T PRK10853 89 IIKRPLLCAPGKPMLLGFS 107 (118)
T ss_pred eeeccEEEeCCCeEEEcCC
Confidence 89999999865 3544444
No 26
>PF02542 YgbB: YgbB family; InterPro: IPR003526 MECDP (2-C-methyl-D-erythritol 2,4-cyclodiphosphate) synthetase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis, isoprenoids being essential in all organisms. Isoprenoids can also be synthesized through the mevalonate pathway. The non-mevolante route is used by many bacteria and human pathogens, including Mycobacterium tuberculosis and Plasmodium falciparum. This route appears to involve seven enzymes. MECDP synthetase catalyses the intramolecular attack by a phosphate group on a diphosphate, with cytidine monophosphate (CMP) acting as the leaving group to give the cyclic diphosphate product MEDCP. The enzyme is a trimer with three active sites shared between adjacent copies of the protein. The enzyme also has two metal binding sites, the metals playing key roles in catalysis[]. A number of proteins from eukaryotes and prokaryotes share this common N-terminal signature and appear to be involved in terpenoid biosynthesis. The YgbB protein is a putative enzyme of this type [].; GO: 0008685 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity, 0016114 terpenoid biosynthetic process; PDB: 3T80_B 3GHZ_A 2PMP_A 3F6M_A 3FPI_A 3RE3_A 1T0A_C 1W57_A 1W55_A 3B6N_A ....
Probab=38.59 E-value=20 Score=30.71 Aligned_cols=21 Identities=38% Similarity=0.590 Sum_probs=16.7
Q ss_pred eeeeCCCCcchhHHhhhhhhc
Q psy5991 100 ALWNRSAGDCLLDSLMQATWG 120 (223)
Q Consensus 100 pL~t~GDGNCLlHA~S~~mWG 120 (223)
-|...+||+.|+||+..|+-|
T Consensus 30 gl~gHSDgDVl~HAi~DAlLG 50 (157)
T PF02542_consen 30 GLEGHSDGDVLLHAIIDALLG 50 (157)
T ss_dssp EEESSSS--HHHHHHHHHHHH
T ss_pred CCcccChHHHHHHHHHHHHHH
Confidence 367789999999999999987
No 27
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=36.74 E-value=26 Score=22.44 Aligned_cols=25 Identities=28% Similarity=0.660 Sum_probs=19.8
Q ss_pred HHHHHHHHHhhCCCcchhhHHHHHH
Q psy5991 168 EEDWASLVSLASQPGAALEQLHVFA 192 (223)
Q Consensus 168 ~~EW~~iv~~As~pg~sLEeiHIFv 192 (223)
+.||-.+|..|-.-|-+.|+|--|-
T Consensus 2 D~EW~~Li~eA~~~Gls~eeir~FL 26 (30)
T PF08671_consen 2 DEEWVELIKEAKESGLSKEEIREFL 26 (30)
T ss_dssp -HHHHHHHHHHHHTT--HHHHHHHH
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 4699999999999999999998873
No 28
>PF00469 F-protein: Negative factor, (F-Protein) or Nef; InterPro: IPR001558 Human immunodeficiency virus 1 (HIV-1) negative factor (Nef protein) accelerates virulent progression of acquired immunodeficiency syndrome (AIDS) by its interaction with specific cellular proteins involved in signal transduction and host cell activation. Nef has been shown to bind specifically to a subset of the Src family of kinases [].; GO: 0005525 GTP binding; PDB: 4EN2_C 4EMZ_C 3IK5_C 2NEF_A 3REA_C 3REB_A 3RBB_A 3QZW_C 3NFN_C 1QVO_C ....
Probab=32.89 E-value=15 Score=33.17 Aligned_cols=71 Identities=21% Similarity=0.254 Sum_probs=39.7
Q ss_pred HHHHHHHhhcCHHHHHHH-hcCCCCCCcchh---hhhhHHHHhhhhcCC---------------CCcccccccccceeee
Q psy5991 40 IQEQLFDELLDKEAQQQL-EAEPHPVINWSH---ELLDKEAQQQLEAEP---------------HPVINWSHEVTAHLYA 100 (223)
Q Consensus 40 ~re~l~~~LlD~~~q~~L-E~~~~~~~~~~~---~~~~~~~~~~~~~~~---------------~~~LNW~~~~~~rL~p 100 (223)
.|..=++..+|-. .-| |.-|--||.||. ++||--+.+ |.|. |-..-|| =+|+|
T Consensus 93 LR~mTyK~a~dls--hflKeKGGLeg~~ys~~R~~iLdl~~~~--~~g~~pdwq~yt~gpG~RyP~~fGw~----~kLvp 164 (220)
T PF00469_consen 93 LRPMTYKLAIDLS--HFLKEKGGLEGIFYSQRRQEILDLYVYN--EQGIFPDWQNYTPGPGIRYPLTFGWL----FKLVP 164 (220)
T ss_dssp CBE--HHHHHHHH--HHHHHTTSSTT-BE-HHHHHHHHHHHHH--HH-BESTTT-B-SSSSSB-BSSTT------EEEEE
T ss_pred ccccccccccchh--HHHHhhccccccccccccccccceEEee--ccccCCCccccCCCCccceeeeccee----EEEEE
Confidence 3444456666543 333 445667899996 888876543 2331 2222233 28999
Q ss_pred eee-----CCCCcchhHHhhhhh
Q psy5991 101 LWN-----RSAGDCLLDSLMQAT 118 (223)
Q Consensus 101 L~t-----~GDGNCLlHA~S~~m 118 (223)
+.. .|+-|||||-+++.-
T Consensus 165 v~~~~~~~~~e~~~Llhp~~~~~ 187 (220)
T PF00469_consen 165 VDPEEEEEEGENNCLLHPAQQHG 187 (220)
T ss_dssp CSCCHHHHHTTTHHHC-GCCSTT
T ss_pred eeccccccccccccCCChhhccC
Confidence 764 688999999999854
No 29
>PF11985 DUF3486: Protein of unknown function (DUF3486); InterPro: IPR021874 This entry is represented by Bacteriophage Mu, Gp27. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=29.92 E-value=28 Score=29.33 Aligned_cols=23 Identities=43% Similarity=0.475 Sum_probs=20.3
Q ss_pred ccccccCCHHHHHHHHHhhcCHH
Q psy5991 30 FSEIENLPPSIQEQLFDELLDKE 52 (223)
Q Consensus 30 P~~i~~~p~~~re~l~~~LlD~~ 52 (223)
|+.|..||+++|+.|...|.|+.
T Consensus 4 ~SkId~LP~eir~~l~~~L~~~~ 26 (180)
T PF11985_consen 4 RSKIDLLPPEIREWLDQMLRDGG 26 (180)
T ss_pred CchHhhCCHHHHHHHHHHHHhCC
Confidence 56789999999999999999963
No 30
>PF05412 Peptidase_C33: Equine arterivirus Nsp2-type cysteine proteinase; InterPro: IPR008743 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases corresponds to MEROPS peptidase family C33 (clan CA). The type example is equine arteritis virus Nsp2-type cysteine proteinase, which is involved in viral polyprotein processing [].; GO: 0016032 viral reproduction, 0019082 viral protein processing
Probab=26.32 E-value=36 Score=27.86 Aligned_cols=17 Identities=12% Similarity=0.173 Sum_probs=14.9
Q ss_pred CCCCcchhHHhhhhhhc
Q psy5991 104 RSAGDCLLDSLMQATWG 120 (223)
Q Consensus 104 ~GDGNCLlHA~S~~mWG 120 (223)
.|||+|=+|.+|+-|-+
T Consensus 5 P~DG~CG~H~i~aI~n~ 21 (108)
T PF05412_consen 5 PGDGSCGWHCIAAIMNH 21 (108)
T ss_pred CCCCchHHHHHHHHHHH
Confidence 79999999999987765
No 31
>KOG1092|consensus
Probab=25.96 E-value=1.4e+02 Score=30.11 Aligned_cols=106 Identities=23% Similarity=0.349 Sum_probs=62.9
Q ss_pred CCcchhhhhhHHHHhhhhcCCCCcccccccccceeeeeeeCCCCcchhHHhhh----hhhccccCchHHH-------HHH
Q psy5991 64 VINWSHELLDKEAQQQLEAEPHPVINWSHEVTAHLYALWNRSAGDCLLDSLMQ----ATWGVFDRENVLR-------RAL 132 (223)
Q Consensus 64 ~~~~~~~~~~~~~~~~~~~~~~~~LNW~~~~~~rL~pL~t~GDGNCLlHA~S~----~mWGv~Drdl~LR-------kaL 132 (223)
++-|.--++..+++..+||. -=||..- ||+.+=. +.=|++-.=..|+ +-|
T Consensus 312 ~~~~d~~~l~~E~~~~iEAD----syWClsk---------------LLD~IQDNYtfaQpGIq~kV~~L~eLv~RID~~~ 372 (484)
T KOG1092|consen 312 VESIDMSLLPAENAEDIEAD----AYWCLSK---------------LLDGIQDNYTFAQPGIQRKVKNLKELVQRIDEPL 372 (484)
T ss_pred ccccchhhccHHHHhhhhhh----HHHHHHH---------------HHHHhhhhhhhcChhHHHHHHHHHHHHHHhcHHH
Confidence 44455556777888899987 6788752 3332211 1123333222333 456
Q ss_pred HHHHHhhh---hhHHHHHHHHHHHhhcccccccChhHHHHHHHHHHHhhCCCcchhhHHHHHHHhhhhc
Q psy5991 133 ADSLAQAS---HLFYPRWKEYEDMHASLLHFSLDESQWEEDWASLVSLASQPGAALEQLHVFALAHILR 198 (223)
Q Consensus 133 ~~~L~~~~---~~f~rRW~~~e~~~s~~~~~~~~e~eW~~EW~~iv~~As~pg~sLEeiHIFvLAnILR 198 (223)
|.+|++.. ..|-.||+-.--+ .++.+..+ -+=|+..++. +.|+.++|+||-|-.|.
T Consensus 373 hkHlq~~gveylQFAFRWmNcLLm--RE~pl~~~----iRlWDTY~aE----~dgf~~FhvYvcAAFL~ 431 (484)
T KOG1092|consen 373 HKHLQEHGVEYLQFAFRWMNCLLM--REFPLRCT----IRLWDTYLAE----PDGFNEFHVYVCAAFLL 431 (484)
T ss_pred HHHHHHhchHHHHHHHHHHHHHHH--hhccchhH----HHHHHHhhcC----ccchHHHHHHHHHHHHH
Confidence 77787654 3588899832222 12333333 4667777664 67889999999887764
No 32
>PF15315 FRG2: Facioscapulohumeral muscular dystrophy candidate 2
Probab=25.70 E-value=1.2e+02 Score=26.91 Aligned_cols=43 Identities=28% Similarity=0.281 Sum_probs=33.2
Q ss_pred ccCchHHHHHHHHHHHhhhhhHHHHHHHHHHHhhcccccccChhHH
Q psy5991 122 FDRENVLRRALADSLAQASHLFYPRWKEYEDMHASLLHFSLDESQW 167 (223)
Q Consensus 122 ~Drdl~LRkaL~~~L~~~~~~f~rRW~~~e~~~s~~~~~~~~e~eW 167 (223)
.|+-+.|||.|--+|+...+.+|+--. .++++..++.++.+|.
T Consensus 105 ~~~pPplRKsLVtslR~~SEaIYqD~a---q~~aQq~~spLt~EQl 147 (181)
T PF15315_consen 105 GDQPPPLRKSLVTSLRAMSEAIYQDLA---QVQAQQHHSPLTWEQL 147 (181)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHH---HHHHHhhcCCCCHHHH
Confidence 677889999999999999888987654 3455566777776554
No 33
>KOG2426|consensus
Probab=22.46 E-value=56 Score=33.27 Aligned_cols=48 Identities=23% Similarity=0.354 Sum_probs=28.4
Q ss_pred HHHHHhcCCCCCCcchhh----hhhHHHHhhhhcCCCCcccccccccceeeeeeeCCCCcchh
Q psy5991 53 AQQQLEAEPHPVINWSHE----LLDKEAQQQLEAEPHPVINWSHEVTAHLYALWNRSAGDCLL 111 (223)
Q Consensus 53 ~q~~LE~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~LNW~~~~~~rL~pL~t~GDGNCLl 111 (223)
-++++|.+.+++..-.-+ .|-.++-+-||.+ |+|||+-.. -|||+|=-
T Consensus 365 s~~~~~~~~~s~vt~d~~~~~~~l~~~~~~ii~~E--p~lt~~D~~---------aGDGDCGt 416 (582)
T KOG2426|consen 365 SLEHLESEKKSGVTVDAQKFAAALKAVAEAIIESE--PHLTELDTI---------AGDGDCGT 416 (582)
T ss_pred chhhcccccCCCccccHHHHHHHHHHHHHHHHhcc--cchhHHhcc---------ccCCcchh
Confidence 345555555554444432 2333334444555 699999876 59999953
Done!