Query 022273
Match_columns 300
No_of_seqs 68 out of 70
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 09:21:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022273.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022273hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10236 hypothetical protein; 100.0 2E-35 4.4E-40 269.7 13.3 125 60-207 8-142 (237)
2 COG4735 Uncharacterized protei 99.8 4E-20 8.7E-25 166.8 0.4 88 98-207 14-103 (211)
3 COG4735 Uncharacterized protei 97.9 5.6E-06 1.2E-10 75.9 1.8 127 132-275 1-137 (211)
4 PF13099 DUF3944: Domain of un 96.2 0.0048 1E-07 42.8 3.0 30 60-89 3-32 (35)
5 PF03250 Tropomodulin: Tropomo 81.1 2.4 5.2E-05 37.7 4.3 31 53-83 109-139 (147)
6 PF03981 Ubiq_cyt_C_chap: Ubiq 73.2 1.6 3.5E-05 35.9 1.0 51 116-196 5-56 (141)
7 PF02173 pKID: pKID domain; I 60.6 6.1 0.00013 28.6 1.7 13 138-150 18-30 (41)
8 cd01915 CODH Carbon monoxide d 43.8 72 0.0016 34.1 7.0 88 143-237 109-211 (613)
9 PF11248 DUF3046: Protein of u 35.5 79 0.0017 24.6 4.4 44 115-158 5-62 (63)
10 PF15008 DUF4518: Domain of un 35.0 66 0.0014 31.1 4.7 89 61-179 7-95 (262)
11 PF04542 Sigma70_r2: Sigma-70 34.5 70 0.0015 22.2 3.7 33 142-177 5-37 (71)
12 TIGR02989 Sig-70_gvs1 RNA poly 33.9 52 0.0011 26.6 3.4 36 141-179 9-44 (159)
13 PF12616 DUF3775: Protein of u 33.0 85 0.0018 24.9 4.3 31 60-90 3-34 (75)
14 cd06406 PB1_P67 A PB1 domain i 30.3 39 0.00084 27.4 2.0 20 137-156 18-37 (80)
15 cd06134 RNaseT DEDDh 3'-5' exo 28.6 53 0.0012 28.7 2.8 33 145-177 151-188 (189)
16 PF01371 Trp_repressor: Trp re 28.5 92 0.002 25.3 3.9 21 65-85 9-29 (87)
17 TIGR00759 aceE pyruvate dehydr 26.9 5.7E+02 0.012 29.0 10.6 136 60-250 338-504 (885)
18 cd02642 R3H_encore_like R3H do 25.5 98 0.0021 23.0 3.3 43 115-157 3-48 (63)
19 PF07176 DUF1400: Alpha/beta h 25.2 91 0.002 26.4 3.5 36 55-90 26-61 (127)
20 COG3426 Butyrate kinase [Energ 22.0 1.7E+02 0.0037 29.5 5.1 49 217-265 231-286 (358)
21 PF04891 NifQ: NifQ; InterPro 22.0 94 0.002 28.0 3.1 53 100-156 97-149 (167)
22 PF02836 Glyco_hydro_2_C: Glyc 21.8 60 0.0013 29.9 1.9 38 118-155 36-73 (298)
23 PF02196 RBD: Raf-like Ras-bin 21.6 54 0.0012 25.1 1.4 32 128-159 8-40 (71)
24 PF08708 PriCT_1: Primase C te 21.5 1.5E+02 0.0033 21.8 3.7 54 108-168 7-60 (71)
25 PRK14082 hypothetical protein; 20.9 75 0.0016 25.1 2.0 16 162-177 33-48 (65)
26 TIGR01702 CO_DH_cata carbon-mo 20.4 2.7E+02 0.0058 30.1 6.5 52 135-189 100-155 (621)
No 1
>PRK10236 hypothetical protein; Provisional
Probab=100.00 E-value=2e-35 Score=269.72 Aligned_cols=125 Identities=20% Similarity=0.362 Sum_probs=116.1
Q ss_pred ChHHHHHHHhhChHHHHHHHHHhc-----CCCCCCccchhhc-cc---CCcchhHHhhhhHHHHHHHHHHHHHHhhhccc
Q 022273 60 DPELRSVLELATDSELYELERILF-----GPSYFSPLLKSFT-KR---ADVDYVMIEQDLEEREDFIASLESRFLFLAAD 130 (300)
Q Consensus 60 ddELr~~LELATdEEL~eLt~ILf-----~~s~fsPLLkSi~-kr---~~~Dy~~i~~~~q~R~~~i~~IEsRFqfLAAD 130 (300)
|++| +||..|++|||.+|++||+ ..|+++.|+++.. ++ +.+||.+ ||+.||+||||||||
T Consensus 8 D~DL-~fL~~cs~edL~~Lv~~Lt~d~dG~~R~te~lt~~~~yk~~~~~~~~~~~----------yw~~Ia~elq~fGgn 76 (237)
T PRK10236 8 DSDL-DFLQHCSEEQLANFARLLTHNEKGKTRLSSVLMRNELFKSMEGHPEQHRR----------NWQLIAGELQHFGGD 76 (237)
T ss_pred CccH-HHHHhCCHHHHHHHHHHHhcCCCCCEeehhhhcccHHHHhhcccchhHHH----------HHHHHHHHHHHhcch
Confidence 4444 7999999999999999999 4577888888854 56 8999999 999999999999999
Q ss_pred h-hhhhcCCCchHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhhccccCCCCCCcccCCchhhhhHHHhhhh
Q 022273 131 A-RSTLRGWRPSYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYASEESGVFPGSWENSEASDAQNSLELGLS 207 (300)
Q Consensus 131 s-~svLRG~~vsYReVLldVckkLkV~~s~klsT~dLEaEIFLhLL~~~ss~~~g~~~~aWekm~~~~e~~sL~~~lq 207 (300)
+ +|+|||+||+|||||+||||||||||++++||++||+|||+|++++ +|+||+++ |+++|+..++
T Consensus 77 t~~n~lRG~Gv~YreIL~DVc~~LKV~y~~~~st~~iE~~il~kll~~-----------a~~kms~e-E~~~L~~~l~ 142 (237)
T PRK10236 77 SIANKLRGHGKLYRAILLDVSKRLKLKADKEMSTFEIEQQLLEQFLRN-----------TWKKMDEE-HKQEFLHAVD 142 (237)
T ss_pred HHHHHHhcCCccHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHH-----------HHHHCCHH-HHHHHHHHHh
Confidence 9 5799999999999999999999999999999999999999999999 99999999 9999999999
No 2
>COG4735 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.77 E-value=4e-20 Score=166.78 Aligned_cols=88 Identities=15% Similarity=0.287 Sum_probs=78.6
Q ss_pred cCCc-chhHHhhhhHHHHHHHHHHHHHHhhhccch-hhhhcCCCchHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHH
Q 022273 98 RADV-DYVMIEQDLEEREDFIASLESRFLFLAADA-RSTLRGWRPSYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLL 175 (300)
Q Consensus 98 r~~~-Dy~~i~~~~q~R~~~i~~IEsRFqfLAADs-~svLRG~~vsYReVLldVckkLkV~~s~klsT~dLEaEIFLhLL 175 (300)
|++. ||.+ |++.|++++|++++|+ ++.|||.|+.||+||+|+|||||++|+++++|.+||++++++++
T Consensus 14 r~g~~~~~k----------y~k~ia~elq~~gg~s~anflr~~G~lyk~il~d~~~~Lk~k~~k~~~tt~Iee~ll~~il 83 (211)
T COG4735 14 REGLIQVCK----------YLKRIAEELQTTGGLSAANFLRDLGQLYKKILCDEKDKLKVKVQKELGTTEIEEPLLLQIL 83 (211)
T ss_pred HhhHHHHHH----------HHHhhHHHHHHhccHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHhhccccccchhHHHHH
Confidence 5555 6666 8999999999999999 79999999999999999999999999999999999999999999
Q ss_pred hhhhccccCCCCCCcccCCchhhhhHHHhhhh
Q 022273 176 QEYASEESGVFPGSWENSEASDAQNSLELGLS 207 (300)
Q Consensus 176 ~~~ss~~~g~~~~aWekm~~~~e~~sL~~~lq 207 (300)
++ +|+||+.. +.+.+.+.+.
T Consensus 84 ~~-----------~l~km~~~-~~~e~~~~l~ 103 (211)
T COG4735 84 RN-----------PLEKMLKG-GKAEAVDSLD 103 (211)
T ss_pred Hh-----------HHHHHhHH-HHHHHHHHhc
Confidence 99 99999887 6665555444
No 3
>COG4735 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=97.87 E-value=5.6e-06 Score=75.86 Aligned_cols=127 Identities=20% Similarity=0.227 Sum_probs=117.4
Q ss_pred hhhhcCC--CchHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhhccccCCCCCCcccCCchhhhhHHHhhhhhh
Q 022273 132 RSTLRGW--RPSYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYASEESGVFPGSWENSEASDAQNSLELGLSQW 209 (300)
Q Consensus 132 ~svLRG~--~vsYReVLldVckkLkV~~s~klsT~dLEaEIFLhLL~~~ss~~~g~~~~aWekm~~~~e~~sL~~~lq~w 209 (300)
+|++||+ ..+||+-++||||+++++|..-..|-++|.++|+|.+++ .|++.+.+ +.+.|...++
T Consensus 1 lt~~l~~~~~~k~r~g~~~~~ky~k~ia~elq~~gg~s~anflr~~G~-----------lyk~il~d-~~~~Lk~k~~-- 66 (211)
T COG4735 1 LTVLLGRSEQFKYREGLIQVCKYLKRIAEELQTTGGLSAANFLRDLGQ-----------LYKKILCD-EKDKLKVKVQ-- 66 (211)
T ss_pred CchhhccchhhHHHhhHHHHHHHHHhhHHHHHHhccHHHHHHHHHHHH-----------HHHHcCHH-HHHHHHHHHH--
Confidence 4778887 999999999999999999999999999999999999999 99999998 8899999899
Q ss_pred HHHHhhhhccCc-------hhHHHHHHhccceeehHHHHH-HHHHHHHHHHHHHHhhhHHHHHHHhhhhccccc
Q 022273 210 KVQALAAFNAGA-------VELKSMMLKGGGIYTLVKIYQ-LLMRNLSGKFFLEAANYQIKKEVLKKVVDNWLP 275 (300)
Q Consensus 210 ~~~~la~~klg~-------~ell~llLKGGsalavssi~~-~l~kqla~q~al~~A~YQ~ake~l~~Gg~~~~~ 275 (300)
+.++.+.+.+ +|++..++|||++.+++++.. .+.+ |.+|+.+|+|.||+||.+..+|+...+-
T Consensus 67 --k~~~tt~Iee~ll~~il~~~l~km~~~~~~e~~~~l~~~~v~~-i~e~~~vl~a~~l~ak~~~~~~S~qla~ 137 (211)
T COG4735 67 --KELGTTEIEEPLLLQILRNPLEKMLKGGKAEAVDSLDAPNVLE-IEEQLQVLIADYLVAKKALGKGSYQLAV 137 (211)
T ss_pred --HhhccccccchhHHHHHHhHHHHHhHHHHHHHHHHhcchhHHH-HHHHHHHHHHHHHHHHHHhccchHHHHH
Confidence 7788888877 999999999999999999999 6777 9999999999999999999999876653
No 4
>PF13099 DUF3944: Domain of unknown function (DUF3944)
Probab=96.23 E-value=0.0048 Score=42.84 Aligned_cols=30 Identities=17% Similarity=0.018 Sum_probs=25.2
Q ss_pred ChHHHHHHHhhChHHHHHHHHHhcCCCCCC
Q 022273 60 DPELRSVLELATDSELYELERILFGPSYFS 89 (300)
Q Consensus 60 ddELr~~LELATdEEL~eLt~ILf~~s~fs 89 (300)
-|+..+||..|++|+|.+|++||+.-+-.+
T Consensus 3 ~D~DLeFL~~cs~edL~~L~~~Lt~dkdG~ 32 (35)
T PF13099_consen 3 YDSDLEFLAECSNEDLKDLVDILTHDKDGK 32 (35)
T ss_pred cCcchHHHHHCCHHHHHHHHHHHhcCCCCC
Confidence 367789999999999999999999655343
No 5
>PF03250 Tropomodulin: Tropomodulin; InterPro: IPR004934 Actin filaments have an intrinsic polarity, each with a fast-growing (barbed) end and a slow-growing (pointed) end. To regulate the dynamics at these ends, capping proteins have evolved that specifically bind to either the barbed or the pointed ends of the filament, where they block the association and dissociation of monomers. Pointed ends, for which actin monomers have significantly lower association and dissociation rate-constants than for barbed, are capped by either the Arp2/3 complex or tropomodulins []. Tropomodulin is a novel tropomyosin regulatory protein that binds to the end of erythrocyte tropomyosin and blocks head-to-tail association of tropomyosin along actin filaments []. Limited proteolysis shows this protein is composed of two domains. The unstructured tropomyosin-binding region at the N terminus has an actin pointed-end-capping activity that is dramatically up-regulated by tropomyosin coating of the actin filament[]. The second region is found near the C terminus. This tropomyosin-independent capping-domain caps pure actin. ; GO: 0005523 tropomyosin binding, 0005856 cytoskeleton
Probab=81.11 E-value=2.4 Score=37.73 Aligned_cols=31 Identities=45% Similarity=0.549 Sum_probs=27.1
Q ss_pred cCCCCCCChHHHHHHHhhChHHHHHHHHHhc
Q 022273 53 SKGQGAFDPELRSVLELATDSELYELERILF 83 (300)
Q Consensus 53 ~~~~~~~ddELr~~LELATdEEL~eLt~ILf 83 (300)
....-..++||.++|.-|||+||.+|+.||-
T Consensus 109 ~ee~v~ldpeleeaL~~Atd~El~dlAaILG 139 (147)
T PF03250_consen 109 KEEQVTLDPELEEALSNATDAELCDLAAILG 139 (147)
T ss_pred cccccccCHHHHHHHhcCcHHHHHHHHHHHh
Confidence 3345678899999999999999999999995
No 6
>PF03981 Ubiq_cyt_C_chap: Ubiquinol-cytochrome C chaperone ; InterPro: IPR021150 Saccharomyces cerevisiae ubiquinol-cytochrome C chaperone is required for assembly of coenzyme QF-2-cytochrome C reductase. It appears to be found in a number of different organisms including Homo sapiens, Caenorhabditis elegans and Rhizobium meliloti. This entry also contains bacterial proteins belonging to the UPF0174 family.
Probab=73.21 E-value=1.6 Score=35.85 Aligned_cols=51 Identities=18% Similarity=0.224 Sum_probs=40.8
Q ss_pred HHHHHHHHHhhhccchh-hhhcCCCchHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhhccccCCCCCCcccCC
Q 022273 116 FIASLESRFLFLAADAR-STLRGWRPSYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYASEESGVFPGSWENSE 194 (300)
Q Consensus 116 ~i~~IEsRFqfLAADs~-svLRG~~vsYReVLldVckkLkV~~s~klsT~dLEaEIFLhLL~~~ss~~~g~~~~aWekm~ 194 (300)
..+.+++||+++..... ...| |+..+ -+..++|++||.++.++ .+++|.
T Consensus 5 ~~dt~~~~f~~~~lh~~l~~~R----------------Lk~~~---~~~~~~~q~l~~~~~~d-----------~~~~l~ 54 (141)
T PF03981_consen 5 VPDTFAGRFQMLGLHVWLVLRR----------------LKAEG---KEGKELEQALFDKFFED-----------MDERLR 54 (141)
T ss_pred CccCHHHHHHHHHHHHHHHHHH----------------Hcccc---ccHHHHHHHHHHHHHHH-----------HHHHHH
Confidence 45689999999998884 4444 77776 55699999999999999 787777
Q ss_pred ch
Q 022273 195 AS 196 (300)
Q Consensus 195 ~~ 196 (300)
+.
T Consensus 55 ~~ 56 (141)
T PF03981_consen 55 EM 56 (141)
T ss_pred Hh
Confidence 65
No 7
>PF02173 pKID: pKID domain; InterPro: IPR003102 The nuclear factor CREB activates transcription of target genes in part through direct interactions with the KIX domain of the coactivator CBP in a phosphorylation-dependent manner. CBP and P300 bind to the pKID (phosphorylated kinase-inducible-domain) domain of CREB [].; GO: 0005515 protein binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1KDX_B.
Probab=60.59 E-value=6.1 Score=28.60 Aligned_cols=13 Identities=46% Similarity=0.810 Sum_probs=11.3
Q ss_pred CCchHHHHHHHHH
Q 022273 138 WRPSYRNVLLAVR 150 (300)
Q Consensus 138 ~~vsYReVLldVc 150 (300)
+|||||.||-++.
T Consensus 18 RRPSYRKIlndLs 30 (41)
T PF02173_consen 18 RRPSYRKILNDLS 30 (41)
T ss_dssp TSTHHHHHHHHHH
T ss_pred hCchHHHHHHHhc
Confidence 5999999998873
No 8
>cd01915 CODH Carbon monoxide dehydrogenase (CODH) is found in acetogenic and methanogenic organisms and is responsible for the synthesis and breakdown of acetyl-CoA, respectively. CODH has two types of metal clusters, a cubane [Fe4-S4] center (B-cluster) similar to that of hybrid cluster protein (HCP) and a Ni-Fe-S center (C-cluster) where carbon monoxide oxidation occurs. Bifunctional CODH forms a heterotetramer with acetyl-CoA synthase (ACS) consisting of two CODH and two ACS subunits while monofunctional CODH forms a homodimer. Bifunctional CODH reduces carbon dioxide to carbon monoxide and ACS then synthesizes acetyl-CoA from carbon monoxide, CoA, and a methyl group donated by another protein (CoFeSP), while monofunctional CODH oxidizes carbon monoxide to carbon dioxide. CODH and ACS each have a metal cluster referred to as the C- and A-clusters, respectively.
Probab=43.85 E-value=72 Score=34.13 Aligned_cols=88 Identities=18% Similarity=0.211 Sum_probs=59.1
Q ss_pred HHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhhccccCCCCCC-----------cccCCchhhhhHHHhhhhhhHH
Q 022273 143 RNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYASEESGVFPGS-----------WENSEASDAQNSLELGLSQWKV 211 (300)
Q Consensus 143 ReVLldVckkLkV~~s~klsT~dLEaEIFLhLL~~~ss~~~g~~~~a-----------Wekm~~~~e~~sL~~~lq~w~~ 211 (300)
.+=|..||++|+|+.+. -+..||=.|+=..+|++|.....+...+. |+++.-- ... .-..+.
T Consensus 109 ~~KL~~~A~~~gi~t~g-~~~~eiA~~va~~~l~d~~~~~~~~~~~~~~~ap~~r~e~w~~lgi~-p~g-i~~ei~---- 181 (613)
T cd01915 109 EEKLKALAKRLGIDTEG-KSINEIAVEVAEIALEDFGRPREEPSRWVEAFAPEKRLELWEELGIL-PGG-IDSEIA---- 181 (613)
T ss_pred HHHHHHHHHHcCCCcCC-CCHHHHHHHHHHHHHHHhcCCCCcchhhHhhhCCHHHHHHHHHcCCC-ChH-HHHHHH----
Confidence 38899999999999665 77899999999999999987655566555 6666421 000 011122
Q ss_pred HHhhhhccCc----hhHHHHHHhccceeeh
Q 022273 212 QALAAFNAGA----VELKSMMLKGGGIYTL 237 (300)
Q Consensus 212 ~~la~~klg~----~ell~llLKGGsalav 237 (300)
.++.....|. .|++...|+-|-+..+
T Consensus 182 e~l~~t~~g~d~D~~~ll~~~Lr~Gla~~~ 211 (613)
T cd01915 182 EAMHRTHTGVDSDPVSLLLHSLRLGLAAGY 211 (613)
T ss_pred HHHHHHccCCCCCHHHHHHHHHHHhhhccH
Confidence 4444445553 6777777777776655
No 9
>PF11248 DUF3046: Protein of unknown function (DUF3046); InterPro: IPR021408 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=35.50 E-value=79 Score=24.63 Aligned_cols=44 Identities=30% Similarity=0.352 Sum_probs=33.5
Q ss_pred HHHHHHHHHHh-----hhccch-hhhhcCC--------CchHHHHHHHHHhhcCCCCC
Q 022273 115 DFIASLESRFL-----FLAADA-RSTLRGW--------RPSYRNVLLAVRKNLNIPCS 158 (300)
Q Consensus 115 ~~i~~IEsRFq-----fLAADs-~svLRG~--------~vsYReVLldVckkLkV~~s 158 (300)
.||++++.+|= .++.|- .+-|-|+ |+.=|+|=..||+-++||-+
T Consensus 5 eFw~~~~~~FG~~~~~~la~dhvL~~LGgrT~~eAL~~G~dpr~VW~AlC~~~dVP~~ 62 (63)
T PF11248_consen 5 EFWQLMEEEFGPAYGRSLARDHVLSELGGRTAAEALEAGVDPRDVWRALCDAFDVPEE 62 (63)
T ss_pred HHHHHHHHHhCchhHHHHHHhcchhhcCCcCHHHHHHcCCCHHHHHHHHHHHcCCCCC
Confidence 58888988883 445554 3555543 89999999999999999954
No 10
>PF15008 DUF4518: Domain of unknown function (DUF4518)
Probab=35.01 E-value=66 Score=31.05 Aligned_cols=89 Identities=21% Similarity=0.336 Sum_probs=64.2
Q ss_pred hHHHHHHHhhChHHHHHHHHHhcCCCCCCccchhhcccCCcchhHHhhhhHHHHHHHHHHHHHHhhhccchhhhhcCCCc
Q 022273 61 PELRSVLELATDSELYELERILFGPSYFSPLLKSFTKRADVDYVMIEQDLEEREDFIASLESRFLFLAADARSTLRGWRP 140 (300)
Q Consensus 61 dELr~~LELATdEEL~eLt~ILf~~s~fsPLLkSi~kr~~~Dy~~i~~~~q~R~~~i~~IEsRFqfLAADs~svLRG~~v 140 (300)
..+|++|.+-++++|..|++.-|.+- ..| - +|+.=++.| .-+--|+..+||. +.
T Consensus 7 ~G~rdlL~~l~~~~LlaL~~TVTn~~-i~~----------e----------~~~EAi~aI----L~~s~~a~~LL~r-kk 60 (262)
T PF15008_consen 7 EGCRDLLGLLDNDDLLALADTVTNRL-IKP----------E----------SRQEAIDAI----LLYSQDAEELLRR-KK 60 (262)
T ss_pred HHHHHHHhcCChHHHHHHHHHHhcCc-eec----------C----------CHHHHHHHH----HHhCcCHHHHHhc-cc
Confidence 45899999999999999999999875 555 2 222222221 2345677788876 56
Q ss_pred hHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhh
Q 022273 141 SYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYA 179 (300)
Q Consensus 141 sYReVLldVckkLkV~~s~klsT~dLEaEIFLhLL~~~s 179 (300)
-+|+||...-..-+|..++..+-.+| ..|.++-..
T Consensus 61 V~RelLFkYLa~kgv~v~p~s~K~~L----I~~~l~~W~ 95 (262)
T PF15008_consen 61 VKRELLFKYLASKGVIVPPDSEKADL----IQRVLQYWS 95 (262)
T ss_pred ccHHHHHHHHHHcCCCCCCCccHHHH----HHHHHHHHh
Confidence 68999999999999999888886554 556666533
No 11
>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 The bacterial core RNA polymerase complex, which consists of five subunits, 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 []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....
Probab=34.46 E-value=70 Score=22.21 Aligned_cols=33 Identities=24% Similarity=0.384 Sum_probs=27.6
Q ss_pred HHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhh
Q 022273 142 YRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQE 177 (300)
Q Consensus 142 YReVLldVckkLkV~~s~klsT~dLEaEIFLhLL~~ 177 (300)
|...+..++.+. ++.....+|+-+|.|+.+++.
T Consensus 5 ~~~~l~~~~~~~---~~~~~~~eD~~qe~~~~l~~~ 37 (71)
T PF04542_consen 5 YYPLLYRYARRY---TGDPEDAEDLVQEAFIKLWRA 37 (71)
T ss_dssp THHHHHHHHHTC---TTCSSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH---hCCHhhHHHHhhHHHHHHHhh
Confidence 667777888887 555579999999999999987
No 12
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=33.88 E-value=52 Score=26.57 Aligned_cols=36 Identities=17% Similarity=0.253 Sum_probs=28.4
Q ss_pred hHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhh
Q 022273 141 SYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYA 179 (300)
Q Consensus 141 sYReVLldVckkLkV~~s~klsT~dLEaEIFLhLL~~~s 179 (300)
.|+..|..++.++.. .....+|+.+|+|+++++...
T Consensus 9 ~~~~~l~~~~~~~~~---~~~~aEDivQe~~l~l~~~~~ 44 (159)
T TIGR02989 9 RHQRSLRAFVRSLVP---DRDDADDVLQETFVTAWRKFD 44 (159)
T ss_pred HhHHHHHHHHHHHcC---ChhhHHHHHHHHHHHHHHHHH
Confidence 477788888888854 445679999999999998743
No 13
>PF12616 DUF3775: Protein of unknown function (DUF3775); InterPro: IPR022254 This domain family is found in bacteria, and is approximately 80 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=32.99 E-value=85 Score=24.91 Aligned_cols=31 Identities=32% Similarity=0.502 Sum_probs=27.4
Q ss_pred ChHHHHHHHhhChHHHHHHHHHhc-CCCCCCc
Q 022273 60 DPELRSVLELATDSELYELERILF-GPSYFSP 90 (300)
Q Consensus 60 ddELr~~LELATdEEL~eLt~ILf-~~s~fsP 90 (300)
-+|||.+++-.+++|..+|+.+.. ||-=|+|
T Consensus 3 ~~el~~~I~~l~~deqaeLvALmwiGRGd~~~ 34 (75)
T PF12616_consen 3 EEELRSFIEDLNEDEQAELVALMWIGRGDFEA 34 (75)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHhcCCCCCH
Confidence 479999999999999999999998 7766666
No 14
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=30.34 E-value=39 Score=27.36 Aligned_cols=20 Identities=25% Similarity=0.474 Sum_probs=18.7
Q ss_pred CCCchHHHHHHHHHhhcCCC
Q 022273 137 GWRPSYRNVLLAVRKNLNIP 156 (300)
Q Consensus 137 G~~vsYReVLldVckkLkV~ 156 (300)
..+++|+++.-.|++|||++
T Consensus 18 p~~~~y~~L~~ki~~kLkl~ 37 (80)
T cd06406 18 ARGLSYATLLQKISSKLELP 37 (80)
T ss_pred CCCCCHHHHHHHHHHHhCCC
Confidence 46999999999999999997
No 15
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=28.55 E-value=53 Score=28.71 Aligned_cols=33 Identities=18% Similarity=0.246 Sum_probs=25.2
Q ss_pred HHHHHHhhcCCCCC---CCC--ChHHHHHHHHHHHHhh
Q 022273 145 VLLAVRKNLNIPCS---SKL--STEDLEAEIFLHLLQE 177 (300)
Q Consensus 145 VLldVckkLkV~~s---~kl--sT~dLEaEIFLhLL~~ 177 (300)
-|-.+|++++|+.. ..- +....-+++|++++++
T Consensus 151 ~L~~l~~~~gi~~~~~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 151 VLAKACQAAGIEFDNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred cHHHHHHHCCCCCCCCCCcChHHHHHHHHHHHHHHHHh
Confidence 38899999999853 333 4455668999999987
No 16
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=28.51 E-value=92 Score=25.29 Aligned_cols=21 Identities=29% Similarity=0.507 Sum_probs=10.9
Q ss_pred HHHHhhChHHHHHHHHHhcCC
Q 022273 65 SVLELATDSELYELERILFGP 85 (300)
Q Consensus 65 ~~LELATdEEL~eLt~ILf~~ 85 (300)
.++.+-+.||.++|-+-|..+
T Consensus 9 ~i~~l~~~ee~~~f~~dL~T~ 29 (87)
T PF01371_consen 9 AILSLKDEEECYDFFEDLCTP 29 (87)
T ss_dssp HHHCHHCHHCHHHHHHHHSSH
T ss_pred HHHHcCCHHHHHHHHHHhCCH
Confidence 344455555555555555433
No 17
>TIGR00759 aceE pyruvate dehydrogenase E1 component, homodimeric type. WARNING: This family is classified as subfamily rather than equivalog because it includes a counterexample from Pseudomonas putida, MdeB, that is active as an E1 component of an alpha-ketoglutarate dehydrogenase complex rather than a pyruvate dehydrogase complex. The second pyruvate dehydrogenase complex E1 protein from Alcaligenes eutrophus, PdhE, complements an aceE mutant of E. coli but is not part of a pyruvate dehydrogenase complex operon, is more similar to the Pseudomonas putida MdeB than to E. coli AceE, and may have also have a different primary specificity.
Probab=26.91 E-value=5.7e+02 Score=28.96 Aligned_cols=136 Identities=19% Similarity=0.290 Sum_probs=0.0
Q ss_pred ChHHHHHHHhhChHHHHHHHHHhcCCCCCCccchhhcccCCcchhHHhhhhHHHHHHHHHHHHHHhhhccch---hhhhc
Q 022273 60 DPELRSVLELATDSELYELERILFGPSYFSPLLKSFTKRADVDYVMIEQDLEEREDFIASLESRFLFLAADA---RSTLR 136 (300)
Q Consensus 60 ddELr~~LELATdEEL~eLt~ILf~~s~fsPLLkSi~kr~~~Dy~~i~~~~q~R~~~i~~IEsRFqfLAADs---~svLR 136 (300)
++|+.+.++-.|||||..| ++++-|+.. ..+.+..--..=+.=. +.|++
T Consensus 338 ~~~l~~lv~~~sD~~i~~l------------------~rgGHD~~~----------I~~A~~~A~~~~grPTvIlA~TvK 389 (885)
T TIGR00759 338 TPELKALVADMSDADIWAL------------------NRGGHDPRK----------VYAAYAAAQEHKGQPTVILAKTIK 389 (885)
T ss_pred cHHHHHHhhccchhhhhhc------------------cCCCCCHHH----------HHHHHHHHHhCCCCCEEEEEeeee
Q ss_pred CCCch---------------HHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhhccccCCCCCCcccCCchhhhhH
Q 022273 137 GWRPS---------------YRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYASEESGVFPGSWENSEASDAQNS 201 (300)
Q Consensus 137 G~~vs---------------YReVLldVckkLkV~~s~klsT~dLEaEIFLhLL~~~ss~~~g~~~~aWekm~~~~e~~s 201 (300)
|+|+. =.+-|.+.+++++|| .+-++||. - .|.+.++....-.
T Consensus 390 G~G~~~~~e~~n~~H~~k~l~~e~l~~~r~~~g~~----~~d~~~~~--------~-----------~~~~~~~~s~e~~ 446 (885)
T TIGR00759 390 GYGMGDAAESRNTAHQVKKLEVDALKNFRDRFELP----LSDAQVEE--------L-----------PYYHPGEGSPEVR 446 (885)
T ss_pred cCCCChhhCCCcccccCCCCCHHHHHHHHHHcCCC----CChhHhcc--------C-----------CCcCCCCCCHHHH
Q ss_pred HHhhhhhhHHHHhh-----------hhccCchhHHHHHHhcc--ceeehHHHHHHHHHHHHH
Q 022273 202 LELGLSQWKVQALA-----------AFNAGAVELKSMMLKGG--GIYTLVKIYQLLMRNLSG 250 (300)
Q Consensus 202 L~~~lq~w~~~~la-----------~~klg~~ell~llLKGG--salavssi~~~l~kqla~ 250 (300)
....-. +.+. +..+++-+...-++||+ .-++-+...--++..|++
T Consensus 447 y~~~rr----~~Lgg~~p~R~~~~~~l~vP~l~~~~~~~~~~~~~~~STt~afvr~l~~L~r 504 (885)
T TIGR00759 447 YLLARR----QALGGYLPARRTFAEHLTVPALEFFGALLKGSGEREVSTTMAFVRILNKLLK 504 (885)
T ss_pred HHHHHH----HHhCCCCCCcCCCCCCCCCCCchhhHHHhcCCCCCCccHHHHHHHHHHHHhc
No 18
>cd02642 R3H_encore_like R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H domain is a potential regulator of DBF1 activity in stress responses. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=25.49 E-value=98 Score=23.02 Aligned_cols=43 Identities=23% Similarity=0.312 Sum_probs=35.2
Q ss_pred HHHHHHHHHHhhhccch-hhh--hcCCCchHHHHHHHHHhhcCCCC
Q 022273 115 DFIASLESRFLFLAADA-RST--LRGWRPSYRNVLLAVRKNLNIPC 157 (300)
Q Consensus 115 ~~i~~IEsRFqfLAADs-~sv--LRG~~vsYReVLldVckkLkV~~ 157 (300)
.|+-.||..|.=|..|+ ... |..-..-+|-++-+||++.|...
T Consensus 3 ~~~l~~E~~i~~Fi~~~~~~~~~f~pm~sy~RllvH~la~~~gL~s 48 (63)
T cd02642 3 LFVLKLEKDLLAFIKDSTRQSLELPPMNSYYRLLAHRVAQYYGLDH 48 (63)
T ss_pred hHHHHHHHHHHHHHhCCCCCeeEcCCCCcHHHHHHHHHHHHhCCee
Confidence 48889999999999888 444 44558899999999999988754
No 19
>PF07176 DUF1400: Alpha/beta hydrolase of unknown function (DUF1400); InterPro: IPR010802 This domain is specific to cyanobacterial proteins, its function and the function of the proteins it is associated with, are uncharacterised.
Probab=25.16 E-value=91 Score=26.39 Aligned_cols=36 Identities=28% Similarity=0.421 Sum_probs=32.9
Q ss_pred CCCCCChHHHHHHHhhChHHHHHHHHHhcCCCCCCc
Q 022273 55 GQGAFDPELRSVLELATDSELYELERILFGPSYFSP 90 (300)
Q Consensus 55 ~~~~~ddELr~~LELATdEEL~eLt~ILf~~s~fsP 90 (300)
..|..++||+..+.+.+.++.++|-++|..+=.++|
T Consensus 26 ~tG~~~~~L~~~~~ll~~~~~~~lr~~L~~~~~~~~ 61 (127)
T PF07176_consen 26 ETGEISPELAFYLNLLSPQQRQQLRELLNTPIPIDP 61 (127)
T ss_pred HcCCCCHHHHHHHHhcCHhhHHHHHHHHcCCCCCCH
Confidence 367889999999999999999999999998887877
No 20
>COG3426 Butyrate kinase [Energy production and conversion]
Probab=22.05 E-value=1.7e+02 Score=29.53 Aligned_cols=49 Identities=27% Similarity=0.304 Sum_probs=35.6
Q ss_pred hccCchhHHHHHHhccceeehH---HHHHHHHHHHHH----HHHHHHhhhHHHHHH
Q 022273 217 FNAGAVELKSMMLKGGGIYTLV---KIYQLLMRNLSG----KFFLEAANYQIKKEV 265 (300)
Q Consensus 217 ~klg~~ell~llLKGGsalavs---si~~~l~kqla~----q~al~~A~YQ~ake~ 265 (300)
.|-.++|++..+..+|+.++.. ...+..-++..+ |++.++-.||+||+.
T Consensus 231 gk~t~~El~k~i~g~gG~~aylGT~d~~~v~~~~~~Gd~~a~~~~~AmayQVaKeI 286 (358)
T COG3426 231 GKYTEEELLKKITGKGGLVAYLGTNDAKEVERRIEQGDEKAKLAYEAMAYQVAKEI 286 (358)
T ss_pred CcccHHHHHHHhhcCCceEEEeccchHHHHHHHHHcccHHHHHHHHHHHHHHHHHH
Confidence 3555699999999999988753 223333333333 889999999999997
No 21
>PF04891 NifQ: NifQ; InterPro: IPR006975 NifQ is involved in early stages of the biosynthesis of the iron-molybdenum cofactor (FeMo-co) [], which is an integral part of the active site of dinitrogenase []. The conserved C-terminal cysteine residues may be involved in metal binding [].; GO: 0030151 molybdenum ion binding, 0009399 nitrogen fixation
Probab=21.96 E-value=94 Score=28.04 Aligned_cols=53 Identities=21% Similarity=0.215 Sum_probs=46.0
Q ss_pred CcchhHHhhhhHHHHHHHHHHHHHHhhhccchhhhhcCCCchHHHHHHHHHhhcCCC
Q 022273 100 DVDYVMIEQDLEEREDFIASLESRFLFLAADARSTLRGWRPSYRNVLLAVRKNLNIP 156 (300)
Q Consensus 100 ~~Dy~~i~~~~q~R~~~i~~IEsRFqfLAADs~svLRG~~vsYReVLldVckkLkV~ 156 (300)
++||.=.+-...+|+..-..+...|-=||+--..=+|-++..||+ +|+.-++.
T Consensus 97 ~~~HLWqDLGL~~R~eLs~Lm~r~Fp~Laa~N~~~MrWKKFfYrq----lCe~eG~~ 149 (167)
T PF04891_consen 97 GPDHLWQDLGLRSRAELSALMRRHFPPLAARNTRNMRWKKFFYRQ----LCEREGLY 149 (167)
T ss_pred CCCccHHhcCCCCHHHHHHHHHHHhHHHHHhccCCCcHHHHHHHH----HHHHcCCC
Confidence 678887888899999999999999999998888888988999998 57777765
No 22
>PF02836 Glyco_hydro_2_C: Glycosyl hydrolases family 2, TIM barrel domain; InterPro: IPR006103 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 2 GH2 from CAZY comprises enzymes with several known activities; beta-galactosidase (3.2.1.23 from EC); beta-mannosidase (3.2.1.25 from EC); beta-glucuronidase (3.2.1.31 from EC). These enzymes contain a conserved glutamic acid residue which has been shown [], in Escherichia coli lacZ (P00722 from SWISSPROT), to be the general acid/base catalyst in the active site of the enzyme. Beta-galactosidase from E. coli has a TIM-barrel-like core surrounded by four other largely beta domains [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3CMG_A 3FN9_C 1YQ2_A 3K4D_B 3LPG_B 3LPF_A 3K4A_B 3K46_B 3GM8_A 3DEC_A ....
Probab=21.77 E-value=60 Score=29.86 Aligned_cols=38 Identities=11% Similarity=0.132 Sum_probs=26.9
Q ss_pred HHHHHHHhhhccchhhhhcCCCchHHHHHHHHHhhcCC
Q 022273 118 ASLESRFLFLAADARSTLRGWRPSYRNVLLAVRKNLNI 155 (300)
Q Consensus 118 ~~IEsRFqfLAADs~svLRG~~vsYReVLldVckkLkV 155 (300)
+.++..++.+-.=++|.+|-..-.+.+-.++.||++||
T Consensus 36 ~~~~~d~~l~k~~G~N~iR~~h~p~~~~~~~~cD~~Gi 73 (298)
T PF02836_consen 36 EAMERDLELMKEMGFNAIRTHHYPPSPRFYDLCDELGI 73 (298)
T ss_dssp HHHHHHHHHHHHTT-SEEEETTS--SHHHHHHHHHHT-
T ss_pred HHHHHHHHHHHhcCcceEEcccccCcHHHHHHHhhcCC
Confidence 45667777777666999997655677888999999998
No 23
>PF02196 RBD: Raf-like Ras-binding domain; InterPro: IPR003116 This is the Ras-binding domain found in proteins related to Ras. It is found in association with the PE-bind and pkinase domains.; GO: 0005057 receptor signaling protein activity, 0007165 signal transduction; PDB: 1RFA_A 1C1Y_B 3KUD_B 1GUA_B 3KUC_B 2L05_A 3NY5_D 1RRB_A 1WFY_A 1WXM_A.
Probab=21.63 E-value=54 Score=25.06 Aligned_cols=32 Identities=13% Similarity=0.102 Sum_probs=22.4
Q ss_pred ccchhhhhcCC-CchHHHHHHHHHhhcCCCCCC
Q 022273 128 AADARSTLRGW-RPSYRNVLLAVRKNLNIPCSS 159 (300)
Q Consensus 128 AADs~svLRG~-~vsYReVLldVckkLkV~~s~ 159 (300)
=++..+++.=+ |.+.|++|..+|+|-+++++.
T Consensus 8 P~~q~t~V~vrpg~ti~d~L~~~~~kr~L~~~~ 40 (71)
T PF02196_consen 8 PNGQRTVVQVRPGMTIRDALSKACKKRGLNPEC 40 (71)
T ss_dssp TTTEEEEEEE-TTSBHHHHHHHHHHTTT--CCC
T ss_pred CCCCEEEEEEcCCCCHHHHHHHHHHHcCCCHHH
Confidence 34445555544 899999999999999998764
No 24
>PF08708 PriCT_1: Primase C terminal 1 (PriCT-1); InterPro: IPR014820 This alpha helical domain is found at the C-terminal of primases.
Probab=21.49 E-value=1.5e+02 Score=21.81 Aligned_cols=54 Identities=19% Similarity=0.279 Sum_probs=38.5
Q ss_pred hhhHHHHHHHHHHHHHHhhhccchhhhhcCCCchHHHHHHHHHhhcCCCCCCCCChHHHHH
Q 022273 108 QDLEEREDFIASLESRFLFLAADARSTLRGWRPSYRNVLLAVRKNLNIPCSSKLSTEDLEA 168 (300)
Q Consensus 108 ~~~q~R~~~i~~IEsRFqfLAADs~svLRG~~vsYReVLldVckkLkV~~s~klsT~dLEa 168 (300)
+++-+|..++=.+..++.|-+-|--. ..++.+.+.|..++-.|+..|+-.|+++
T Consensus 7 ~~~g~RN~~lf~~a~~~~~~~v~~~~-------~~~~~v~~~~~~~N~~~~~PL~~~Ev~~ 60 (71)
T PF08708_consen 7 IVEGGRNCTLFRLARRLAYRGVDQEE-------QFRQEVLSLAQAINSNFSPPLPESEVKA 60 (71)
T ss_pred CCCCCcHHHHHHHHHHHHHhCCCHhH-------HHHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence 34556777776666666655554433 7778888899999988888888877765
No 25
>PRK14082 hypothetical protein; Provisional
Probab=20.91 E-value=75 Score=25.12 Aligned_cols=16 Identities=31% Similarity=0.640 Sum_probs=14.6
Q ss_pred ChHHHHHHHHHHHHhh
Q 022273 162 STEDLEAEIFLHLLQE 177 (300)
Q Consensus 162 sT~dLEaEIFLhLL~~ 177 (300)
.-+|||+||=+++.++
T Consensus 33 eREDLeQElk~Ki~eK 48 (65)
T PRK14082 33 EREDLEQELKIKIIEK 48 (65)
T ss_pred hHHHHHHHHHHHHHHH
Confidence 4799999999999988
No 26
>TIGR01702 CO_DH_cata carbon-monoxide dehydrogenase, catalytic subunit. This model represents the carbon-monoxide dehydrogenase catalytic subunit. This protein is related to prismane (also called hybrid cluster protein), a complex whose activity is not yet fully described; the two share similar sets of ligands to unusual metal-containing clusters.
Probab=20.45 E-value=2.7e+02 Score=30.12 Aligned_cols=52 Identities=21% Similarity=0.221 Sum_probs=37.7
Q ss_pred hcCCCchHH----HHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhhccccCCCCCC
Q 022273 135 LRGWRPSYR----NVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYASEESGVFPGS 189 (300)
Q Consensus 135 LRG~~vsYR----eVLldVckkLkV~~s~klsT~dLEaEIFLhLL~~~ss~~~g~~~~a 189 (300)
-+|+.+ |+ +=|..+++.++|+... -++ |+=.++=-.+|+++.....+...+.
T Consensus 100 a~g~~~-y~Ikd~~Kl~~~a~~~gI~te~-~~~-eia~~va~~~l~D~~~~~~~~~~~~ 155 (621)
T TIGR01702 100 AEGKTP-YSIKDEAKLKWLAKKLGIDTEG-DSN-ELAVEVAEIVLSDFRKPREEKAELV 155 (621)
T ss_pred hcCCcc-cccccHHHHHHHHHHCCCCCCC-chH-HHHHHHHHHHHHHhccccccchhhH
Confidence 346555 76 7899999999999865 333 8889999999999875544444443
Done!