Query 036335
Match_columns 122
No_of_seqs 102 out of 326
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 11:38:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036335.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036335hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02668 indole-3-acetate carb 100.0 1.1E-36 2.4E-41 249.2 11.7 116 1-120 268-385 (386)
2 PF03492 Methyltransf_7: SAM d 100.0 1.7E-36 3.8E-41 244.1 12.2 120 1-121 212-334 (334)
3 PRK01683 trans-aconitate 2-met 78.4 23 0.0005 26.8 8.5 90 16-121 162-257 (258)
4 PHA00457 inhibitor of host bac 71.0 5.5 0.00012 24.9 2.7 33 9-41 23-58 (63)
5 PF14904 FAM86: Family of unkn 66.8 8.2 0.00018 26.5 3.2 31 69-99 67-99 (100)
6 PF02375 JmjN: jmjN domain; I 64.2 2.5 5.5E-05 23.3 0.2 15 16-30 1-15 (34)
7 PRK14103 trans-aconitate 2-met 57.0 84 0.0018 23.8 8.7 73 16-104 159-232 (255)
8 smart00545 JmjN Small domain f 55.0 7.5 0.00016 22.4 1.2 16 15-30 2-17 (42)
9 COG4342 Uncharacterized protei 54.4 7.8 0.00017 31.1 1.5 36 2-37 94-141 (291)
10 COG1232 HemY Protoporphyrinoge 43.1 25 0.00055 29.9 3.0 27 75-101 136-162 (444)
11 COG4090 Uncharacterized protei 42.4 23 0.00051 25.7 2.3 37 13-49 95-135 (154)
12 KOG3262 H/ACA small nucleolar 41.5 18 0.00038 27.8 1.6 38 5-42 71-113 (215)
13 PF06043 Reo_P9: Reovirus P9-l 37.1 27 0.00057 28.5 2.1 29 13-41 251-279 (333)
14 PF12631 GTPase_Cys_C: Catalyt 34.6 26 0.00057 22.0 1.4 31 65-96 38-72 (73)
15 PF12426 DUF3674: RNA dependen 33.6 25 0.00053 20.3 1.0 17 5-21 20-36 (41)
16 PF00990 GGDEF: GGDEF domain; 33.3 1E+02 0.0022 20.2 4.3 28 79-106 45-72 (161)
17 PF07288 DUF1447: Protein of u 32.2 68 0.0015 20.6 3.0 27 19-45 26-52 (69)
18 PF14205 Cys_rich_KTR: Cystein 30.5 21 0.00046 21.9 0.5 9 13-21 25-33 (55)
19 PF08427 DUF1741: Domain of un 30.3 1.1E+02 0.0023 24.0 4.4 34 18-52 181-215 (237)
20 PF08704 GCD14: tRNA methyltra 29.6 61 0.0013 25.4 3.0 33 17-49 144-179 (247)
21 PF07466 DUF1517: Protein of u 27.9 92 0.002 25.0 3.8 37 14-51 233-269 (289)
22 PF07742 BTG: BTG family; Int 27.5 1.3E+02 0.0029 20.8 4.2 36 64-99 8-45 (118)
23 TIGR02021 BchM-ChlM magnesium 27.5 52 0.0011 24.2 2.2 29 15-44 180-208 (219)
24 PF09921 DUF2153: Uncharacteri 27.2 70 0.0015 22.8 2.7 40 65-104 39-82 (126)
25 cd08788 CARD_NOD2_2_CARD15 Cas 26.8 27 0.00059 23.1 0.5 28 2-30 26-53 (81)
26 PF07340 Herpes_IE1: Cytomegal 26.4 40 0.00087 28.4 1.5 17 15-31 362-378 (392)
27 TIGR03762 exosort_arch archaea 24.8 85 0.0019 25.2 3.1 29 67-96 226-254 (274)
28 PF02095 Extensin_1: Extensin- 24.6 29 0.00062 14.2 0.2 8 16-23 2-9 (10)
29 PF08221 HTH_9: RNA polymerase 23.8 61 0.0013 19.7 1.7 20 77-96 4-26 (62)
30 PF11888 DUF3408: Protein of u 23.7 1E+02 0.0022 21.6 3.1 22 74-95 109-132 (136)
31 PF03721 UDPG_MGDP_dh_N: UDP-g 22.6 56 0.0012 24.1 1.6 34 5-38 31-67 (185)
32 PF02901 PFL: Pyruvate formate 22.4 48 0.001 29.5 1.4 75 21-116 558-639 (648)
33 PF11115 DUF2623: Protein of u 22.2 42 0.0009 22.8 0.7 13 81-93 2-14 (95)
34 COG1458 Predicted DNA-binding 21.9 3.4E+02 0.0073 21.1 5.7 34 13-46 45-82 (221)
35 smart00828 PKS_MT Methyltransf 21.9 1.1E+02 0.0024 22.3 3.1 29 15-44 118-146 (224)
36 KOG0362 Chaperonin complex com 21.8 96 0.0021 27.2 3.0 57 63-119 33-107 (537)
37 PF09630 DUF2024: Domain of un 21.7 75 0.0016 21.0 1.8 17 22-38 64-80 (81)
38 PRK11705 cyclopropane fatty ac 21.2 4.7E+02 0.01 21.5 9.8 25 18-44 290-314 (383)
39 PF09584 Phageshock_PspD: Phag 20.8 87 0.0019 19.9 1.9 20 73-97 46-65 (66)
40 KOG2025 Chromosome condensatio 20.6 22 0.00048 32.5 -1.1 88 10-101 679-768 (892)
41 PF09066 B2-adapt-app_C: Beta2 20.3 1.1E+02 0.0023 20.4 2.5 30 12-41 28-57 (114)
No 1
>PLN02668 indole-3-acetate carboxyl methyltransferase
Probab=100.00 E-value=1.1e-36 Score=249.16 Aligned_cols=116 Identities=28% Similarity=0.438 Sum_probs=106.6
Q ss_pred CCCCcccccCCccccCccCCCHHHHHHHHHhcCceeEeeeeeeeccCCCCcccccccCCcchhhHHHHHHHHHHHHHHHH
Q 036335 1 MQGLIEEEKLDSFNAPYYGPCPEELKMEIQKEGSFIIDRLDHFEIDWDGGVEELTSTMSLPLARGQRVAKTIRAVVESMF 80 (122)
Q Consensus 1 ~eGlI~eeklDsFNiP~Y~ps~eEv~~~Ie~eGsF~I~~le~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~RAv~Epll 80 (122)
+||+|++||+||||+|+|+||++||+++|+++|||+|+++|+++.+|+++++. ..|....|+++|+++||++||||
T Consensus 268 ~eGlI~eek~dsFniP~Y~ps~eEv~~~Ie~~gsF~I~~le~~~~~~~~~~~~----~~d~~~~g~~~a~~~RA~~E~ll 343 (386)
T PLN02668 268 QEGLVTSEKRDSFNIPVYAPSLQDFKEVVEANGSFAIDKLEVFKGGSPLVVNE----PDDAAEVGRAMANSCRSVAGVLV 343 (386)
T ss_pred HcCCCCHHHHhcccCcccCCCHHHHHHHHhhcCCEEeeeeEEeeccCcccccC----cccHHHHHHHHHHHHHHHHHHHH
Confidence 48999999999999999999999999999999999999999999999875432 24556789999999999999999
Q ss_pred HHhhhhhhHHHHHHHHHHHHhhhhhh--cCCCeEEEEEEEee
Q 036335 81 ELHFGRGIMDLLFTRYAQIVDGYLSK--NSANYINLVISIIK 120 (122)
Q Consensus 81 ~~HFG~~i~deLF~r~~~~v~~~~~~--~~~~~~~i~vsL~r 120 (122)
++|||++|||+||+||+++++++++. ++.+++++++||.-
T Consensus 344 ~~HFG~~i~D~lF~r~~~~v~~~~~~~~~~~~~~~~~~sL~~ 385 (386)
T PLN02668 344 DAHIGEELSNELFLRVERRATSHAKELLEKLQFFHIVASLSF 385 (386)
T ss_pred HHHcCHHHHHHHHHHHHHHHHHHHHhhcccCceEEEEEEEec
Confidence 99999999999999999999999988 88899999999963
No 2
>PF03492 Methyltransf_7: SAM dependent carboxyl methyltransferase; InterPro: IPR005299 This family of plant methyltransferases contains enzymes that act on a variety of substrates including salicylic acid, jasmonic acid and 7-Methylxanthine. Caffeine is synthesized through sequential three-step methylation of xanthine derivatives at positions 7-N, 3-N, and 1-N. The protein 7-methylxanthine methyltransferase (designated as CaMXMT) catalyses the second step to produce theobromine [].; GO: 0008168 methyltransferase activity; PDB: 2EFJ_A 1M6E_X 2EG5_C 3B5I_B.
Probab=100.00 E-value=1.7e-36 Score=244.08 Aligned_cols=120 Identities=43% Similarity=0.690 Sum_probs=98.2
Q ss_pred CCCCcccccCCccccCccCCCHHHHHHHHHhcCceeEeeeeeeeccCCCCcccccccCCcchhhHHHHHHHHHHHHHHHH
Q 036335 1 MQGLIEEEKLDSFNAPYYGPCPEELKMEIQKEGSFIIDRLDHFEIDWDGGVEELTSTMSLPLARGQRVAKTIRAVVESMF 80 (122)
Q Consensus 1 ~eGlI~eeklDsFNiP~Y~ps~eEv~~~Ie~eGsF~I~~le~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~RAv~Epll 80 (122)
+||+|++||+|+||+|+|+||++||+++|+++|||+|++||+++.+|.....+ .....|...+|+.+|+++||++||+|
T Consensus 212 ~eGlI~~ek~dsfniP~Y~ps~eEv~~~I~~~gsF~I~~le~~~~~~~~~~~~-~~~~~d~~~~~~~~~~~iRA~~e~~l 290 (334)
T PF03492_consen 212 AEGLISEEKVDSFNIPIYFPSPEEVRAIIEEEGSFEIEKLELFEQPWWSVPDD-ESWKEDAKEYARNVANYIRAVFEPLL 290 (334)
T ss_dssp HTTSS-HCCCCTG--SBB---HHHHHHHHHHHTSEEEEEEEEEEEETCCTCTT-T-STTTHHCHHHHHHHHHHHHHHHHH
T ss_pred HcCCcCHHHhhceeCCccCCCHHHHHHHHhcCCCEEEEEEEEEeecccccchh-hhcccchhhhHHHHHHhHHHHHHHHH
Confidence 48999999999999999999999999999999999999999999664432211 11234567899999999999999999
Q ss_pred HHhhhhhhHHHHHHHHHHHHhhhhhhcC---CCeEEEEEEEeec
Q 036335 81 ELHFGRGIMDLLFTRYAQIVDGYLSKNS---ANYINLVISIIKK 121 (122)
Q Consensus 81 ~~HFG~~i~deLF~r~~~~v~~~~~~~~---~~~~~i~vsL~rk 121 (122)
++|||++|||+||+||+++++++++..+ .+++++++||+||
T Consensus 291 ~~hfG~ei~D~LF~r~~~~v~~~~~~~~~~~~~~~~i~~~L~Rk 334 (334)
T PF03492_consen 291 KAHFGEEIMDELFERYAKKVAEHLEKEKSRNMKFVNIVVSLTRK 334 (334)
T ss_dssp HHHH-HHHHHHHHHHHHHHHHHHHHHTHTT-BEEEEEEEEEEE-
T ss_pred HHHhChHHHHHHHHHHHHHHHHHHHHhhccCCCcEEEEEEEeeC
Confidence 9999999999999999999999997655 8899999999998
No 3
>PRK01683 trans-aconitate 2-methyltransferase; Provisional
Probab=78.37 E-value=23 Score=26.76 Aligned_cols=90 Identities=9% Similarity=0.103 Sum_probs=57.0
Q ss_pred CccCCCHHHHHHHHHhcCceeEeeeeeeeccCCCCcccccccCCcchhhHHHHHHHHHHH-HHHHHHHhhhhhhHHHHHH
Q 036335 16 PYYGPCPEELKMEIQKEGSFIIDRLDHFEIDWDGGVEELTSTMSLPLARGQRVAKTIRAV-VESMFELHFGRGIMDLLFT 94 (122)
Q Consensus 16 P~Y~ps~eEv~~~Ie~eGsF~I~~le~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~RAv-~Epll~~HFG~~i~deLF~ 94 (122)
+.+.|+++++...+.+.| |.++..+.. +...- .+...+..++++. +.|++ ++++.+-.+++-+
T Consensus 162 ~~~~~~~~~~~~~l~~~g-~~v~~~~~~---~~~~~-----------~~~~~~~~~~~~~~~~~~~-~~l~~~~~~~f~~ 225 (258)
T PRK01683 162 RAPLPPPHAYYDALAPAA-CRVDIWHTT---YYHPM-----------PSAQAIVEWVKGTGLRPFL-DPLTESEQAAFLA 225 (258)
T ss_pred CcCCCCHHHHHHHHHhCC-Cceeeeeee---eeeec-----------CCchhhhhhhhhccHHHHH-hhCCHHHHHHHHH
Confidence 346689999999999999 445444432 11100 1233444566653 46665 7899888999999
Q ss_pred HHHHHHhhhhh-hcC----CCeEEEEEEEeec
Q 036335 95 RYAQIVDGYLS-KNS----ANYINLVISIIKK 121 (122)
Q Consensus 95 r~~~~v~~~~~-~~~----~~~~~i~vsL~rk 121 (122)
.|...+.+... ... ..+.-++++-+|+
T Consensus 226 ~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ 257 (258)
T PRK01683 226 AYLARIAEAYPLQADGKVLLAFPRLFIVARRK 257 (258)
T ss_pred HHHHHHHHHCCCCCCCcEEcccceEEEEEEec
Confidence 99998887753 221 3344556666664
No 4
>PHA00457 inhibitor of host bacterial RNA polymerase
Probab=70.98 E-value=5.5 Score=24.92 Aligned_cols=33 Identities=24% Similarity=0.406 Sum_probs=27.2
Q ss_pred cCCccccCccCCCHHHHHHHHH---hcCceeEeeee
Q 036335 9 KLDSFNAPYYGPCPEELKMEIQ---KEGSFIIDRLD 41 (122)
Q Consensus 9 klDsFNiP~Y~ps~eEv~~~Ie---~eGsF~I~~le 41 (122)
.-.||-+|+|+-|.+|-.+.-+ .+--|.+.|+.
T Consensus 23 ~~~sfEVPV~A~SLeeA~e~AE~~Y~~aGf~VtRiR 58 (63)
T PHA00457 23 SGQSFEVPVYAKSLEEATELAEWQYVPAGFVVTRIR 58 (63)
T ss_pred cCceEEeeeecccHHHHHHHHHHhhhccCcEEEEec
Confidence 4579999999999999888877 46778888874
No 5
>PF14904 FAM86: Family of unknown function
Probab=66.85 E-value=8.2 Score=26.50 Aligned_cols=31 Identities=19% Similarity=0.322 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHh--hhhhhHHHHHHHHHHH
Q 036335 69 AKTIRAVVESMFELH--FGRGIMDLLFTRYAQI 99 (122)
Q Consensus 69 a~~~RAv~Epll~~H--FG~~i~deLF~r~~~~ 99 (122)
.+|.|+++.-+|..| .|.++.|+|++.|+..
T Consensus 67 ~kY~~~FLk~lI~k~Ea~~~EplDeLYealae~ 99 (100)
T PF14904_consen 67 VKYRRCFLKELIKKHEAVHCEPLDELYEALAEV 99 (100)
T ss_pred hhHHHHHHHHHHHHHHHhcCCcHHHHHHHHHhh
Confidence 678999999999876 5789999999999864
No 6
>PF02375 JmjN: jmjN domain; InterPro: IPR003349 Jumonji protein is required for neural tube formation in mice [].There is evidence of domain swapping within the jumonji family of transcription factors []. This domain is often associated with JmjC (see IPR003347 from INTERPRO).; PDB: 2XML_A 2W2I_C 3DXT_A 3DXU_A 2OX0_B 2OQ6_B 2WWJ_A 2Q8D_A 3PDQ_A 2YBK_A ....
Probab=64.24 E-value=2.5 Score=23.35 Aligned_cols=15 Identities=40% Similarity=0.594 Sum_probs=8.3
Q ss_pred CccCCCHHHHHHHHH
Q 036335 16 PYYGPCPEELKMEIQ 30 (122)
Q Consensus 16 P~Y~ps~eEv~~~Ie 30 (122)
|+|.||.+|.+..+.
T Consensus 1 Pvf~Pt~eEF~dp~~ 15 (34)
T PF02375_consen 1 PVFYPTMEEFKDPIK 15 (34)
T ss_dssp EEE---HHHHS-HHH
T ss_pred CcccCCHHHHhCHHH
Confidence 788899999876654
No 7
>PRK14103 trans-aconitate 2-methyltransferase; Provisional
Probab=57.01 E-value=84 Score=23.81 Aligned_cols=73 Identities=8% Similarity=0.045 Sum_probs=47.3
Q ss_pred CccCCCHHHHHHHHHhcCceeEeeeeeeeccCCCCcccccccCCcchhhHHHHHHHHHHH-HHHHHHHhhhhhhHHHHHH
Q 036335 16 PYYGPCPEELKMEIQKEGSFIIDRLDHFEIDWDGGVEELTSTMSLPLARGQRVAKTIRAV-VESMFELHFGRGIMDLLFT 94 (122)
Q Consensus 16 P~Y~ps~eEv~~~Ie~eGsF~I~~le~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~RAv-~Epll~~HFG~~i~deLF~ 94 (122)
+.+.++++++.+++++.| |++...+..... +.. ....+...+++. +.|++. .++++-.+++-+
T Consensus 159 ~~~~~~~~~~~~~l~~aG-f~v~~~~~~~~~--~~~------------~~~~~~~~~~~~~~~~~~~-~l~~~~~~~~~~ 222 (255)
T PRK14103 159 GAVVQTPAGYAELLTDAG-CKVDAWETTYVH--QLT------------GEDPVLDWITGTALRPVRE-RLSDDSWEQFRA 222 (255)
T ss_pred CcCCCCHHHHHHHHHhCC-CeEEEEeeeeee--eCC------------Cchhhhhhhhccchhhhhh-hCCHHHHHHHHH
Confidence 445679999999999999 887666542211 101 111233334432 345554 889888899999
Q ss_pred HHHHHHhhhh
Q 036335 95 RYAQIVDGYL 104 (122)
Q Consensus 95 r~~~~v~~~~ 104 (122)
.+.+.+.+.+
T Consensus 223 ~~~~~l~~~~ 232 (255)
T PRK14103 223 ELIPLLREAY 232 (255)
T ss_pred HHHHHHHHHC
Confidence 9998888775
No 8
>smart00545 JmjN Small domain found in the jumonji family of transcription factors. To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).
Probab=55.04 E-value=7.5 Score=22.41 Aligned_cols=16 Identities=31% Similarity=0.480 Sum_probs=13.4
Q ss_pred cCccCCCHHHHHHHHH
Q 036335 15 APYYGPCPEELKMEIQ 30 (122)
Q Consensus 15 iP~Y~ps~eEv~~~Ie 30 (122)
+|+|.||.+|.+.-+.
T Consensus 2 iPvf~Pt~eEF~Dp~~ 17 (42)
T smart00545 2 IPVFYPTMEEFKDPLA 17 (42)
T ss_pred CCeEcCCHHHHHCHHH
Confidence 6999999999887665
No 9
>COG4342 Uncharacterized protein conserved in archaea [Function unknown]
Probab=54.39 E-value=7.8 Score=31.07 Aligned_cols=36 Identities=36% Similarity=0.491 Sum_probs=28.6
Q ss_pred CCCcccc---------cCCccc-cCccCCCHHHHH--HHHHhcCceeE
Q 036335 2 QGLIEEE---------KLDSFN-APYYGPCPEELK--MEIQKEGSFII 37 (122)
Q Consensus 2 eGlI~ee---------klDsFN-iP~Y~ps~eEv~--~~Ie~eGsF~I 37 (122)
+|+|+++ |++-+| .-.|.||.+|++ ..+.++-++.+
T Consensus 94 rgiise~~Ae~lrk~lk~k~~~g~dlyIp~de~ir~~~~l~r~~~e~~ 141 (291)
T COG4342 94 RGIISEEFAEKLRKPLKVKKSNGVDLYIPSDEEIRATEELAREYSERA 141 (291)
T ss_pred cccccHHHHHHHHHHhccCcCCCcceecCCHHHHHHHHHHHHHhcchH
Confidence 5788876 678899 999999999999 77776655543
No 10
>COG1232 HemY Protoporphyrinogen oxidase [Coenzyme metabolism]
Probab=43.13 E-value=25 Score=29.93 Aligned_cols=27 Identities=11% Similarity=0.247 Sum_probs=22.7
Q ss_pred HHHHHHHHhhhhhhHHHHHHHHHHHHh
Q 036335 75 VVESMFELHFGRGIMDLLFTRYAQIVD 101 (122)
Q Consensus 75 v~Epll~~HFG~~i~deLF~r~~~~v~ 101 (122)
-++.++..|||+++++.+|+.|...+-
T Consensus 136 sv~~f~r~~fG~ev~~~~~~pll~giy 162 (444)
T COG1232 136 SVGEFIRRRFGEEVVERFIEPLLEGIY 162 (444)
T ss_pred CHHHHHHHHHhHHHHHHHHHHHhhchh
Confidence 367789999999999999999877554
No 11
>COG4090 Uncharacterized protein conserved in archaea [Function unknown]
Probab=42.36 E-value=23 Score=25.73 Aligned_cols=37 Identities=24% Similarity=0.496 Sum_probs=25.8
Q ss_pred cccCccCCCHHHHHHHHHhcCceeEee---eeeee-ccCCC
Q 036335 13 FNAPYYGPCPEELKMEIQKEGSFIIDR---LDHFE-IDWDG 49 (122)
Q Consensus 13 FNiP~Y~ps~eEv~~~Ie~eGsF~I~~---le~~~-~~~~~ 49 (122)
--+|.|+.+++.+|+++++.|.=.+-- |-+|+ ..|+.
T Consensus 95 LaMP~~gv~~d~~kel~ee~~~kkliGvCfm~mF~ragW~e 135 (154)
T COG4090 95 LAMPKIGVTPDDAKELLEELGNKKLIGVCFMNMFERAGWDE 135 (154)
T ss_pred cccCcCCCCHHHHHHHHHhcCCCceEEeeHHHHHHHcCcch
Confidence 458999999999999999766543322 22454 34765
No 12
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=41.55 E-value=18 Score=27.78 Aligned_cols=38 Identities=26% Similarity=0.356 Sum_probs=29.6
Q ss_pred cccccCCccccCccCCCHHHHHHHHH-----hcCceeEeeeee
Q 036335 5 IEEEKLDSFNAPYYGPCPEELKMEIQ-----KEGSFIIDRLDH 42 (122)
Q Consensus 5 I~eeklDsFNiP~Y~ps~eEv~~~Ie-----~eGsF~I~~le~ 42 (122)
.+..|+--||.|+|.-+.+.|=.+=| .+-+|+|.-.+-
T Consensus 71 ~~~~kIPyfNAPIylenk~qIGKVDEIfG~i~d~~fsIK~~dg 113 (215)
T KOG3262|consen 71 LTNKKIPYFNAPIYLENKEQIGKVDEIFGPINDVHFSIKPSDG 113 (215)
T ss_pred eccccCCCCCCceeecchhhhcchhhhcccccccEEEEecCCC
Confidence 35678889999999999888765554 567888877773
No 13
>PF06043 Reo_P9: Reovirus P9-like family; InterPro: IPR009268 These proteins of unknown function are found in Rice black streaked dwarf virus (RBSDV) and other viruses.; PDB: 3VJJ_B.
Probab=37.13 E-value=27 Score=28.49 Aligned_cols=29 Identities=24% Similarity=0.305 Sum_probs=15.9
Q ss_pred cccCccCCCHHHHHHHHHhcCceeEeeee
Q 036335 13 FNAPYYGPCPEELKMEIQKEGSFIIDRLD 41 (122)
Q Consensus 13 FNiP~Y~ps~eEv~~~Ie~eGsF~I~~le 41 (122)
|-+|--.-.+.++++.|.++|.|++-...
T Consensus 251 ~~L~s~is~p~~i~q~i~k~GLFk~i~s~ 279 (333)
T PF06043_consen 251 FQLSSLISVPNSILQRIAKDGLFKIITSA 279 (333)
T ss_dssp HH-SS-----HHHHHHHHHS-SEEE----
T ss_pred HHhhhhcCChHHHHHHHHhcCceEEEeec
Confidence 44666677899999999999999985544
No 14
>PF12631 GTPase_Cys_C: Catalytic cysteine-containing C-terminus of GTPase, MnmE; PDB: 1XZQ_A 1XZP_A 2GJ8_D 3GEH_A 3GEI_B 3GEE_A.
Probab=34.64 E-value=26 Score=21.97 Aligned_cols=31 Identities=29% Similarity=0.470 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhh----hhhHHHHHHHH
Q 036335 65 GQRVAKTIRAVVESMFELHFG----RGIMDLLFTRY 96 (122)
Q Consensus 65 ~~~~a~~~RAv~Epll~~HFG----~~i~deLF~r~ 96 (122)
...+|-.+|.+.+.| ..-.| ++|+|.+|++|
T Consensus 38 ~dl~a~~L~~A~~~L-~~ItG~~~~ediLd~IFs~F 72 (73)
T PF12631_consen 38 LDLVAEDLREALESL-GEITGEVVTEDILDNIFSNF 72 (73)
T ss_dssp HHHHHHHHHHHHHHH-HHHCTSS--HHHHHHHHCTS
T ss_pred HHHHHHHHHHHHHHH-HHHhCCCChHHHHHHHHHhh
Confidence 445666677766653 33334 78999999876
No 15
>PF12426 DUF3674: RNA dependent RNA polymerase; InterPro: IPR024378 This domain is found in the RNA-directed RNA polymerase. It is located towards the N terminus and is approximately 40 amino acids in length. There is a conserved MFNLKF sequence motif. There are two completely conserved residues (E and P) that may be functionally important.
Probab=33.60 E-value=25 Score=20.31 Aligned_cols=17 Identities=24% Similarity=0.333 Sum_probs=13.2
Q ss_pred cccccCCccccCccCCC
Q 036335 5 IEEEKLDSFNAPYYGPC 21 (122)
Q Consensus 5 I~eeklDsFNiP~Y~ps 21 (122)
|.-.|...|+||-|-|-
T Consensus 20 i~~~k~~~y~IP~Y~~~ 36 (41)
T PF12426_consen 20 IGGPKTQPYYIPDYRGI 36 (41)
T ss_pred eCCcccccccCCCCCCc
Confidence 45568889999999764
No 16
>PF00990 GGDEF: GGDEF domain; InterPro: IPR000160 This domain appears to be ubiquitous in bacteria and is often linked to a regulatory domain, such as a phosphorylation receiver or oxygen sensing domain. Its function is to synthesize cyclic di-GMP, which is used as an intracellular signalling molecule in a wide variety of bacteria [,]. Enzymatic activity can be strongly influenced by the adjacent domains. Processes regulated by this domain include exopolysaccharide synthesis, biofilm formation, motility and cell differentiation. Structural studies of PleD from Caulobacter crescentus show that this domain forms a five-stranded beta sheet surrounded by helices, similar to the catalytic core of adenylate cyclase [].; PDB: 3IGN_A 3BRE_B 3EZU_A 3ICL_B 3PJX_A 3PJW_A 3HVW_A 3HVA_B 3I5C_B 3I5B_B ....
Probab=33.27 E-value=1e+02 Score=20.25 Aligned_cols=28 Identities=14% Similarity=0.248 Sum_probs=22.1
Q ss_pred HHHHhhhhhhHHHHHHHHHHHHhhhhhh
Q 036335 79 MFELHFGRGIMDLLFTRYAQIVDGYLSK 106 (122)
Q Consensus 79 ll~~HFG~~i~deLF~r~~~~v~~~~~~ 106 (122)
-|..++|....|++..+++..+...+..
T Consensus 45 ~l~~~~G~~~~~~~l~~i~~~L~~~~~~ 72 (161)
T PF00990_consen 45 ELNEKYGYEVGDEILRQIAKRLKKQLRE 72 (161)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHCCT
T ss_pred cccccccccccccccccccccccccccc
Confidence 4567888888888888888888877644
No 17
>PF07288 DUF1447: Protein of unknown function (DUF1447); InterPro: IPR009907 This family consists of several bacterial proteins of around 70 residues in length. The function of this family is unknown.
Probab=32.16 E-value=68 Score=20.56 Aligned_cols=27 Identities=7% Similarity=0.165 Sum_probs=24.1
Q ss_pred CCCHHHHHHHHHhcCceeEeeeeeeec
Q 036335 19 GPCPEELKMEIQKEGSFIIDRLDHFEI 45 (122)
Q Consensus 19 ~ps~eEv~~~Ie~eGsF~I~~le~~~~ 45 (122)
+.|..|+|..|+.+-.|+|+-++.+.-
T Consensus 26 a~s~~evR~~ve~~t~yNIEfI~~L~~ 52 (69)
T PF07288_consen 26 AESEVEVRKLVEDNTPYNIEFIQPLSG 52 (69)
T ss_pred cCCHHHHHHHHHhCCCcCEEEEeeccc
Confidence 568999999999999999999998753
No 18
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=30.49 E-value=21 Score=21.86 Aligned_cols=9 Identities=44% Similarity=0.608 Sum_probs=7.2
Q ss_pred cccCccCCC
Q 036335 13 FNAPYYGPC 21 (122)
Q Consensus 13 FNiP~Y~ps 21 (122)
=|.|+|+|-
T Consensus 25 kNfPlyCpK 33 (55)
T PF14205_consen 25 KNFPLYCPK 33 (55)
T ss_pred ccccccCCC
Confidence 388999984
No 19
>PF08427 DUF1741: Domain of unknown function (DUF1741); InterPro: IPR013636 This is a eukaryotic domain of unknown function.
Probab=30.31 E-value=1.1e+02 Score=24.04 Aligned_cols=34 Identities=15% Similarity=0.335 Sum_probs=24.9
Q ss_pred cCCCHHHHHHHHHhc-CceeEeeeeeeeccCCCCcc
Q 036335 18 YGPCPEELKMEIQKE-GSFIIDRLDHFEIDWDGGVE 52 (122)
Q Consensus 18 Y~ps~eEv~~~Ie~e-GsF~I~~le~~~~~~~~~~~ 52 (122)
=.+|++||-++|+++ .+-+|.--|.++ .|..+.+
T Consensus 181 ~~lt~~qV~~VIk~~YdtLsl~~~e~Ld-~~ery~E 215 (237)
T PF08427_consen 181 SNLTPEQVLEVIKQNYDTLSLKLQEGLD-QWERYRE 215 (237)
T ss_pred CCCCHHHHHHHHHhCccceecchhhccc-ccccccc
Confidence 358999999999987 567777666664 3666544
No 20
>PF08704 GCD14: tRNA methyltransferase complex GCD14 subunit; InterPro: IPR014816 GCD14 is a subunit of the tRNA methyltransferase complex and is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA []. ; GO: 0016429 tRNA (adenine-N1-)-methyltransferase activity, 0030488 tRNA methylation; PDB: 2YVL_C 1YB2_A 2B25_B 1O54_A 2PWY_B 1I9G_A 3LGA_B 3LHD_C 3MB5_A.
Probab=29.63 E-value=61 Score=25.35 Aligned_cols=33 Identities=18% Similarity=0.555 Sum_probs=26.8
Q ss_pred ccCCCHHHHHHHHH---hcCceeEeeeeeeeccCCC
Q 036335 17 YYGPCPEELKMEIQ---KEGSFIIDRLDHFEIDWDG 49 (122)
Q Consensus 17 ~Y~ps~eEv~~~Ie---~eGsF~I~~le~~~~~~~~ 49 (122)
.|.||.++|...++ +.|--.|+-+|++...|..
T Consensus 144 ~fsP~ieQv~~~~~~L~~~gf~~i~~~Evl~R~~~v 179 (247)
T PF08704_consen 144 CFSPCIEQVQKTVEALREHGFTDIETVEVLLREWEV 179 (247)
T ss_dssp EEESSHHHHHHHHHHHHHTTEEEEEEEEEEEEEEEE
T ss_pred EECCCHHHHHHHHHHHHHCCCeeeEEEEEEeeEEEE
Confidence 58999999998776 5787778888888777765
No 21
>PF07466 DUF1517: Protein of unknown function (DUF1517); InterPro: IPR010903 This family consists of several hypothetical glycine rich plant and bacterial proteins of around 300 residues in length. The function of this family is unknown.
Probab=27.87 E-value=92 Score=24.98 Aligned_cols=37 Identities=30% Similarity=0.409 Sum_probs=33.7
Q ss_pred ccCccCCCHHHHHHHHHhcCceeEeeeeeeeccCCCCc
Q 036335 14 NAPYYGPCPEELKMEIQKEGSFIIDRLDHFEIDWDGGV 51 (122)
Q Consensus 14 NiP~Y~ps~eEv~~~Ie~eGsF~I~~le~~~~~~~~~~ 51 (122)
.+|- ..+.+++|+.+++=|+..-++|..+++.|.|..
T Consensus 233 ~lp~-~~~~~~l~~aL~~l~~~~~~~l~a~evlWtP~~ 269 (289)
T PF07466_consen 233 KLPT-INSAEDLREALRKLGSISSDRLLAVEVLWTPQA 269 (289)
T ss_pred CCCC-CCCHHHHHHHHHHHhCCChhheeeEEEEECCCC
Confidence 7888 889999999999999999999999999999943
No 22
>PF07742 BTG: BTG family; InterPro: IPR002087 Anti-proliferative proteins have been shown to include mammalian and avian protein BTG1 (which appears to be involved in negative regulation of cell proliferation) and rat/mouse NGF-inducible protein PC3/TIS21 (BTG2) [, , ]. These proteins have from 158 to 363 amino acid residues, that are highly similar and include 3 conserved cysteine residues. BTG2 seems to have a signal sequence; while the other proteins may lack such a domain. The sequence of the N-terminal half of these proteins is well conserved.; PDB: 3DJU_B 3E9V_A 2Z15_D 2D5R_B 3DJN_B.
Probab=27.54 E-value=1.3e+02 Score=20.83 Aligned_cols=36 Identities=14% Similarity=0.132 Sum_probs=27.3
Q ss_pred hHHHHHHHHHHH--HHHHHHHhhhhhhHHHHHHHHHHH
Q 036335 64 RGQRVAKTIRAV--VESMFELHFGRGIMDLLFTRYAQI 99 (122)
Q Consensus 64 ~~~~~a~~~RAv--~Epll~~HFG~~i~deLF~r~~~~ 99 (122)
....+++++++- +-+=-...|++.+.+.|.+||+.+
T Consensus 8 av~Fl~~~l~~~~~l~~~~~~~F~~~L~~~L~~ry~~H 45 (118)
T PF07742_consen 8 AVNFLTRLLYNKGRLPRRQVDRFAEELENLLCERYKGH 45 (118)
T ss_dssp HHHHHHHHHHHHC-B-HHHHHHHHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhCC
Confidence 445677777777 777777889999999999999644
No 23
>TIGR02021 BchM-ChlM magnesium protoporphyrin O-methyltransferase. This model represents the S-adenosylmethionine-dependent O-methyltransferase responsible for methylation of magnesium protoporphyrin IX. This step is essentiasl for the biosynthesis of both chlorophyll and bacteriochlorophyll. This model encompasses two closely related clades, from cyanobacteria (and plants) where it is called ChlM and other photosynthetic bacteria where it is known as BchM.
Probab=27.47 E-value=52 Score=24.23 Aligned_cols=29 Identities=17% Similarity=0.134 Sum_probs=24.4
Q ss_pred cCccCCCHHHHHHHHHhcCceeEeeeeeee
Q 036335 15 APYYGPCPEELKMEIQKEGSFIIDRLDHFE 44 (122)
Q Consensus 15 iP~Y~ps~eEv~~~Ie~eGsF~I~~le~~~ 44 (122)
.+.|.++++|+++++++.| |.|.+.+.+.
T Consensus 180 ~~~~~~~~~~~~~~l~~~G-f~v~~~~~~~ 208 (219)
T TIGR02021 180 TSAYLHPMTDLERALGELG-WKIVREGLVS 208 (219)
T ss_pred cceEEecHHHHHHHHHHcC-ceeeeeeccc
Confidence 3567889999999999999 9998888664
No 24
>PF09921 DUF2153: Uncharacterized protein conserved in archaea (DUF2153); InterPro: IPR014450 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=27.17 E-value=70 Score=22.82 Aligned_cols=40 Identities=20% Similarity=0.405 Sum_probs=31.2
Q ss_pred HHHHHHHHHHH----HHHHHHHhhhhhhHHHHHHHHHHHHhhhh
Q 036335 65 GQRVAKTIRAV----VESMFELHFGRGIMDLLFTRYAQIVDGYL 104 (122)
Q Consensus 65 ~~~~a~~~RAv----~Epll~~HFG~~i~deLF~r~~~~v~~~~ 104 (122)
-+.+++.+.|+ -.|+|.+|...+.+.++..+.-+.+.+.+
T Consensus 39 fqhm~RTlKaFd~WLqdP~ItshMPreML~dv~~~~~~il~~ll 82 (126)
T PF09921_consen 39 FQHMMRTLKAFDQWLQDPMITSHMPREMLEDVWETLREILEQLL 82 (126)
T ss_pred HHHHHHHHHHHHHHHcCchhHhcCCHHHHHHHHHHHHHHHHHHH
Confidence 34667777775 46999999999999999888877776654
No 25
>cd08788 CARD_NOD2_2_CARD15 Caspase activation and recruitment domain of NOD2, repeat 2. Caspase activation and recruitment domain (CARD) similar to that found in human NOD2 (CARD15), repeat 2. NOD2 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD2, as well as NOD1, the N-terminal effector domain is a CARD. NOD2 contains two N-terminal CARD repeats. Mutations in NOD2 have been associated with Crohns disease and Blau syndrome. Nod2-CARDs have been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are pr
Probab=26.77 E-value=27 Score=23.05 Aligned_cols=28 Identities=14% Similarity=0.401 Sum_probs=22.3
Q ss_pred CCCcccccCCccccCccCCCHHHHHHHHH
Q 036335 2 QGLIEEEKLDSFNAPYYGPCPEELKMEIQ 30 (122)
Q Consensus 2 eGlI~eeklDsFNiP~Y~ps~eEv~~~Ie 30 (122)
.|.|+++.-|+--.|.|.||.. .|.+|.
T Consensus 26 ~G~is~~Ecd~Ir~p~~T~sqq-ARrLLD 53 (81)
T cd08788 26 RGFFSSYDCDEIRLPIFTPSQQ-ARRLLD 53 (81)
T ss_pred cCCccHhhcchhhcCCCChHHH-HHHHHH
Confidence 4899999999999999999854 454443
No 26
>PF07340 Herpes_IE1: Cytomegalovirus IE1 protein; InterPro: IPR010855 Expression from a human cytomegalovirus early promoter (E1.7) has been shown to be activated in trans by the IE2 gene product. Although the IE1 gene product alone had no effect on this early viral promoter, maximal early promoter activity was detected when both IE1 and IE2 gene products were present []. The IE1 protein from cytomegalovirus is also known as UL123.; GO: 0050792 regulation of viral reproduction, 0042025 host cell nucleus
Probab=26.44 E-value=40 Score=28.36 Aligned_cols=17 Identities=24% Similarity=0.227 Sum_probs=14.5
Q ss_pred cCccCCCHHHHHHHHHh
Q 036335 15 APYYGPCPEELKMEIQK 31 (122)
Q Consensus 15 iP~Y~ps~eEv~~~Ie~ 31 (122)
+=+|.||++|+|+|++.
T Consensus 362 ~k~~~~Sv~elR~Ia~d 378 (392)
T PF07340_consen 362 MKVCTPSVEELREIAND 378 (392)
T ss_pred ccccCCCHHHHHHHhcc
Confidence 34799999999999975
No 27
>TIGR03762 exosort_arch archaeal exosortase. Members of this family are archaeal homologs to bacterial PEP-CTERM-sorting protein exosortase (TIGR02602). Members of this family are found in species with an archaeal variant sorting motif, PEF-CTERM (TIGR03024). Members are found in the thermoacidophilic Aciduliprofundum boonei and the mesophilic psychromethanogens Methanosarcina mazei and Methanococcoides burtonii.
Probab=24.77 E-value=85 Score=25.24 Aligned_cols=29 Identities=21% Similarity=0.340 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhHHHHHHHH
Q 036335 67 RVAKTIRAVVESMFELHFGRGIMDLLFTRY 96 (122)
Q Consensus 67 ~~a~~~RAv~Epll~~HFG~~i~deLF~r~ 96 (122)
.++|.+|...=.++..|+|.+.++ .|.-+
T Consensus 226 ~vaN~lRV~iL~lL~~~~g~Eaae-f~H~~ 254 (274)
T TIGR03762 226 YIVNLIRVTILYLIAYYYGMEIMQ-LVHTH 254 (274)
T ss_pred HHHHHHHHHHHHHHHHhcCHHHHH-HHHcc
Confidence 779999999999999999999887 66544
No 28
>PF02095 Extensin_1: Extensin-like protein repeat; InterPro: IPR003883 Extensins are plant cell-wall proteins; they can account for up to 20% of the dry weight of the cell wall. They are highly-glycosylated, possibly reflecting their interactions with cell-wall carbohydrates. Amongst their functions is cell wall strengthening in response to mechanical stress (e.g., during attack by pests, plant-bending in the wind, etc.). This repeat occurs within extensin-like proteins.; GO: 0005199 structural constituent of cell wall
Probab=24.55 E-value=29 Score=14.17 Aligned_cols=8 Identities=50% Similarity=0.812 Sum_probs=5.4
Q ss_pred CccCCCHH
Q 036335 16 PYYGPCPE 23 (122)
Q Consensus 16 P~Y~ps~e 23 (122)
|+|-|..+
T Consensus 2 P~ykPpve 9 (10)
T PF02095_consen 2 PVYKPPVE 9 (10)
T ss_pred CccCCCcc
Confidence 77877653
No 29
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=23.84 E-value=61 Score=19.74 Aligned_cols=20 Identities=30% Similarity=0.556 Sum_probs=12.6
Q ss_pred HHHHHHhhhh---hhHHHHHHHH
Q 036335 77 ESMFELHFGR---GIMDLLFTRY 96 (122)
Q Consensus 77 Epll~~HFG~---~i~deLF~r~ 96 (122)
.-++..|||+ .|.+-|+.+-
T Consensus 4 ~~ii~~~fG~~~~~V~~~Ll~~G 26 (62)
T PF08221_consen 4 TLIIEEHFGEIVAKVGEVLLSRG 26 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHC-
T ss_pred HHHHHHHcChHHHHHHHHHHHcC
Confidence 3578888985 4666666543
No 30
>PF11888 DUF3408: Protein of unknown function (DUF3408); InterPro: IPR021823 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 128 to 160 amino acids in length.
Probab=23.69 E-value=1e+02 Score=21.64 Aligned_cols=22 Identities=14% Similarity=0.472 Sum_probs=13.5
Q ss_pred HHHHHHHHHhhh--hhhHHHHHHH
Q 036335 74 AVVESMFELHFG--RGIMDLLFTR 95 (122)
Q Consensus 74 Av~Epll~~HFG--~~i~deLF~r 95 (122)
+.++-+|..||- .+.+++||.+
T Consensus 109 ~yidNIL~~Hle~~~eeI~~l~~~ 132 (136)
T PF11888_consen 109 GYIDNILRHHLEEYREEINELYEK 132 (136)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344557777776 3566666654
No 31
>PF03721 UDPG_MGDP_dh_N: UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain; InterPro: IPR001732 The UDP-glucose/GDP-mannose dehydrogenases are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [, ]. The enzymes have a wide range of functions. In plants UDP-glucose dehydrogenase, 1.1.1.22 from EC, is an important enzyme in the synthesis of hemicellulose and pectin [], which are the components of newly formed cell walls; while in zebrafish UDP-glucose dehydrogenase is required for cardiac valve formation []. In Xanthomonas campestris, a plant pathogen, UDP-glucose dehydrogenase is required for virulence []. GDP-mannose dehydrogenase, 1.1.1.132 from EC, catalyses the formation of GDP-mannuronic acid, which is the monomeric unit from which the exopolysaccharide alginate is formed. Alginate is secreted by a number of bacteria, which include Pseudomonas aeruginosa and Azotobacter vinelandii. In P. aeruginosa, alginate is believed to play an important role in the bacteria's resistance to antibiotics and the host immune response [], while in A. vinelandii it is essential for the encystment process []. This entry represents the N-terminal NAD(+)-binding domain. Structural studies indicate that this domain forms an alpha-beta structure containing the six-stranded parallel beta sheet characteristic of the dinucleotide binding Rossman fold [, ].; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 3OJO_A 3OJL_A 1MV8_B 1MUU_A 1MFZ_C 3GG2_D 1DLJ_A 1DLI_A 3G79_B 2Y0E_D ....
Probab=22.60 E-value=56 Score=24.08 Aligned_cols=34 Identities=35% Similarity=0.549 Sum_probs=26.0
Q ss_pred cccccCCccc---cCccCCCHHHHHHHHHhcCceeEe
Q 036335 5 IEEEKLDSFN---APYYGPCPEELKMEIQKEGSFIID 38 (122)
Q Consensus 5 I~eeklDsFN---iP~Y~ps~eEv~~~Ie~eGsF~I~ 38 (122)
+++++++..| .|+|-|-.+|+-+-..++|.|...
T Consensus 31 ~~~~~v~~l~~g~~p~~E~~l~~ll~~~~~~~~l~~t 67 (185)
T PF03721_consen 31 IDEEKVEALNNGELPIYEPGLDELLKENVSAGRLRAT 67 (185)
T ss_dssp S-HHHHHHHHTTSSSS-CTTHHHHHHHHHHTTSEEEE
T ss_pred CChHHHHHHhhccccccccchhhhhccccccccchhh
Confidence 4567777777 999999999998888878887774
No 32
>PF02901 PFL: Pyruvate formate lyase; InterPro: IPR004184 Pyruvate formate-lyase 2.3.1.54 from EC (also known as formate C-acetyltransferase) is an enzyme which converts acetyl-CoA and formate to CoA and pyruvate. Acetyl-CoA + formate = CoA + pyruvate In Escherichia coli, it uses a radical mechanism to reversibly cleave the C1-C2 bond of pyruvate using the Gly 734 radical and two cysteine residues (Cys 418, Cys 419) [].; GO: 0008861 formate C-acetyltransferase activity, 0006006 glucose metabolic process, 0005737 cytoplasm; PDB: 1QHM_A 1MZO_B 3PFL_B 1H18_A 2PFL_A 1CM5_B 1H16_A 1H17_A 1R9E_A 1R8W_A ....
Probab=22.42 E-value=48 Score=29.47 Aligned_cols=75 Identities=16% Similarity=0.343 Sum_probs=40.2
Q ss_pred CHHHHHHHHHhcCceeEeee-eeeeccCCCCcccccccCCcchhhHHHHHHHHHHHHHHHHHHhhhh------hhHHHHH
Q 036335 21 CPEELKMEIQKEGSFIIDRL-DHFEIDWDGGVEELTSTMSLPLARGQRVAKTIRAVVESMFELHFGR------GIMDLLF 93 (122)
Q Consensus 21 s~eEv~~~Ie~eGsF~I~~l-e~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~RAv~Epll~~HFG~------~i~deLF 93 (122)
|.-=||.+|=.++.+|++.| +.+..+|..++. +|..+-- ..+||. +|..+++
T Consensus 558 SLaAIKklVFd~k~~T~~eL~~Al~~nfeg~E~-------------------lr~~l~~--~PKyGNDd~~aD~ia~~v~ 616 (648)
T PF02901_consen 558 SLAAIKKLVFDEKKYTMEELLDALKANFEGYEE-------------------LRQMLLN--APKYGNDDDYADEIAREVY 616 (648)
T ss_dssp HHHHHHHHTTTSCSSEHHHHHHHHHTTTTTEHH-------------------HHHHHHH--S--TTSS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCccHHHHHHHHHhcCCchHH-------------------HHHHccC--CCCCCCCChHHHHHHHHHH
Confidence 44557777777888988884 456667765211 4444444 679993 4455555
Q ss_pred HHHHHHHhhhhhhcCCCeEEEEE
Q 036335 94 TRYAQIVDGYLSKNSANYINLVI 116 (122)
Q Consensus 94 ~r~~~~v~~~~~~~~~~~~~i~v 116 (122)
+.|...+.++.......+..-+.
T Consensus 617 ~~~~~~~~~~~~~rg~~~~~~~~ 639 (648)
T PF02901_consen 617 DFFCDEVEKYKNYRGGQYTPGLY 639 (648)
T ss_dssp HHHHHHHTTSB-TTSSEEEEEE-
T ss_pred HHHHHHHhcCCCCCCCeeeeeEE
Confidence 55555555444333444443333
No 33
>PF11115 DUF2623: Protein of unknown function (DUF2623); InterPro: IPR022574 This family is conserved in the Enterobacteriaceae family. Several members are named as YghW. The function is not known.
Probab=22.22 E-value=42 Score=22.77 Aligned_cols=13 Identities=46% Similarity=0.774 Sum_probs=10.6
Q ss_pred HHhhhhhhHHHHH
Q 036335 81 ELHFGRGIMDLLF 93 (122)
Q Consensus 81 ~~HFG~~i~deLF 93 (122)
..|||..+|+-|=
T Consensus 2 ~NHFG~GlmaGl~ 14 (95)
T PF11115_consen 2 KNHFGKGLMAGLK 14 (95)
T ss_pred CcchhhHHHhhhc
Confidence 4799999998774
No 34
>COG1458 Predicted DNA-binding protein containing PIN domain [General function prediction only]
Probab=21.94 E-value=3.4e+02 Score=21.10 Aligned_cols=34 Identities=18% Similarity=0.391 Sum_probs=23.2
Q ss_pred cccCccCC-CH-HHHHHHHHhcCce--eEeeeeeeecc
Q 036335 13 FNAPYYGP-CP-EELKMEIQKEGSF--IIDRLDHFEID 46 (122)
Q Consensus 13 FNiP~Y~p-s~-eEv~~~Ie~eGsF--~I~~le~~~~~ 46 (122)
+|+..|.| |. .|++...+.|||= .+-+++++-+.
T Consensus 45 ~~iscyiPPsVY~El~~fm~r~gc~~e~~~ki~twivk 82 (221)
T COG1458 45 LGISCYIPPSVYRELMGFMERNGCPEEVIAKIETWIVK 82 (221)
T ss_pred cCeEEEeChHHHHHHHHHHHhCCCcHHHHHhhheeeEe
Confidence 34444554 33 7999999999997 56777766443
No 35
>smart00828 PKS_MT Methyltransferase in polyketide synthase (PKS) enzymes.
Probab=21.94 E-value=1.1e+02 Score=22.32 Aligned_cols=29 Identities=10% Similarity=-0.019 Sum_probs=23.6
Q ss_pred cCccCCCHHHHHHHHHhcCceeEeeeeeee
Q 036335 15 APYYGPCPEELKMEIQKEGSFIIDRLDHFE 44 (122)
Q Consensus 15 iP~Y~ps~eEv~~~Ie~eGsF~I~~le~~~ 44 (122)
++.|.|+.+++.+.+++.| |++.+.+.+.
T Consensus 118 ~~~~~~s~~~~~~~l~~~G-f~~~~~~~~~ 146 (224)
T smart00828 118 TTSYLVTREEWAELLARNN-LRVVEGVDAS 146 (224)
T ss_pred cccccCCHHHHHHHHHHCC-CeEEEeEECc
Confidence 6678999999999998876 8887777654
No 36
>KOG0362 consensus Chaperonin complex component, TCP-1 theta subunit (CCT8) [Posttranslational modification, protein turnover, chaperones]
Probab=21.81 E-value=96 Score=27.16 Aligned_cols=57 Identities=21% Similarity=0.236 Sum_probs=39.2
Q ss_pred hhHHHHHHHHHHHHHH-----HHHHhhh--------hhhHHHHHH--HHHHHHhhhh---hhcCCCeEEEEEEEe
Q 036335 63 ARGQRVAKTIRAVVES-----MFELHFG--------RGIMDLLFT--RYAQIVDGYL---SKNSANYINLVISII 119 (122)
Q Consensus 63 ~~~~~~a~~~RAv~Ep-----ll~~HFG--------~~i~deLF~--r~~~~v~~~~---~~~~~~~~~i~vsL~ 119 (122)
..-+..++.+|+.++| ||..|.| ..|+++|=- =.++.+...- +.+-...+|+||+|+
T Consensus 33 ~a~~ela~~~rs~yGpng~nK~vvnh~~k~~~TndaatIlrelev~HPaakllv~a~~~q~~~iGDgtnfvvvla 107 (537)
T KOG0362|consen 33 AAVRELANVIRSAYGPNGRNKMVVNHLGKTFVTNDAATILRELEVEHPAAKLLVEATQMQEEEIGDGTNFVVVLA 107 (537)
T ss_pred HHHHHHHHHHHhhcCCCCcceeeecccceEEEcCChHHHHHHhhccCcHHHHHHHHHHHHHHhhCCCceEeehhH
Confidence 3566889999999998 8999999 368887742 2233333332 335567788888874
No 37
>PF09630 DUF2024: Domain of unknown function (DUF2024); InterPro: IPR018592 This protein of 86 residues is expressed in bacteria. It consists of two alpha helices and four beta strands. Its function is unknown.; PDB: 2HFQ_A.
Probab=21.68 E-value=75 Score=20.96 Aligned_cols=17 Identities=41% Similarity=0.815 Sum_probs=13.8
Q ss_pred HHHHHHHHHhcCceeEe
Q 036335 22 PEELKMEIQKEGSFIID 38 (122)
Q Consensus 22 ~eEv~~~Ie~eGsF~I~ 38 (122)
++||++.|+++|-|.|.
T Consensus 64 ~~ev~~~I~~~Gy~I~~ 80 (81)
T PF09630_consen 64 PPEVEQAIKQQGYFIIK 80 (81)
T ss_dssp -HHHHHHHHHHSEEEE-
T ss_pred CHHHHHHHHHCCeEEEe
Confidence 57999999999998764
No 38
>PRK11705 cyclopropane fatty acyl phospholipid synthase; Provisional
Probab=21.18 E-value=4.7e+02 Score=21.50 Aligned_cols=25 Identities=16% Similarity=0.414 Sum_probs=19.7
Q ss_pred cCCCHHHHHHHHHhcCceeEeeeeeee
Q 036335 18 YGPCPEELKMEIQKEGSFIIDRLDHFE 44 (122)
Q Consensus 18 Y~ps~eEv~~~Ie~eGsF~I~~le~~~ 44 (122)
+.|+++++....+ +.|+|..++.+.
T Consensus 290 ~lps~~~i~~~~~--~~~~v~d~~~~~ 314 (383)
T PRK11705 290 CLPSVRQIAQASE--GLFVMEDWHNFG 314 (383)
T ss_pred cCCCHHHHHHHHH--CCcEEEEEecCh
Confidence 6899999999866 459988887653
No 39
>PF09584 Phageshock_PspD: Phage shock protein PspD (Phageshock_PspD); InterPro: IPR014321 Members of this entry are phage shock protein PspD, they are found in a minority of bacteria that carry the defining genes of the phage shock regulon (pspA, pspB, pspC, and pspF). It is found in Escherichia coli, Yersinia pestis, and closely related species, where it is part of the phage shock operon. It is known to be expressed but its function is unknown.
Probab=20.75 E-value=87 Score=19.88 Aligned_cols=20 Identities=25% Similarity=0.358 Sum_probs=12.2
Q ss_pred HHHHHHHHHHhhhhhhHHHHHHHHH
Q 036335 73 RAVVESMFELHFGRGIMDLLFTRYA 97 (122)
Q Consensus 73 RAv~Epll~~HFG~~i~deLF~r~~ 97 (122)
.=++||||.. .++.++.||.
T Consensus 46 a~~LEPllrr-----~~~~~~~r~~ 65 (66)
T PF09584_consen 46 ALALEPLLRR-----GLNKLSRRYA 65 (66)
T ss_pred HHHHHHHHHH-----HHHHHHHHhc
Confidence 3456777765 4556666664
No 40
>KOG2025 consensus Chromosome condensation complex Condensin, subunit G [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]
Probab=20.63 E-value=22 Score=32.49 Aligned_cols=88 Identities=18% Similarity=0.253 Sum_probs=39.3
Q ss_pred CCccccCccCCCHHHHHHHHHhcCceeEeeeeeeecc--CCCCcccccccCCcchhhHHHHHHHHHHHHHHHHHHhhhhh
Q 036335 10 LDSFNAPYYGPCPEELKMEIQKEGSFIIDRLDHFEID--WDGGVEELTSTMSLPLARGQRVAKTIRAVVESMFELHFGRG 87 (122)
Q Consensus 10 lDsFNiP~Y~ps~eEv~~~Ie~eGsF~I~~le~~~~~--~~~~~~~~~~~~~~~~~~~~~~a~~~RAv~Epll~~HFG~~ 87 (122)
+=-||+|+|+||..|. ..-|.=....+|...++ |++...............+..+....|.+-.-..+--+|..
T Consensus 679 ll~y~ipvy~fs~hen----~~r~~tl~~dle~s~lp~~~dlam~k~~l~~~~i~~~~~~lvd~tg~~~r~tq~~dd~d~ 754 (892)
T KOG2025|consen 679 LLFYNIPVYLFSEHEN----DQRGKTLVKDLERSELPRCWDLAMTKKILFCCSIVARKHGLVDSTGEVIRRTQEIDDGDP 754 (892)
T ss_pred HHHHHHhhhcchhhhH----HHhhhHHHHHHHHhhhhhhcchhhccccchHHHHHHHHhhhhhcccchhccccccccccH
Confidence 3458999999997776 22222222333333333 66522211000011112344444444444444444455554
Q ss_pred hHHHHHHHHHHHHh
Q 036335 88 IMDLLFTRYAQIVD 101 (122)
Q Consensus 88 i~deLF~r~~~~v~ 101 (122)
+....-.-.++.+.
T Consensus 755 i~~~vh~~lkk~I~ 768 (892)
T KOG2025|consen 755 ISQEVHCDLKKDIE 768 (892)
T ss_pred HHHHHHHHHHHHHH
Confidence 44444443333333
No 41
>PF09066 B2-adapt-app_C: Beta2-adaptin appendage, C-terminal sub-domain; InterPro: IPR015151 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. AP (adaptor protein) complexes are found in coated vesicles and clathrin-coated pits. AP complexes connect cargo proteins and lipids to clathrin at vesicle budding sites, as well as binding accessory proteins that regulate coat assembly and disassembly (such as AP180, epsins and auxilin). There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes []. AP2 associates with the plasma membrane and is responsible for endocytosis []. AP3 is responsible for protein trafficking to lysosomes and other related organelles []. AP4 is less well characterised. AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). For example, in AP1 these subunits are gamma-1-adaptin, beta-1-adaptin, mu-1 and sigma-1, while in AP2 they are alpha-adaptin, beta-2-adaptin, mu-2 and sigma-2. Each subunit has a specific function. Adaptins recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal ear (appendage) domains. Mu recognises tyrosine-based sorting signals within the cytoplasmic domains of transmembrane cargo proteins []. One function of clathrin and AP2 complex-mediated endocytosis is to regulate the number of GABA(A) receptors available at the cell surface []. This entry represents a subdomain of the appendage (ear) domain of beta-adaptin from AP clathrin adaptor complexes. This domain has a three-layer arrangement, alpha-beta-alpha, with a bifurcated antiparallel beta-sheet []. This domain is required for binding to clathrin, and its subsequent polymerisation. Furthermore, a hydrophobic patch present in the domain also binds to a subset of D-phi-F/W motif-containing proteins that are bound by the alpha-adaptin appendage domain (epsin, AP180, eps15) []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030131 clathrin adaptor complex; PDB: 1E42_B 2G30_A 2IV9_B 2IV8_A 3HS9_A 3H1Z_A.
Probab=20.27 E-value=1.1e+02 Score=20.37 Aligned_cols=30 Identities=20% Similarity=0.293 Sum_probs=20.5
Q ss_pred ccccCccCCCHHHHHHHHHhcCceeEeeee
Q 036335 12 SFNAPYYGPCPEELKMEIQKEGSFIIDRLD 41 (122)
Q Consensus 12 sFNiP~Y~ps~eEv~~~Ie~eGsF~I~~le 41 (122)
++.+|...++++.+.+..+.++-|+|-+=.
T Consensus 28 ~~~~~~~~~~~~~i~~~L~~~nI~~iA~~~ 57 (114)
T PF09066_consen 28 SIQLNASVPSPDAIEEKLQANNIFTIASGK 57 (114)
T ss_dssp EEEETT----HHHHHHHHHCTT-EEEEEEE
T ss_pred EEeccccCCcHHHHHHHHHHCCEEEEecCC
Confidence 455667789999999999999999996654
Done!