Query 020828
Match_columns 321
No_of_seqs 204 out of 475
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 05:28:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020828.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020828hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00719 Plus3 Short conserv 100.0 1.6E-33 3.5E-38 233.3 11.2 104 164-269 1-109 (109)
2 PF03126 Plus-3: Plus-3 domain 100.0 1.1E-31 2.3E-36 221.3 5.9 102 168-270 1-107 (108)
3 KOG2402 Paf1/RNA polymerase II 100.0 1.8E-29 3.8E-34 254.3 13.2 139 163-304 214-357 (525)
4 KOG1946 RNA polymerase I trans 100.0 3.7E-30 8.1E-35 239.4 5.9 135 39-175 96-240 (240)
5 COG5296 Transcription factor i 99.9 9.4E-25 2E-29 213.2 13.2 138 160-302 205-347 (521)
6 PF02201 SWIB: SWIB/MDM2 domai 99.9 2.3E-23 4.9E-28 162.6 2.5 70 42-117 7-76 (76)
7 smart00151 SWIB SWI complex, B 99.9 2.9E-22 6.3E-27 156.7 7.3 71 42-118 7-77 (77)
8 COG5531 SWIB-domain-containing 99.8 3.3E-19 7.1E-24 165.7 5.9 71 42-118 127-197 (237)
9 PRK14724 DNA topoisomerase III 99.7 2.1E-18 4.6E-23 187.0 7.2 70 42-117 918-987 (987)
10 PRK06319 DNA topoisomerase I/S 99.3 8.6E-13 1.9E-17 142.1 4.5 71 42-118 790-860 (860)
11 KOG2570 SWI/SNF transcription 99.2 3E-12 6.5E-17 126.7 0.7 145 42-196 211-371 (420)
12 KOG2522 Filamentous baseplate 78.3 2.9 6.3E-05 43.3 4.5 53 46-98 367-419 (560)
13 PF10281 Ish1: Putative stress 73.7 6.6 0.00014 26.6 3.9 37 38-74 1-38 (38)
14 PHA02696 hypothetical protein; 67.1 3.7 7.9E-05 32.3 1.7 23 247-269 40-62 (79)
15 PRK05350 acyl carrier protein; 65.6 6.9 0.00015 30.4 3.0 58 61-121 2-59 (82)
16 TIGR03759 conj_TIGR03759 integ 63.0 9.2 0.0002 35.6 3.8 66 256-321 14-87 (200)
17 PRK05828 acyl carrier protein; 55.7 22 0.00047 28.4 4.3 58 61-121 1-58 (84)
18 PRK12449 acyl carrier protein; 49.4 30 0.00066 26.3 4.2 58 61-121 1-58 (80)
19 CHL00124 acpP acyl carrier pro 43.0 26 0.00057 26.8 2.9 58 61-121 1-58 (82)
20 PF06627 DUF1153: Protein of u 33.8 24 0.00052 29.1 1.4 27 250-276 55-81 (90)
21 cd00454 Trunc_globin Truncated 33.1 76 0.0017 25.5 4.3 41 254-294 71-115 (116)
22 PTZ00171 acyl carrier protein; 32.8 53 0.0011 29.0 3.5 61 58-121 63-123 (148)
23 TIGR02530 flg_new flagellar op 28.1 60 0.0013 27.0 2.9 25 293-317 29-53 (96)
24 cd00238 ERp29c ERp29 and ERp38 27.0 59 0.0013 26.4 2.6 39 252-290 54-92 (93)
25 PF02037 SAP: SAP domain; Int 26.7 1.4E+02 0.0031 19.8 4.0 32 41-74 4-35 (35)
26 PF01152 Bac_globin: Bacterial 23.1 1.2E+02 0.0025 24.7 3.7 41 254-294 75-119 (120)
27 cd00238 ERp29c ERp29 and ERp38 22.9 96 0.0021 25.2 3.1 17 293-309 55-71 (93)
28 PF08349 DUF1722: Protein of u 22.5 2.6E+02 0.0057 23.2 5.8 57 257-313 27-83 (117)
29 PF00010 HLH: Helix-loop-helix 22.2 84 0.0018 22.3 2.4 21 56-76 33-53 (55)
No 1
>smart00719 Plus3 Short conserved domain in transcriptional regulators. Plus3 domains occur in the Saccharomyces cerevisiae Rtf1p protein, which interacts with Spt6p, and in parsley CIP, which interacts with the bZIP protein CPRF1.
Probab=100.00 E-value=1.6e-33 Score=233.33 Aligned_cols=104 Identities=48% Similarity=0.664 Sum_probs=96.2
Q ss_pred ccCccccceeeeeHHHHHHHhcCcccccccccccEEEEecCCCCCCCcCceeEEEEeeeeecCC---CCccccceeEEEe
Q 020828 164 AIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPG---TDDKSTEILLKVS 240 (321)
Q Consensus 164 ai~~~nI~~I~L~Rs~l~~l~~~P~~Fe~~VvGcFVRI~ig~~~~t~~~~YRL~qV~Gv~~~~~---~G~~~Td~~L~v~ 240 (321)
|++.+||++|||+|+.|++||+.| +|+++|+||||||+||++++++ ++||||||+||.++.+ .|+++||++|.+.
T Consensus 1 ~~~l~~l~~i~L~R~~l~~~~~~p-~Fe~~v~GcFVRv~ig~~~~~~-~~Yrl~qI~gv~~~~k~Y~~~~~~t~~~L~v~ 78 (109)
T smart00719 1 AIVFDNLNLLRLRRSLVEELLKPP-TFESKVVGCFVRVKIGPNDQKQ-PIYRLVQVTGVKEADKPYELGGKTTNVLLEVL 78 (109)
T ss_pred CCChHHhheEEEEHHHHHHHhcCC-chhHhceEeEEEEEECCCCCCC-CeEEEEEEeeEEecCcceecCCceeeEEEEEe
Confidence 568999999999999999999999 8999999999999999999987 8999999999999655 5789999999994
Q ss_pred C--CceeEEeeeecCCCCCHHHHHHHHHHHH
Q 020828 241 N--FVKDIRIATLSDDNFSEEECEDLRQRVK 269 (321)
Q Consensus 241 ~--~~k~~~i~~~Sd~~FTEeE~~r~~q~~~ 269 (321)
+ ..+.|+|++|||+||||+||++|++.|+
T Consensus 79 ~g~~~~~~~i~~iSn~~fte~E~~~w~~~~~ 109 (109)
T smart00719 79 NGDSEKVVQINFISNQDFTEEEFQRWKQAIK 109 (109)
T ss_pred cCCceEEEEEEEecCCCCCHHHHHHHHHHhC
Confidence 3 4579999999999999999999999984
No 2
>PF03126 Plus-3: Plus-3 domain; InterPro: IPR004343 The yeast Paf1 complex consists of Pfa1, Rtf1, Cdc73, Ctr9, and Leo1. The complex regulates histone H2B ubiquitination, histone H3 methylation, RNA polymerase II carboxy-terminal domain (CTD) Ser2 phosphorylation, and RNA 3' end processing. The conservation of Paf1 complex function in higher eukaryotes has been confirmed in human cells, Drosophila and Arabidopsis. The Plus3 domain spans the most conserved regions of the Rtf1 protein and is surrounded by regions of low complexity and coiled-coil propensity []. It contains only a limited number of highly conserved amino acids, among which are three positively charged residues that gave the Plus3 domain its name. The capacity to bind single-stranded DNA is at least one function of the Plus3 domain []. The plus-3 domain is about 90 residues in length and is often found associated with the GYF domain (IPR003169 from INTERPRO). The Plus3 domain structure consists of six alpha helices intervened by a sequence of six beta strands in a mixed alpha/beta topology. Beta strands 1, 2, 5, and 6 compose a four-stranded antiparallel beta sheet with a beta-hairpin insertion formed by strands 3 and 4. The N-terminal helices alpha1-alpha3 and C-terminal helix alpha6 pack together to form an alpha subdomain, while the beta strands and the small 3(10) helix alpha 4 form a beta subdomain. The two subdomains pack together to form a compact, globular protein [].; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent, 0016570 histone modification, 0005634 nucleus; PDB: 2BZE_A 3U1U_B 2DB9_A.
Probab=99.97 E-value=1.1e-31 Score=221.30 Aligned_cols=102 Identities=35% Similarity=0.492 Sum_probs=86.1
Q ss_pred cccceeeeeHHHHHHHhcCcccccccccccEEEEecCCCCCCCcCceeEEEEeeeeecCC---CCccccceeEEEe-C-C
Q 020828 168 DNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPG---TDDKSTEILLKVS-N-F 242 (321)
Q Consensus 168 ~nI~~I~L~Rs~l~~l~~~P~~Fe~~VvGcFVRI~ig~~~~t~~~~YRL~qV~Gv~~~~~---~G~~~Td~~L~v~-~-~ 242 (321)
+||++|||+||+|++||++| +|+++|+||||||+||++++++.++||||||+||.++++ .|++.||++|.+. | .
T Consensus 1 e~i~~i~l~Rs~l~~~~~~P-~Fe~~v~G~fVRv~ig~~~~~~~~~Yrl~qI~~v~~~~k~Y~~~~~~t~~~L~l~~g~~ 79 (108)
T PF03126_consen 1 EDIKRIRLSRSQLEKWLFKP-FFEDAVVGCFVRVNIGPNDYTQNPVYRLCQIVGVKEGKKPYKLGSKKTNKYLVLRHGNS 79 (108)
T ss_dssp HHHHHTBE-HHHHHHHTTST-THHHHHTT-EEEEEEETTSSS-E--EEEEEEEEEEEEEEEEEETTEEEEEEEEEEETTE
T ss_pred CchHeEEEEHHHHHHHHcCC-ChhHheeEEEEEEEecCCCCCCceeEEEEEEEEEecccccEecCCeEEEEEEEEEECCc
Confidence 58999999999999999999 899999999999999999998877899999999999984 5899999999995 4 4
Q ss_pred ceeEEeeeecCCCCCHHHHHHHHHHHHh
Q 020828 243 VKDIRIATLSDDNFSEEECEDLRQRVKD 270 (321)
Q Consensus 243 ~k~~~i~~~Sd~~FTEeE~~r~~q~~~~ 270 (321)
.+.|+|++|||++|||+||++|++.|++
T Consensus 80 ~r~~~i~~vSn~~~te~E~~~w~~~~~~ 107 (108)
T PF03126_consen 80 ERDFPIDMVSNSPFTEEEFERWKQSCEK 107 (108)
T ss_dssp EEEEEGGGBBSS---HHHHHHHHHHH--
T ss_pred eeEEEeEeeECCCCCHHHHHHHHHHhcc
Confidence 4799999999999999999999999986
No 3
>KOG2402 consensus Paf1/RNA polymerase II complex, RTF1 component (involved in regulation of TATA box-binding protein) [Transcription]
Probab=99.96 E-value=1.8e-29 Score=254.28 Aligned_cols=139 Identities=22% Similarity=0.267 Sum_probs=127.5
Q ss_pred cccCccccceeeeeHHHHHHHhcCcccccccccccEEEEecCCCCCCCcCceeEEEEeeeeecCC---CCccccceeEEE
Q 020828 163 AAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPG---TDDKSTEILLKV 239 (321)
Q Consensus 163 aai~~~nI~~I~L~Rs~l~~l~~~P~~Fe~~VvGcFVRI~ig~~~~t~~~~YRL~qV~Gv~~~~~---~G~~~Td~~L~v 239 (321)
...+..++++++|+|+.|+.||+.| +|+++|+||||||+||..+ ++++||||+|+||.++.. .|.+.||.||.+
T Consensus 214 ~v~~~~dln~~rlsR~~vak~~~~P-~Fe~~V~gCfvRv~ig~~~--~~p~YRv~~I~gV~es~k~Y~l~~~~Tnk~l~~ 290 (525)
T KOG2402|consen 214 RVPSISDLNALRLSRHKVAKWLFSP-FFESTVTGCFVRVGIGGEG--SKPVYRVAEIVGVLESDKPYKLEGVKTNKYLRV 290 (525)
T ss_pred CCCCHHHHHHHHhhHHHHHHHHhhh-HHHHHhhhheEEeeecCcC--CCCceeEEEEeeecccCccccccceeecceeee
Confidence 3448899999999999999999999 9999999999999999994 468999999999999777 479999999999
Q ss_pred -eC-CceeEEeeeecCCCCCHHHHHHHHHHHHhCCCCCCcHHHHHHHHHHHHHHHhccchHHHHHHH
Q 020828 240 -SN-FVKDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITKHWLVRELALL 304 (321)
Q Consensus 240 -~~-~~k~~~i~~~Sd~~FTEeE~~r~~q~~~~~~~~~PTv~dl~eKa~~i~~~i~~~w~e~El~rL 304 (321)
+| ..++|.|.+|||++|||+||++|+..|....+.+||++.|.+|..+|.+++++.+.++++..+
T Consensus 291 ~~G~s~r~f~m~~iSn~~f~e~Efq~w~~~~~~s~~~~PT~~~i~~K~~~i~~a~~~~~sd~~v~~~ 357 (525)
T KOG2402|consen 291 RHGRSERVFRMNFISNGEFTEEEFQDWLRACKNSHGIMPTVDLISRKKLDIVKALNYRLSDKEVDQM 357 (525)
T ss_pred ecCcchhhcchhhhcCCcccHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHhcCccCcccHHHH
Confidence 56 336999999999999999999999999999999999999999999999999999988888443
No 4
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]
Probab=99.96 E-value=3.7e-30 Score=239.45 Aligned_cols=135 Identities=35% Similarity=0.526 Sum_probs=100.8
Q ss_pred cCCCCHHHHHHHhhcCCCC-CCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhccc
Q 020828 39 DGWGSIPLIEFLQSLGKDT-TQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYA 117 (321)
Q Consensus 39 ~~w~S~eL~~fl~~~g~~~-~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~ 117 (321)
.+|||..|..|+.+|++++ +++|||++|+++||+|||+||||||.||+.|+||++|++|||+++|+||+|++||++||.
T Consensus 96 ~~~g~~kl~~ls~~L~~~~G~~~lsR~~vvk~iw~YIke~nLqDP~nkr~IlCDekL~~iF~~k~v~~fem~KLL~~H~~ 175 (240)
T KOG1946|consen 96 ASWGSTKLIPLSPSLARFVGTSELSRTDVVKKIWAYIKEHNLQDPKNKREILCDEKLKSIFGKKRVGMFEMLKLLTKHFL 175 (240)
T ss_pred cCcCcccccccCHHHHhhcccccccHHHHHHHHHHHHHHhccCCccccCeeeeHHHHHHHhccCccceeeHHHHHHHhcc
Confidence 3499888888888888877 999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCC--------C-cccchhhhccccCchhhhccccccccccccCCcccccccCccccceeee
Q 020828 118 ENQFESDD--------D-FLFSSDEENNLFSSEKQKSRKVPLKKLCLETPKSCWAAIVPDNIKLVYL 175 (321)
Q Consensus 118 ~~~~~s~d--------~-~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aai~~~nI~~I~L 175 (321)
++++...- + ..+.++++.+...+...+.++...+. .-.++..||++..++++++|+
T Consensus 176 ~~~d~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~e~~~k~~~~~--~~~~~~~~a~~~~~~~~l~~~ 240 (240)
T KOG1946|consen 176 KNQDMVGTDLKQGEETETKEFKEEEDKSQDPCLSEKEAKETKKV--VKKPRGTFAAIVSDNIKLLYL 240 (240)
T ss_pred CccccccchhhcCccccccccccccccccccchhhhhhhhhhhc--ccccccchhhhhccccccccC
Confidence 98864311 1 11111222222211112222222111 122233999999999999986
No 5
>COG5296 Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]
Probab=99.92 E-value=9.4e-25 Score=213.16 Aligned_cols=138 Identities=22% Similarity=0.287 Sum_probs=125.2
Q ss_pred ccccccCccccceeeeeHHHHHHHhcCcccccccccccEEEEecCCCCCCCcCceeEEEEeeeeecCC---CCcccccee
Q 020828 160 SCWAAIVPDNIKLVYLKRSLVQDLLKDSETFECKVVGSFVRVKSDPNDYLQKNSHQLLQVIGTKKVPG---TDDKSTEIL 236 (321)
Q Consensus 160 ~~~aai~~~nI~~I~L~Rs~l~~l~~~P~~Fe~~VvGcFVRI~ig~~~~t~~~~YRL~qV~Gv~~~~~---~G~~~Td~~ 236 (321)
+.||. .-|+|.++|+|+.++++|++| +|++.|+|||+||+||..+ |+-+||||+|.++..... .|++.||.|
T Consensus 205 d~~a~--l~Dfn~~rvgR~~VA~~~f~P-~Fed~v~Gcf~Rv~Ig~R~--g~~vyRiv~V~~~~~~~kpy~~~~v~Tn~y 279 (521)
T COG5296 205 DDFAE--LYDFNQCRVGRDMVARNVFKP-IFEDEVIGCFTRVRIGERG--GYLVYRIVGVGKGSTYSKPYGRKEVKTNRY 279 (521)
T ss_pred chhhh--hhhhhhhhhhHHHHHHHhccc-chhhhhcceeeEEEecccC--CeeEEEEEEeccceeccccccccceeeeee
Confidence 56665 468999999999999999999 7999999999999999443 457999999999999665 479999999
Q ss_pred EEEe-CCc-eeEEeeeecCCCCCHHHHHHHHHHHHhCCCCCCcHHHHHHHHHHHHHHHhccchHHHHH
Q 020828 237 LKVS-NFV-KDIRIATLSDDNFSEEECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITKHWLVRELA 302 (321)
Q Consensus 237 L~v~-~~~-k~~~i~~~Sd~~FTEeE~~r~~q~~~~~~~~~PTv~dl~eKa~~i~~~i~~~w~e~El~ 302 (321)
|.|+ |-. |+|+|..+||+||.++||+||...++.|.+.+|++.-|.+|...|-..+++..+++|+.
T Consensus 280 l~v~~Gr~~kvF~in~~Sn~pf~~~eyQr~~r~~~~~kl~~PS~~~v~~k~~~l~d~~~~~LSdkeis 347 (521)
T COG5296 280 LDVSTGRTYKVFRINNISNSPFLREEYQRVWRSFKVGKLSMPSIAKVKEKYDKLVDTMGRRLSDKEIS 347 (521)
T ss_pred EeeecCcceeeeEeecccCCcccHHHHHHHHHHHhccccccchHHHHHHHHHHHHHHhCCcCchhHHH
Confidence 9995 544 59999999999999999999999999999999999999999999999999999999983
No 6
>PF02201 SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SWI/SNF family of complexes, which are conserved from yeast to humans, are ATP-dependent chromatin-remodelling proteins that facilitate transcription activation []. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors). The BAF60 family have at least three members: BAF60a, which is ubiquitous, BAF60b and BAF60c, which are expressed in muscle and pancreatic tissues, respectively. BAF60b is present in alternative forms of the SWI/SNF complex, including complex B (SWIB), which lacks BAF60a. The SWIB domain is a conserved region found within the BAF60b proteins [], and can be found fused to the C terminus of DNA topoisomerase in Chlamydia. MDM2 is an oncoprotein that acts as a cellular inhibitor of the p53 tumour suppressor by binding to the transactivation domain of p53 and suppressing its ability to activate transcription []. p53 acts in response to DNA damage, inducing cell cycle arrest and apoptosis. Inactivation of p53 is a common occurrence in neoplastic transformations. The core of MDM2 folds into an open bundle of four helices, which is capped by two small 3-stranded beta-sheets. It consists of a duplication of two structural repeats. MDM2 has a deep hydrophobic cleft on which the p53 alpha-helix binds; p53 residues involved in transactivation are buried deep within the cleft of MDM2, thereby concealing the p53 transactivation domain. The SWIB and MDM2 domains are homologous and share a common fold.; GO: 0005515 protein binding; PDB: 1V31_A 3FE7_A 3JZQ_B 3EQY_B 2VYR_A 3JZO_A 3DAB_E 3LBJ_E 3FEA_A 3FDO_A ....
Probab=99.87 E-value=2.3e-23 Score=162.56 Aligned_cols=70 Identities=36% Similarity=0.511 Sum_probs=65.5
Q ss_pred CCHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhccc
Q 020828 42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYA 117 (321)
Q Consensus 42 ~S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~ 117 (321)
+|++|++|+| ..++||++|++.||+|||+||||||+||+.|+||++|+.|||+++|++|+|+++|.+|+.
T Consensus 7 ls~~L~~~lg------~~~~sr~~v~~~lw~YIk~~~L~dp~~k~~I~cD~~L~~lf~~~~v~~~~i~~~l~~hl~ 76 (76)
T PF02201_consen 7 LSPELAEFLG------EDELSRSEVVKRLWQYIKENNLQDPKDKRIIICDEKLKKLFGKDSVNFFEIPKLLKPHLI 76 (76)
T ss_dssp HHHHHHHHTT-------SCEEHHHHHHHHHHHHHHTTSBESSSTTEEE-TTSHHHHHHTSECSEEETTHHHHHHHE
T ss_pred CCHHHHHHhC------CCCCCHHHHHHHHHHHHHHhcCCCcccCceEecCHHHHHHhCCCeecHhhHHHHHHHhcC
Confidence 5899999998 467999999999999999999999999999999999999999999999999999999984
No 7
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=99.87 E-value=2.9e-22 Score=156.69 Aligned_cols=71 Identities=23% Similarity=0.420 Sum_probs=68.3
Q ss_pred CCHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhcccc
Q 020828 42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAE 118 (321)
Q Consensus 42 ~S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~~ 118 (321)
.|++|++|+| .+++||++|++.||+|||+||||||.||+.|+||+.|+.+||+++|.+++|+++|.+|+.+
T Consensus 7 ls~~L~~~lg------~~~~tr~ev~~~lw~YIk~n~L~d~~~k~~i~~D~~L~~l~~~~~v~~~~~~~ll~~Hl~~ 77 (77)
T smart00151 7 LSPELAKVLG------APEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIFGKDRMDMFEMNKLLTPHLIK 77 (77)
T ss_pred CCHHHHHHhC------CCcCcHHHHHHHHHHHHHHhcccCCccCCEEecCHHHHHHHCcCeecHHHHHHHHHHHcCC
Confidence 6999999998 4899999999999999999999999999999999999999999999999999999999863
No 8
>COG5531 SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics]
Probab=99.77 E-value=3.3e-19 Score=165.68 Aligned_cols=71 Identities=18% Similarity=0.275 Sum_probs=69.2
Q ss_pred CCHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhcccc
Q 020828 42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAE 118 (321)
Q Consensus 42 ~S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~~ 118 (321)
+|+.|+.||| ..++||+|||+.||+|||+||||||+|||.|+||++|+.|||.+.+.||+|+++|.+|+.+
T Consensus 127 lS~~La~ilG------~~~~tr~~~v~~lw~YIk~h~lq~~~nkr~I~~D~~L~~v~g~~p~~mf~~~k~l~~hl~~ 197 (237)
T COG5531 127 LSPKLAAILG------LEPGTRPEAVKKLWKYIKKHNLQDPNNKRLILCDSKLKKVLGSDPIDMFELTKPLSPHLIK 197 (237)
T ss_pred cCHHHHHHhC------CCCCCccHHHHHHHHHHHHhcCCCccccceecccHHHHHHhCCCchhhhhhhcccccceec
Confidence 7999999998 5899999999999999999999999999999999999999998899999999999999997
No 9
>PRK14724 DNA topoisomerase III; Provisional
Probab=99.74 E-value=2.1e-18 Score=187.04 Aligned_cols=70 Identities=20% Similarity=0.399 Sum_probs=67.8
Q ss_pred CCHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhccc
Q 020828 42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYA 117 (321)
Q Consensus 42 ~S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~ 117 (321)
+|++|++||| ..++||++|++.||+|||+||||||.|||.|+||++|+.|||+++|.||+|+++|.+|+.
T Consensus 918 ls~~La~~lg------~~~~~r~~v~~~lW~YIK~~~Lqdp~~k~~i~cD~~L~~vfg~~~~~~~~~~~~l~~hl~ 987 (987)
T PRK14724 918 PSAALAAVIG------AEPVARPEVIKKLWDYIKANNLQDPADKRAINADAKLRPVFGKDQVTMFELAGIVGKHLS 987 (987)
T ss_pred CCHHHHHHhC------CCcCCHHHHHHHHHHHHHHccCCCcccCCeeccchHHHHHhCCCcccHHHHHHHHHHhcC
Confidence 7999999998 579999999999999999999999999999999999999999999999999999999983
No 10
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=99.32 E-value=8.6e-13 Score=142.06 Aligned_cols=71 Identities=20% Similarity=0.332 Sum_probs=67.6
Q ss_pred CCHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhcccc
Q 020828 42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAE 118 (321)
Q Consensus 42 ~S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~~ 118 (321)
.|++|+.|+| +.+++|.++++.||+|||+|+||||.+|+.|+||++|+++||++++.||.|+++|+.|+.+
T Consensus 790 ~S~~La~~~g------~~~~sr~~~~~~lw~yIk~~~lqdp~~Kr~i~~d~kl~kvf~~~~~~~~~~~k~l~~hl~~ 860 (860)
T PRK06319 790 PSPALAAMIG------AEPVGRGEATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVIGPDPIDMFQLSKKLSQHLIK 860 (860)
T ss_pred cccccccccC------cCccCchHHHHHHHHHHHHhcccCccccccCCCchhhhhhhCcCccchhhhHHHHHhhhcC
Confidence 6999999987 5899999999999999999999999999999999999999999999999999999999864
No 11
>KOG2570 consensus SWI/SNF transcription activation complex subunit [Chromatin structure and dynamics; Transcription]
Probab=99.20 E-value=3e-12 Score=126.68 Aligned_cols=145 Identities=17% Similarity=0.165 Sum_probs=104.1
Q ss_pred CCHHHHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhccccCCC
Q 020828 42 GSIPLIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQF 121 (321)
Q Consensus 42 ~S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~~~~~ 121 (321)
+||-|+..|| -..=+|++++..||.|||-|+||||.++..|.||.-|+.+||++++.+.+++.+|.+|+.+.+|
T Consensus 211 lsp~La~lLG------i~t~Trp~iI~alWqYIk~n~Lqd~~e~~~incD~~l~qif~~~rl~F~elp~~l~~lL~P~dP 284 (420)
T KOG2570|consen 211 LSPRLANLLG------IHTGTRPDIVTALWQYIKTNKLQDPEDSDFINCDKALEQIFGVDRLKFPELPQLLNPLLSPPDP 284 (420)
T ss_pred cCHHHHHHhh------hccCcchHHHHHHHHHHHHhccCCcccchhhcchHHHHHhhcccccccccchhhhhhccCCCCC
Confidence 8999999998 3666899999999999999999999999999999999999999999999999999999998887
Q ss_pred CC-CCCcccch--------hhhccccC-chhhhccccccccccccCCcccccc------cCccccceeeeeHHHHHHHhc
Q 020828 122 ES-DDDFLFSS--------DEENNLFS-SEKQKSRKVPLKKLCLETPKSCWAA------IVPDNIKLVYLKRSLVQDLLK 185 (321)
Q Consensus 122 ~s-~d~~~~~s--------~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~aa------i~~~nI~~I~L~Rs~l~~l~~ 185 (321)
+- ++.|..|. +|+++-+. |.+..-+.- +.......+-+| -..+.|+...-+|.+|.+|..
T Consensus 285 Ivi~h~I~v~~~~~~~tacyDIdV~v~~p~~~q~~nf----l~~~~~~~eI~alD~kI~~li~~ine~~~rr~Ff~~Fs~ 360 (420)
T KOG2570|consen 285 IVIDHTISVDGNDTKVTACYDIDVEVEDPRKSQMSNF----LASTESQKEIAALDRKITELIQQINESKERRDFFLEFSK 360 (420)
T ss_pred eeecceeccCCCcccceeEEeeeeccCCccchhhhhh----hcchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 53 33343332 22222111 111100000 000001111111 134678889999999999999
Q ss_pred Ccccccccccc
Q 020828 186 DSETFECKVVG 196 (321)
Q Consensus 186 ~P~~Fe~~VvG 196 (321)
+|..|-...+-
T Consensus 361 dPvefin~wi~ 371 (420)
T KOG2570|consen 361 DPVEFINEWIE 371 (420)
T ss_pred CHHHHHHHHHH
Confidence 99778766553
No 12
>KOG2522 consensus Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=78.31 E-value=2.9 Score=43.33 Aligned_cols=53 Identities=17% Similarity=0.364 Sum_probs=44.2
Q ss_pred HHHHHhhcCCCCCCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhh
Q 020828 46 LIEFLQSLGKDTTQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLF 98 (321)
Q Consensus 46 L~~fl~~~g~~~~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lF 98 (321)
..+.+.+.|-+-..-++-.||...+..||++|||-|+.||..|+-|+=|-...
T Consensus 367 ~~~Lf~evg~~kg~lyt~seir~~V~kYi~knnLad~~nKg~VrLDpILfd~~ 419 (560)
T KOG2522|consen 367 AKDLFKEVGLAKGTLYTSSEIRSAVSKYISKNNLADTKNKGKVRLDPILFDMV 419 (560)
T ss_pred HHHHHHhcCccccceeeHHHHHHHHHHHhhhhhccccccCCcEEeccHHHHHH
Confidence 34555666766678899999999999999999999999999998888877743
No 13
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=73.73 E-value=6.6 Score=26.60 Aligned_cols=37 Identities=24% Similarity=0.452 Sum_probs=31.5
Q ss_pred ccCCCCHHHHHHHhhcCCCCCCcc-ChHHHHHHHHHHh
Q 020828 38 FDGWGSIPLIEFLQSLGKDTTQQI-SRYDVTDIINKYV 74 (321)
Q Consensus 38 ~~~w~S~eL~~fl~~~g~~~~~~l-sr~~vvk~lw~YI 74 (321)
|..|-..+|.+||.+-|-...... +|.+.++.+-+|+
T Consensus 1 fdtWs~~~L~~wL~~~gi~~~~~~~~rd~Ll~~~k~~y 38 (38)
T PF10281_consen 1 FDTWSDSDLKSWLKSHGIPVPKSAKTRDELLKLAKKNY 38 (38)
T ss_pred CCCCCHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHhC
Confidence 567999999999999888777776 9999999987764
No 14
>PHA02696 hypothetical protein; Provisional
Probab=67.10 E-value=3.7 Score=32.34 Aligned_cols=23 Identities=48% Similarity=0.569 Sum_probs=19.6
Q ss_pred EeeeecCCCCCHHHHHHHHHHHH
Q 020828 247 RIATLSDDNFSEEECEDLRQRVK 269 (321)
Q Consensus 247 ~i~~~Sd~~FTEeE~~r~~q~~~ 269 (321)
-|..|.|.-|||+||++=+|.+.
T Consensus 40 ViQtCdDDYFTEeEFdDgkQvVa 62 (79)
T PHA02696 40 VIQTCDDDYFTEEEFDDGKQVVA 62 (79)
T ss_pred eeeecccccccHhhcccHHHHHH
Confidence 46789999999999999888763
No 15
>PRK05350 acyl carrier protein; Provisional
Probab=65.61 E-value=6.9 Score=30.37 Aligned_cols=58 Identities=9% Similarity=0.092 Sum_probs=49.0
Q ss_pred cChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhccccCCC
Q 020828 61 ISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQF 121 (321)
Q Consensus 61 lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~~~~~ 121 (321)
|+|.++...|.++|.+. +.-|. -.|-.|..|..-+|-+++.+.++.-.|+.||--..+
T Consensus 2 m~~~~i~~~v~~ii~~~-~~~~~--~~i~~d~~l~~dlg~DSld~veli~~lE~~fgI~i~ 59 (82)
T PRK05350 2 MTREEILERLRAILVEL-FEIDP--EDITPEANLYEDLDLDSIDAVDLVVHLQKLTGKKIK 59 (82)
T ss_pred CCHHHHHHHHHHHHHHH-hCCCH--HHCCCCccchhhcCCCHHHHHHHHHHHHHHHCCccC
Confidence 78999999999999987 54333 359999999888899999999999999999975543
No 16
>TIGR03759 conj_TIGR03759 integrating conjugative element protein, PFL_4693 family. Members of this protein family, such as model protein PFL_4693 from Pseudomonas fluorescens Pf-5, belong to extended genomic regions that appear to be spread by conjugative transfer. Most members have a predicted N-terminal signal sequence. The function is unknown.
Probab=63.01 E-value=9.2 Score=35.62 Aligned_cols=66 Identities=17% Similarity=0.255 Sum_probs=46.2
Q ss_pred CCHHHHHHHHHHHHh------CCCCCCcHHHHHHHHHHHHHHHhccchHHHHHHHHHH--HHHHHHccccccCC
Q 020828 256 FSEEECEDLRQRVKD------GLLKRPTVVELQEKTQILHEDITKHWLVRELALLQKL--IDRANVKGMAQRTP 321 (321)
Q Consensus 256 FTEeE~~r~~q~~~~------~~~~~PTv~dl~eKa~~i~~~i~~~w~e~El~rL~~l--id~A~ekG~~~~~~ 321 (321)
+|++|+.||++.|.- -++...|.=-|+.+-.+=.+-...-|-..|-.|.++. .++|-.+.|.+-||
T Consensus 14 Lt~~Ew~RY~~LmqG~rG~~SPgLdPLtaLGIeArsd~ERrryAEl~vk~E~~rvekeLA~qrayd~A~~RL~p 87 (200)
T TIGR03759 14 LTEDEWQRYQQLMQGPRGVYSPGLDPLTALGIEARSDEERRRYAELWVKQEAQRVEKELAFQRAYDAAWQRLYP 87 (200)
T ss_pred CCHHHHHHHHHHhcCCccCcCCCCChhhhhccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 799999999999982 2345556656665555555555556667777777774 56677777887776
No 17
>PRK05828 acyl carrier protein; Validated
Probab=55.74 E-value=22 Score=28.35 Aligned_cols=58 Identities=9% Similarity=0.083 Sum_probs=47.3
Q ss_pred cChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhccccCCC
Q 020828 61 ISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQF 121 (321)
Q Consensus 61 lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~~~~~ 121 (321)
|+|.++..+|-+-|.+.++.=+.+ .|-+|..|.. +|-+++.+.++--.|+.+|--..+
T Consensus 1 m~~~eI~~~i~~ii~e~~~~~~~d--~i~~~~~~~d-Lg~DSLd~velv~~lE~~f~I~i~ 58 (84)
T PRK05828 1 MQEMEILLKIKEIAKKKNFAVTLD--ESNINKPYRE-LKIDSLDMFSIIVSLESEFNIEFS 58 (84)
T ss_pred CCHHHHHHHHHHHHHHhccCCCcc--cccCCCCHHh-cCCCHHHHHHHHHHHHHHHCCCcC
Confidence 689999999999999866543332 3677888976 999999999999999999975554
No 18
>PRK12449 acyl carrier protein; Provisional
Probab=49.39 E-value=30 Score=26.30 Aligned_cols=58 Identities=9% Similarity=0.111 Sum_probs=47.1
Q ss_pred cChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhccccCCC
Q 020828 61 ISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQF 121 (321)
Q Consensus 61 lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~~~~~ 121 (321)
|+|.++...|-+++.+.-=.+|. .|-.|..|..-+|-+++.+.++.-.|+..|--..+
T Consensus 1 m~~~~i~~~l~~il~~~~~~~~~---~i~~~~~l~~dlg~DSl~~~~li~~lE~~f~i~i~ 58 (80)
T PRK12449 1 MTREEIFERLINLIQKQRSYLSL---AITEQTHLKDDLAVDSIELVEFIINVEDEFHIAIP 58 (80)
T ss_pred CCHHHHHHHHHHHHHHHhCCCcc---ccCCCCcHHHHcCCcHHHHHHHHHHHHHHhCCCCC
Confidence 56888888888888875433433 49999999999999999999999999998865543
No 19
>CHL00124 acpP acyl carrier protein; Validated
Probab=42.99 E-value=26 Score=26.79 Aligned_cols=58 Identities=14% Similarity=0.200 Sum_probs=48.3
Q ss_pred cChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhccccCCC
Q 020828 61 ISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQF 121 (321)
Q Consensus 61 lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~~~~~ 121 (321)
|+|.+|...|-++|.+.==.+|. .|-.|..|..-+|-+++.+.++.-.|+.+|--..+
T Consensus 1 M~~~~i~~~l~~ii~~~~~~~~~---~i~~d~~l~~dlg~DSl~~~eli~~le~~f~i~i~ 58 (82)
T CHL00124 1 MTKNDIFEKVQSIVAEQLGIEKS---EVTLDANFTRDLGADSLDVVELVMAIEEKFDIEIP 58 (82)
T ss_pred CCHHHHHHHHHHHHHHHHCCCHH---HCCCCcchhhhcCCcHHHHHHHHHHHHHHHCCccC
Confidence 57888999999999887323443 49999999999999999999999999999876554
No 20
>PF06627 DUF1153: Protein of unknown function (DUF1153); InterPro: IPR009534 This family consists of several short, hypothetical bacterial proteins of unknown function.; PDB: 2OA4_A 2JRT_A.
Probab=33.78 E-value=24 Score=29.05 Aligned_cols=27 Identities=22% Similarity=0.115 Sum_probs=19.9
Q ss_pred eecCCCCCHHHHHHHHHHHHhCCCCCC
Q 020828 250 TLSDDNFSEEECEDLRQRVKDGLLKRP 276 (321)
Q Consensus 250 ~~Sd~~FTEeE~~r~~q~~~~~~~~~P 276 (321)
.|.-=.+|++||..|.+.+..++..-.
T Consensus 55 A~~rY~Ls~eEf~~W~~av~rhge~aL 81 (90)
T PF06627_consen 55 ACRRYGLSEEEFESWQRAVDRHGENAL 81 (90)
T ss_dssp HHHCTTSSHHHHHHHHHHCCT--TTSS
T ss_pred HHHHhCCCHHHHHHHHHHHHHHhHHHH
Confidence 344457899999999999999887654
No 21
>cd00454 Trunc_globin Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct from the three-over-three pattern found in other globins. A subset of these have been demonstrated to form homodimers.
Probab=33.09 E-value=76 Score=25.48 Aligned_cols=41 Identities=10% Similarity=0.110 Sum_probs=33.0
Q ss_pred CCCCHHHHHHHHH----HHHhCCCCCCcHHHHHHHHHHHHHHHhc
Q 020828 254 DNFSEEECEDLRQ----RVKDGLLKRPTVVELQEKTQILHEDITK 294 (321)
Q Consensus 254 ~~FTEeE~~r~~q----~~~~~~~~~PTv~dl~eKa~~i~~~i~~ 294 (321)
-++|+++|++|.. ++..-+.+-+...++...+..+...+++
T Consensus 71 ~~I~~~~f~~~l~~l~~al~~~~~~~~~~~~~~~~~~~~~~~~v~ 115 (116)
T cd00454 71 FPITEEEFDAWLELLRDALDELGVPAELADALLARAERIADHMVN 115 (116)
T ss_pred CCCCHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 3899999999986 5556667778888888888888777765
No 22
>PTZ00171 acyl carrier protein; Provisional
Probab=32.80 E-value=53 Score=29.00 Aligned_cols=61 Identities=15% Similarity=0.214 Sum_probs=51.3
Q ss_pred CCccChHHHHHHHHHHhhhCCCCCCCCCCeeecchhhhhhhCCCccchHhHHHHHHhccccCCC
Q 020828 58 TQQISRYDVTDIINKYVNENKLVHSVKKKRVVSDERLLSLFGKKSFLRIKIYDLLEAHYAENQF 121 (321)
Q Consensus 58 ~~~lsr~~vvk~lw~YIK~nnLqdP~~Kr~I~CDekLk~lFgk~~v~~f~m~klL~~H~~~~~~ 121 (321)
..-|++.+|...|.++|.+.-=-+|. .|..|..+..-+|-+++.+.++--.|+.+|--..+
T Consensus 63 ~~~~~~~~v~~~l~eiiae~l~vd~~---~I~~ds~~~~dLg~DSLd~veLv~~LEdeFgI~Ip 123 (148)
T PTZ00171 63 QYLLSKEDVLTRVKKVVKNFEKVDAS---KITPESNFVKDLGADSLDVVELLIAIEQEFNLTIP 123 (148)
T ss_pred ccccCHHHHHHHHHHHHHHHhCCCHh---hCCCCcchhhhcCCCHHHHHHHHHHHHHHHCCccC
Confidence 35688999999999999988533433 48899999999999999999999999999876554
No 23
>TIGR02530 flg_new flagellar operon protein. Members of this family are found in a subset of bacterial flagellar operons, generally between genes designated flgD and flgE, in species as diverse as Bacillus halodurans and various other Firmicutes, Geobacter sulfurreducens, and Bdellovibrio bacteriovorus. The specific molecular function is unknown.
Probab=28.06 E-value=60 Score=27.00 Aligned_cols=25 Identities=16% Similarity=0.171 Sum_probs=22.4
Q ss_pred hccchHHHHHHHHHHHHHHHHcccc
Q 020828 293 TKHWLVRELALLQKLIDRANVKGMA 317 (321)
Q Consensus 293 ~~~w~e~El~rL~~lid~A~ekG~~ 317 (321)
+=.+++.++.+|+..++.|.+||-+
T Consensus 29 ~I~l~~~~~~~i~~av~~A~~KG~k 53 (96)
T TIGR02530 29 NISINPDDWKKLLEAVEEAESKGVK 53 (96)
T ss_pred CCCCCHHHHHHHHHHHHHHHhcCCC
Confidence 3458999999999999999999987
No 24
>cd00238 ERp29c ERp29 and ERp38, C-terminal domain; composed of the protein disulfide isomerase (PDI)-like proteins ERp29 and ERp38. ERp29 (also called ERp28) is a ubiquitous endoplasmic reticulum (ER)-resident protein expressed in high levels in secretory cells. It contains a redox inactive TRX-like domain at the N-terminus. The expression profile of ERp29 suggests a role in secretory protein production, distinct from that of PDI. It has also been identified as a member of the thyroglobulin folding complex and is essential in regulating the secretion of thyroglobulin. The Drosophila homolog, Wind, is the product of windbeutel, an essential gene in the development of dorsal-ventral patterning. Wind is required for correct targeting of Pipe, a Golgi-resident type II transmembrane protein with homology to 2-O-sulfotransferase. ERp38 is a P5-like protein, first isolated from alfalfa (the cDNA clone was named G1), which contains two redox active TRX domains at the N-terminus, like human P5.
Probab=27.05 E-value=59 Score=26.42 Aligned_cols=39 Identities=21% Similarity=0.308 Sum_probs=34.3
Q ss_pred cCCCCCHHHHHHHHHHHHhCCCCCCcHHHHHHHHHHHHH
Q 020828 252 SDDNFSEEECEDLRQRVKDGLLKRPTVVELQEKTQILHE 290 (321)
Q Consensus 252 Sd~~FTEeE~~r~~q~~~~~~~~~PTv~dl~eKa~~i~~ 290 (321)
-+.+|-+.|..|+...+..+.+..-+.+++..|...|..
T Consensus 54 kg~~yv~~E~~RL~~iL~~~~ls~~K~del~~R~NIL~~ 92 (93)
T cd00238 54 KGEDYVEKELARLERLLEKKGLAPEKADELTRRLNILRS 92 (93)
T ss_pred cchhHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhc
Confidence 478899999999999999888899999999998887764
No 25
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=26.71 E-value=1.4e+02 Score=19.76 Aligned_cols=32 Identities=16% Similarity=0.191 Sum_probs=24.3
Q ss_pred CCCHHHHHHHhhcCCCCCCccChHHHHHHHHHHh
Q 020828 41 WGSIPLIEFLQSLGKDTTQQISRYDVTDIINKYV 74 (321)
Q Consensus 41 w~S~eL~~fl~~~g~~~~~~lsr~~vvk~lw~YI 74 (321)
|--++|.+++...|-.++. ++.+++.+|-+||
T Consensus 4 l~v~eLk~~l~~~gL~~~G--~K~~Li~Rl~~~l 35 (35)
T PF02037_consen 4 LTVAELKEELKERGLSTSG--KKAELIERLKEHL 35 (35)
T ss_dssp SHHHHHHHHHHHTTS-STS--SHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHCCCCCCC--CHHHHHHHHHHhC
Confidence 3447899999888876655 4899999998886
No 26
>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=23.12 E-value=1.2e+02 Score=24.69 Aligned_cols=41 Identities=17% Similarity=0.218 Sum_probs=31.2
Q ss_pred CCCCHHHHHHHHH----HHHhCCCCCCcHHHHHHHHHHHHHHHhc
Q 020828 254 DNFSEEECEDLRQ----RVKDGLLKRPTVVELQEKTQILHEDITK 294 (321)
Q Consensus 254 ~~FTEeE~~r~~q----~~~~~~~~~PTv~dl~eKa~~i~~~i~~ 294 (321)
-++|+.+|++|.+ ++..-+++-+...++.+.+..+...|++
T Consensus 75 l~it~~~f~~~~~~~~~al~~~~v~~~~~~~~~~~~~~~~~~i~n 119 (120)
T PF01152_consen 75 LGITEEHFDRWLELLKQALDELGVPEELIDELLARLESLRDDIVN 119 (120)
T ss_dssp S-BBHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhcC
Confidence 3899999999975 5566677777888888888888777764
No 27
>cd00238 ERp29c ERp29 and ERp38, C-terminal domain; composed of the protein disulfide isomerase (PDI)-like proteins ERp29 and ERp38. ERp29 (also called ERp28) is a ubiquitous endoplasmic reticulum (ER)-resident protein expressed in high levels in secretory cells. It contains a redox inactive TRX-like domain at the N-terminus. The expression profile of ERp29 suggests a role in secretory protein production, distinct from that of PDI. It has also been identified as a member of the thyroglobulin folding complex and is essential in regulating the secretion of thyroglobulin. The Drosophila homolog, Wind, is the product of windbeutel, an essential gene in the development of dorsal-ventral patterning. Wind is required for correct targeting of Pipe, a Golgi-resident type II transmembrane protein with homology to 2-O-sulfotransferase. ERp38 is a P5-like protein, first isolated from alfalfa (the cDNA clone was named G1), which contains two redox active TRX domains at the N-terminus, like human P5.
Probab=22.93 E-value=96 Score=25.20 Aligned_cols=17 Identities=29% Similarity=0.645 Sum_probs=15.3
Q ss_pred hccchHHHHHHHHHHHH
Q 020828 293 TKHWLVRELALLQKLID 309 (321)
Q Consensus 293 ~~~w~e~El~rL~~lid 309 (321)
..+|.++|+.||+++++
T Consensus 55 g~~yv~~E~~RL~~iL~ 71 (93)
T cd00238 55 GEDYVEKELARLERLLE 71 (93)
T ss_pred chhHHHHHHHHHHHHHh
Confidence 78899999999999874
No 28
>PF08349 DUF1722: Protein of unknown function (DUF1722); InterPro: IPR013560 This domain of unknown function is found in bacteria and archaea and is homologous to the hypothetical protein ybgA from Escherichia coli.
Probab=22.54 E-value=2.6e+02 Score=23.16 Aligned_cols=57 Identities=21% Similarity=0.140 Sum_probs=51.5
Q ss_pred CHHHHHHHHHHHHhCCCCCCcHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHH
Q 020828 257 SEEECEDLRQRVKDGLLKRPTVVELQEKTQILHEDITKHWLVRELALLQKLIDRANV 313 (321)
Q Consensus 257 TEeE~~r~~q~~~~~~~~~PTv~dl~eKa~~i~~~i~~~w~e~El~rL~~lid~A~e 313 (321)
.++-++.|.+.+.......||....-+=+..|--.+.++.+++|.+.+..+|+.=.+
T Consensus 27 ~~~~~~~Y~~~l~~al~~~~~~~~~~Nvl~Hi~Gyfk~~ls~~EK~~~~~~i~~yr~ 83 (117)
T PF08349_consen 27 LEEVFEEYEELLMEALSKPPTRGSHINVLQHIFGYFKKKLSSEEKQHFLDLIEDYRE 83 (117)
T ss_pred hHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHc
Confidence 678899999999999999999999999999999999999999999999998875443
No 29
>PF00010 HLH: Helix-loop-helix DNA-binding domain only nuclear translocator protein (Arnt).; InterPro: IPR011598 The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways []. bHLH proteins include MyoD [], SREBPs (sterol regulatory element binding proteins) [], and yeast Pho4 (phosphatase system) []. In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding []. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf [, ]. This entry is bHLHZip, which covers the bHLH domain and the leucine zipper motif, when present.; PDB: 1NLW_A 1NKP_D 1A93_A 2A93_A 1AM9_C 3U5V_A 1A0A_B 2QL2_C 1UKL_C 1AN4_B ....
Probab=22.17 E-value=84 Score=22.26 Aligned_cols=21 Identities=10% Similarity=0.366 Sum_probs=18.3
Q ss_pred CCCCccChHHHHHHHHHHhhh
Q 020828 56 DTTQQISRYDVTDIINKYVNE 76 (321)
Q Consensus 56 ~~~~~lsr~~vvk~lw~YIK~ 76 (321)
+....+|..+|+....+||+.
T Consensus 33 ~~~~k~~K~~iL~~ai~yI~~ 53 (55)
T PF00010_consen 33 GSSRKLSKASILQKAIDYIKQ 53 (55)
T ss_dssp CTTSSSSHHHHHHHHHHHHHH
T ss_pred cccccCCHHHHHHHHHHHHHH
Confidence 356789999999999999985
Done!