Query 015642
Match_columns 403
No_of_seqs 175 out of 1351
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 08:13:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015642.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015642hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2439 Nuclear architecture r 100.0 3E-102 7E-107 757.1 24.8 379 1-403 78-459 (459)
2 COG4624 Iron only hydrogenase 100.0 3.2E-85 6.8E-90 639.2 20.3 350 1-390 50-403 (411)
3 PF02906 Fe_hyd_lg_C: Iron onl 100.0 1.9E-83 4.2E-88 626.6 24.0 284 18-331 1-285 (285)
4 TIGR02512 Fe_only_hydrog hydro 100.0 4.7E-79 1E-83 616.5 33.2 301 4-332 70-373 (374)
5 PF02256 Fe_hyd_SSU: Iron hydr 99.3 4.1E-13 8.9E-18 101.0 2.2 54 339-392 4-59 (60)
6 PRK12809 putative oxidoreducta 74.8 1.8 3.8E-05 47.4 2.0 47 17-63 151-198 (639)
7 PF09756 DDRGK: DDRGK domain; 61.5 11 0.00024 34.9 4.0 50 6-62 100-149 (188)
8 PF06574 FAD_syn: FAD syntheta 50.4 12 0.00027 33.3 2.4 60 18-81 38-100 (157)
9 PF04914 DltD_C: DltD C-termin 44.9 60 0.0013 28.2 5.7 58 5-63 36-96 (130)
10 PRK13011 formyltetrahydrofolat 42.2 1.3E+02 0.0029 29.5 8.4 73 5-82 101-187 (286)
11 cd01965 Nitrogenase_MoFe_beta_ 41.8 87 0.0019 32.4 7.4 20 197-216 170-189 (428)
12 cd01966 Nitrogenase_NifN_1 Nit 40.7 1.3E+02 0.0028 31.2 8.5 89 18-128 22-125 (417)
13 PRK07114 keto-hydroxyglutarate 40.4 2.9E+02 0.0063 26.2 10.1 129 7-211 5-134 (222)
14 PF02236 Viral_DNA_bi: Viral D 33.3 36 0.00078 27.5 2.3 41 109-150 44-84 (86)
15 PF13592 HTH_33: Winged helix- 33.1 30 0.00065 25.5 1.8 36 27-64 9-44 (60)
16 TIGR00083 ribF riboflavin kina 31.5 1.2E+02 0.0025 30.0 6.1 63 18-82 31-93 (288)
17 KOG1611 Predicted short chain- 31.0 11 0.00024 36.0 -1.1 33 25-57 102-137 (249)
18 cd01977 Nitrogenase_VFe_alpha 27.6 4.9E+02 0.011 26.8 10.2 46 61-117 66-120 (415)
19 COG1105 FruK Fructose-1-phosph 26.7 1.8E+02 0.0038 29.2 6.4 56 2-66 111-170 (310)
20 smart00421 HTH_LUXR helix_turn 25.5 1.2E+02 0.0026 20.6 3.9 30 29-58 21-50 (58)
21 PF03096 Ndr: Ndr family; Int 25.2 89 0.0019 30.8 4.0 98 31-142 72-172 (283)
22 KOG2931 Differentiation-relate 24.1 1.3E+02 0.0028 30.0 4.8 73 31-114 95-170 (326)
23 PF11576 DUF3236: Protein of u 24.0 73 0.0016 28.2 2.8 36 17-57 118-154 (154)
24 PF04343 DUF488: Protein of un 22.0 1.5E+02 0.0032 24.9 4.3 55 6-69 1-58 (122)
25 PF01927 Mut7-C: Mut7-C RNAse 21.5 1.1E+02 0.0024 26.7 3.6 21 44-64 9-29 (147)
26 PF00325 Crp: Bacterial regula 21.1 1.9E+02 0.0041 18.9 3.6 28 28-56 4-31 (32)
27 cd01979 Pchlide_reductase_N Pc 21.0 8.9E+02 0.019 24.6 11.1 16 198-213 169-184 (396)
28 cd07025 Peptidase_S66 LD-Carbo 20.8 2E+02 0.0044 28.0 5.6 54 21-82 1-59 (282)
29 cd00068 GGL G protein gamma su 20.6 51 0.0011 24.3 1.0 23 99-121 22-46 (57)
30 PRK05569 flavodoxin; Provision 20.1 3.7E+02 0.0081 22.6 6.5 65 6-80 68-138 (141)
31 PF01418 HTH_6: Helix-turn-hel 20.1 1.3E+02 0.0027 23.2 3.2 25 29-57 37-61 (77)
No 1
>KOG2439 consensus Nuclear architecture related protein [Nuclear structure]
Probab=100.00 E-value=3.3e-102 Score=757.14 Aligned_cols=379 Identities=47% Similarity=0.828 Sum_probs=347.4
Q ss_pred CcccccHHHHHHHHhCCC---eEEEEeCccchHHHHHHhCCChHHHHHHHHHHHHHcCCcEEEechhHHHHhHHHHHHHH
Q 015642 1 MLEKQSLDEFLSNINKGK---AVIISLSPQSRASLAEHFGISPLQVFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNEF 77 (403)
Q Consensus 1 l~~~qs~~~~~~~l~~~k---~~Vv~iaPq~r~sl~~~f~~~~~~~~~kl~~~lk~LGf~~V~dt~~gadi~~~e~~~E~ 77 (403)
|+++||+.+|++.|+..| .+||++|||+|+|||++||++..++..+|..|+|+|||+||+||++++++++.|.++||
T Consensus 78 lls~Qs~~~~~k~l~~~k~~~~lvvsvSPQ~~~slAa~~gls~~e~~~~L~~F~kklgvhyv~DT~~sR~~sl~es~~Ef 157 (459)
T KOG2439|consen 78 LLSEQSHKEFLKVLQKSKQQKVLVVSVSPQSRASLAAKYGLSLREAALRLTSFFKKLGVHYVVDTSFSRDFSLSESYEEF 157 (459)
T ss_pred hhhhhhHHHHHHhhhhccccceEEEecChhHHHHHHHHhCCCHHHHHHHHHHHHHhcCeeEEeehHHHHHHHHHHHHHHH
Confidence 689999999999998876 77999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhcccCcccccCCCCCceecCChHHHHHHHHhcCCCCCCCCCCCCCHHHHHHHHHHHHHhHhhCCCCCCeEEEEEE
Q 015642 78 IARYKQSQESDDERSNSSLPMLSSACPGWICYAEKQLGSYILPYISSVKSPQQTIGATIKHHICQKLGFRPDEIYHVTVM 157 (403)
Q Consensus 78 ~~~~~~~~~~~~~~~~~~~P~isS~CPgwV~yiEk~~~P~lip~Ls~vkSPq~i~g~liK~~~~~~~~~~~~~i~~V~I~ 157 (403)
+.|++++.. ....||++|+|||||||+||+| |.||||||+|||||||||+|||.+++.+.+++|++||||++|
T Consensus 158 v~~~r~~~~------~~~~PlLsSaCPG~v~YaEkt~-~~Lip~ls~vkSPQQi~Gslikd~~~~q~~l~p~~v~hvsvM 230 (459)
T KOG2439|consen 158 VARYRQHSE------EERTPLLSSACPGWVCYAEKTH-GRLIPHLSRVKSPQQIMGSLIKDFFASQQSLSPEKVFHVSVM 230 (459)
T ss_pred HHHhhcccc------cccccchhhcCCceeEEeeccc-cccchhhhccCCHHHhhhHHHHHHHHHhcCCCccceeeEeec
Confidence 998875432 2457999999999999999999 889999999999999999999999999999999999999999
Q ss_pred ccchhhHhhhcchhhcccccchhccccCCCCCCCceEEEcHHHHHHHHHhcCCCCCCCCCCcccccCCCCCCCCcccccc
Q 015642 158 PCYDKKLEAAREDFVFQLDSQEETYRDEGLEIPEVDSVLTTGEVLDLIQLKAVNFEALEESPLDKMLTNVDDEGHLYGVA 237 (403)
Q Consensus 158 PC~aKK~Ea~r~~~~~~~~~~~~~~~~~~~~~~~VD~VLTt~El~~~l~~~~i~~~~l~~~~~d~~~~~~s~~~~~~~~~ 237 (403)
||+|||+||+|++|.. .+.++||||||++|+.+++++.++++.....+ .|..+...+........|
T Consensus 231 PCfDKKLEAsR~~f~~-------------~~~r~~DcVlT~~Ei~k~l~e~~~~l~~~~~~-~d~l~~~~~~~~~~~~~G 296 (459)
T KOG2439|consen 231 PCFDKKLEASREEFKE-------------HGVRDVDCVLTTGEIFKLLEELDFDLPVRDAE-VDTLPSGLSRETVTSNDG 296 (459)
T ss_pred ccccHhhhccchhhhc-------------cCCcccceEeehHHHHHHHHhcCcccccccch-hhcccccccccceeeccC
Confidence 9999999999999951 15789999999999999999999998776544 455444444444556669
Q ss_pred CCCccHHHHHHHHHHHHhhccccccccceeeecCCCcEEEEEEeCCeeeEEEEEEechHHHHHHHHHHhcCCCCCcEEEe
Q 015642 238 GSSGGYAETVFRHAAKTLFGKVIEGHLEFKTIRNSDFREVALEVEGKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVEV 317 (403)
Q Consensus 238 ~~SGG~~e~i~~~~~~~l~~~~~~~~~~~~~~rn~d~~e~~l~~~g~~~~~~a~v~G~~ni~~~l~~lk~gk~~~~fIEv 317 (403)
|+||||+++|+|++++++||.++. ++.|+..||.||+|+++.-+|++++++|.+||||||||+++++++||.+||||||
T Consensus 297 gsSGGYa~~i~r~aak~lfg~~v~-~~t~k~~rN~Df~e~tl~~~geill~~a~~yGFRNiQNlvrklkk~k~pyhyvEV 375 (459)
T KOG2439|consen 297 GSSGGYAEHIFRHAAKELFGEIVE-PVTYKELRNSDFREVTLEKNGEILLRFAAAYGFRNIQNLVRKLKKGKFPYHYVEV 375 (459)
T ss_pred CCCcchHHHHHHHHHHHhcCCccc-chhhhhhccccceeeeeecCchHHHHHHHhhhhhHHHHHHHHHhccCCCcceeEE
Confidence 999999999999999999999885 8899999999999999999999999999999999999999999999999999999
Q ss_pred cCCcccccCCCCCcCCCCCCChhHHHHHHHHHHhhcccCCCCCCChHHHHHHHHHhcCCCChhhhcceeeeecccccccc
Q 015642 318 MACPSGCLNGGGQIKPKPGQSPKELIKTLETIYLENVMLADPFKNPLVRSLYDEWLEQPGSEKAKKHVHTEYHPVVKSIT 397 (403)
Q Consensus 318 mACpgGCinGgGq~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~n~~v~~ly~~~l~~~~~~~~~~llht~y~~~~~~~~ 397 (403)
|||||||+|||||++.++...+++++++++++|.+.+. +.+...|.+.+||++|+.+ ++..+.++|||+||+|+++.+
T Consensus 376 mACpgGC~NGgGQl~~~~~~~~~~llq~ve~ly~e~~~-~~~e~~~~~~~L~E~w~k~-~~~~~r~~Lht~y~avek~~~ 453 (459)
T KOG2439|consen 376 MACPGGCINGGGQLQTPDGHARKELLQQVEALYGEIPR-RRDESSPTVPKLEEEWLKG-DSKKARKVLHTDYQAVEKDVT 453 (459)
T ss_pred eccCccccCCCccccCCccchHHHHHHHHHHhhccCcc-ccCccccchhHHHHHHHhc-Cchhhhhhhcccchhhhcchh
Confidence 99999999999999988878889999999999988877 4555668999999999998 778899999999999999999
Q ss_pred cccCCC
Q 015642 398 AQLHNW 403 (403)
Q Consensus 398 ~~~~~w 403 (403)
+..++|
T Consensus 454 sl~~kW 459 (459)
T KOG2439|consen 454 SLGNKW 459 (459)
T ss_pred hhccCC
Confidence 988899
No 2
>COG4624 Iron only hydrogenase large subunit, C-terminal domain [General function prediction only]
Probab=100.00 E-value=3.2e-85 Score=639.22 Aligned_cols=350 Identities=34% Similarity=0.617 Sum_probs=306.9
Q ss_pred CcccccHHHHHHHHhC---CCeEEEEeCccchHHHHHHhCCChHHHH-HHHHHHHHHcCCcEEEechhHHHHhHHHHHHH
Q 015642 1 MLEKQSLDEFLSNINK---GKAVIISLSPQSRASLAEHFGISPLQVF-KKLTTFLKSLGVKSIFDTSCSRDLTLIEACNE 76 (403)
Q Consensus 1 l~~~qs~~~~~~~l~~---~k~~Vv~iaPq~r~sl~~~f~~~~~~~~-~kl~~~lk~LGf~~V~dt~~gadi~~~e~~~E 76 (403)
|++.|+...+++.|.+ .+.+++++|||+|++++.+||++.+++. .++..|+|++||++||||++|||++++|+++|
T Consensus 50 li~~~s~~~~~~~le~~~~~k~v~v~~apsvR~al~~~~gl~~~~~~a~~~~~f~k~~gf~~vvdt~fgad~vi~eea~E 129 (411)
T COG4624 50 AISLQSGKKVLEELEDLFCDKIVLVSNAPSVRAALAEEFGLSEGEAVAVLMSFFLKKLGFDKVVDTNFGADMVIMEEAAE 129 (411)
T ss_pred hhhhcchHHHHHHhhccccceEEEecCCHHHHHHHHHHhCCChhHHHHHHHHHHHHHcChHhhhhhhhccchHHHHHHHH
Confidence 5788999999999988 5888999999999999999999999887 88899999999999999999999999999999
Q ss_pred HHHHHhhcccCcccccCCCCCceecCChHHHHHHHHhcCCCCCCCCCCCCCHHHHHHHHHHHHHhHhhCCCCCCeEEEEE
Q 015642 77 FIARYKQSQESDDERSNSSLPMLSSACPGWICYAEKQLGSYILPYISSVKSPQQTIGATIKHHICQKLGFRPDEIYHVTV 156 (403)
Q Consensus 77 ~~~~~~~~~~~~~~~~~~~~P~isS~CPgwV~yiEk~~~P~lip~Ls~vkSPq~i~g~liK~~~~~~~~~~~~~i~~V~I 156 (403)
|.+|+++ +..+|+|||||||||+|+||+| |+|+||||+|||||||+|+++|+++++++|+.|++||||||
T Consensus 130 f~~r~~~---------n~~lP~~tscCPgwV~~~Ekt~-P~Ll~~LS~vkSPQq~~g~~iK~~~~~~~~~~~e~~~~Vsi 199 (411)
T COG4624 130 FLERVKK---------NDDLPLFTSCCPGWVNYAEKTY-PNLLPNLSSVKSPQQALGSLIKTYYAEKLGIAPEDVYHVSI 199 (411)
T ss_pred HHHHHhc---------CCCCceeeccChHHHHHHHHhh-HHHHhhccccCCHHHHHHHHHHHHhhhhcCCCccceeEEEE
Confidence 9999874 4679999999999999999999 99999999999999999999999999999999999999999
Q ss_pred EccchhhHhhhcchhhcccccchhccccCCCCCCCceEEEcHHHHHHHHHhcCCCCCCCCCCcccccCCCCCCCCccccc
Q 015642 157 MPCYDKKLEAAREDFVFQLDSQEETYRDEGLEIPEVDSVLTTGEVLDLIQLKAVNFEALEESPLDKMLTNVDDEGHLYGV 236 (403)
Q Consensus 157 ~PC~aKK~Ea~r~~~~~~~~~~~~~~~~~~~~~~~VD~VLTt~El~~~l~~~~i~~~~l~~~~~d~~~~~~s~~~~~~~~ 236 (403)
|||+|||+||.|++- +.++||+||||+||.+||+..+||++.+|+.++|.+.+..++++.+||.
T Consensus 200 MPC~aKK~Ea~r~~~----------------ng~~iD~vLTtrEL~~ml~~l~id~~~lp~~~~~s~~g~~sga~~lfG~ 263 (411)
T COG4624 200 MPCIAKKLEADRDED----------------NGRAIDFVLTTRELVKMLKELRIDFARLPDGHYDSPAGFSSGAGLLFGS 263 (411)
T ss_pred ecchhhhhhhcCccc----------------cCcceeEEecHHHHHHHHHHhCCCHhHCCCCCccccccccccccccCCC
Confidence 999999999999831 2389999999999999999999999999999999999888888888888
Q ss_pred cCCCccHHHHHHHHHHHHhhccccccccceeeecCCCcEEEEEEeCCeeeEEEEEEechHHHHHHHHHHhcCCCCCcEEE
Q 015642 237 AGSSGGYAETVFRHAAKTLFGKVIEGHLEFKTIRNSDFREVALEVEGKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVE 316 (403)
Q Consensus 237 ~~~SGG~~e~i~~~~~~~l~~~~~~~~~~~~~~rn~d~~e~~l~~~g~~~~~~a~v~G~~ni~~~l~~lk~gk~~~~fIE 316 (403)
+|||++++.+. +.+.+..+ ..+.++..| .+|++....+.|.. .+.++++|.+|+++++++.+.+...|+|||
T Consensus 264 ---tGgv~e~v~~~--~l~~~~~~-e~v~~~~~~-~gI~~~e~~l~g~~-~k~~vv~G~~n~~~~~~~~~~~~~~~~fiE 335 (411)
T COG4624 264 ---TGGVMEAVLRT--RLLHDKHI-EAVDSEEVR-RGIQEAERKLGGSS-RKIAVVEGVKNVRNFFKSTTADEYRYDFIE 335 (411)
T ss_pred ---cccEEEEeecc--ccccccch-hhhhhhhhh-ccchhhhhhccCcc-eeeeeeehHHHHHHHHHhcccCCCcceEEE
Confidence 99999999874 33444333 235565566 67888888777766 699999999999999999988889999999
Q ss_pred ecCCcccccCCCCCcCCCCCCChhHHHHHHHHHHhhcccCCCCCCChHHHHHHHHHhcCCCChhhhcceeeeec
Q 015642 317 VMACPSGCLNGGGQIKPKPGQSPKELIKTLETIYLENVMLADPFKNPLVRSLYDEWLEQPGSEKAKKHVHTEYH 390 (403)
Q Consensus 317 vmACpgGCinGgGq~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~n~~v~~ly~~~l~~~~~~~~~~llht~y~ 390 (403)
||||||||||||||+........|++..+....+ .+.+.+++|+.+..+|++|++.| .+|++|||.|+
T Consensus 336 vmACpGGCinGgGq~~~~~~~~~R~~~~~~~~~~---~~~~~svd~~~~~k~le~~~~~p---l~~e~lh~~y~ 403 (411)
T COG4624 336 VMACPGGCINGGGQPYVERNDKERASVLQTKNGR---EPKLKSVDNLALKKMLEEYVKDP---LSHELLHTKYK 403 (411)
T ss_pred EeccCccccCCCCCcChhhhHHHHHHHHHhhhcc---CCceeecCcHHHHHHHHHHhcCc---ccHHHhcchhh
Confidence 9999999999999999833222333332222221 34568899999999999999988 78899999999
No 3
>PF02906 Fe_hyd_lg_C: Iron only hydrogenase large subunit, C-terminal domain; InterPro: IPR004108 Proteins containing this domain may be involved in the mechanism of biological hydrogen activation and contain 4FE-4S clusters. They can use molecular hydrogen for the reduction of a variety of substances.; PDB: 3LX4_A 1HFE_L 1GX7_A 1E08_A 1C4C_A 1FEH_A 3C8Y_A 1C4A_A.
Probab=100.00 E-value=1.9e-83 Score=626.55 Aligned_cols=284 Identities=44% Similarity=0.822 Sum_probs=244.4
Q ss_pred CeEEEEeCccchHHHHHHhCCChHHHHHHHHHHHHHcCCcEEEechhHHHHhHHHHHHHHHHHHhhcccCcccccCCCCC
Q 015642 18 KAVIISLSPQSRASLAEHFGISPLQVFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIARYKQSQESDDERSNSSLP 97 (403)
Q Consensus 18 k~~Vv~iaPq~r~sl~~~f~~~~~~~~~kl~~~lk~LGf~~V~dt~~gadi~~~e~~~E~~~~~~~~~~~~~~~~~~~~P 97 (403)
|++||+||||++++|+..|+++++++.++|.++||+|||++|+||++|||+++.++++||++++.+ +.++|
T Consensus 1 K~vva~iaPs~~~~f~~~~~~~~~~~~~~l~~~Lk~lGf~~V~d~a~gadl~~~~~~~e~~~~~~~---------~~~~p 71 (285)
T PF02906_consen 1 KKVVASIAPSFRAQFAEKFGLSPGEAPGQLVSALKKLGFDYVFDTAFGADLVILEEAEEFIERKEE---------GKPLP 71 (285)
T ss_dssp -EEEEEE-HHHHHTGGGGGT--TTSSHHHHHHHHHHTT-SEEEEHHHHHHHHHHHHHHHHHHHHCC---------TSSSS
T ss_pred CEEEEEECchhHHHHHhHhCcChhhHHHHHHHHHHHcCCCEEEECHHHHHHHHHHHHHHHHHhhcc---------cCCCc
Confidence 679999999999999999999999999999999999999999999999999999999999999753 34679
Q ss_pred ceecCChHHHHHHHHhcCCCCCCCCCCCCCHHHHHHHHHHHHHhHhhCCCCCCeEEEEEEccchhhHhhhcchhhccccc
Q 015642 98 MLSSACPGWICYAEKQLGSYILPYISSVKSPQQTIGATIKHHICQKLGFRPDEIYHVTVMPCYDKKLEAAREDFVFQLDS 177 (403)
Q Consensus 98 ~isS~CPgwV~yiEk~~~P~lip~Ls~vkSPq~i~g~liK~~~~~~~~~~~~~i~~V~I~PC~aKK~Ea~r~~~~~~~~~ 177 (403)
|||||||||||||||+| |+|+||||+++|||+++|+++|++++++.++.+.+++|||||||+|||+||.|+++..
T Consensus 72 ~itS~CP~~V~~iek~~-P~li~~ls~v~SP~~~~g~~~K~~~~~~~~~~~~~i~~V~I~PC~aKK~Ea~r~~~~~---- 146 (285)
T PF02906_consen 72 MITSCCPGWVCYIEKYY-PELIPNLSPVKSPMQIMGRLIKKYFAEESGIKPPDIYVVFIMPCIAKKLEASRPEFSG---- 146 (285)
T ss_dssp EE-TTSHHHHHHHHHH--GGGGGGB-SB-THHHHHHHHHTTHHHHHCT--GGGEEEEEEES-SHHHHHHTSTTCEC----
T ss_pred eEecccHHHHHHHHHhC-cccccccCCCccHHHHHHHHHHHHHHHhcCCCCCCEEEEEEEcCccccccccCccccC----
Confidence 99999999999999999 9999999999999999999999999999999999999999999999999999998732
Q ss_pred chhccccCCCCCCCceEEEcHHHHHHHHHhcCCCCCCCCCCcccccCCCCCCCCccccccCCCccHHHHHHHHHHHHhhc
Q 015642 178 QEETYRDEGLEIPEVDSVLTTGEVLDLIQLKAVNFEALEESPLDKMLTNVDDEGHLYGVAGSSGGYAETVFRHAAKTLFG 257 (403)
Q Consensus 178 ~~~~~~~~~~~~~~VD~VLTt~El~~~l~~~~i~~~~l~~~~~d~~~~~~s~~~~~~~~~~~SGG~~e~i~~~~~~~l~~ 257 (403)
+.++||+||||+||.+||++.+||+.++++.++|.++...++.+++|+. ||||++++++++.+.++|
T Consensus 147 ----------~~~~vD~VLT~~El~~~l~~~~i~~~~~~~~~~d~~~~~~s~~~~~f~~---sGG~~~~v~~~~~~~~~~ 213 (285)
T PF02906_consen 147 ----------GSPDVDYVLTFEELAELLKEKGIDLAELEPEPFDNPFGESSGAGRIFGS---SGGVAEAVLRYAAEKLFG 213 (285)
T ss_dssp ----------TCESSSEEEEHHHHHHHHHHTT--GGGSS--B--CTTSSSCHHHCCCCS---TTHHHHHHHHHHHHHHHS
T ss_pred ----------CCcccCEechHHHHHHHHHHcCCChhHCCCccccchHHHhhhhhhcccc---CchHHHHHHHHHHHHhcC
Confidence 2469999999999999999999999999999999987777888888887 999999999999999999
Q ss_pred cccccccceeeecCC-CcEEEEEEeCCeeeEEEEEEechHHHHHHHHHHhcCCCCCcEEEecCCcccccCCCCCc
Q 015642 258 KVIEGHLEFKTIRNS-DFREVALEVEGKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVEVMACPSGCLNGGGQI 331 (403)
Q Consensus 258 ~~~~~~~~~~~~rn~-d~~e~~l~~~g~~~~~~a~v~G~~ni~~~l~~lk~gk~~~~fIEvmACpgGCinGgGq~ 331 (403)
.+++ .++|+.+||. |++|+++.++. . ++++++|||+|+||+|+++++|+.+|||||+|||||||+|||||+
T Consensus 214 ~~~~-~~~~~~~r~~~~~~e~~~~~g~-~-~~~~~~~G~~n~~~~l~~ik~g~~~~~~iEvmaCpgGCinGgGq~ 285 (285)
T PF02906_consen 214 EDLP-NVEIEKVRGKEDIKEATVEIGK-E-LRFAVVYGFRNIQNLLRKIKKGKSEYDFIEVMACPGGCINGGGQP 285 (285)
T ss_dssp STTS--S--GGGTSSTSEEEEEEEETT-E-EEEEEEESHHHHHHHHHHHHTTSS--SEEEEESSTTSGGGCTTS-
T ss_pred CCCC-cceeEeccCCCCeEEEEEeccc-c-eEEEEecCHHHHHHHHHHhhccCCCCeEEEECCCCCcccCCCCCC
Confidence 8885 5889999995 89999999955 4 699999999999999999999999999999999999999999996
No 4
>TIGR02512 Fe_only_hydrog hydrogenases, Fe-only. This model describes iron-only hydrogenases of anaerobic and microaerophilic bacteria and protozoa. This model is narrower, and covers a longer stretch of sequence, than Pfam model pfam02906. This family represents a division among families that belong to pfam02906, which also includes proteins such as nuclear prelamin A recognition factor in animals. Note that this family shows some heterogeneity in terms of periplasmic, cytosolic, or hydrogenosome location, NAD or NADP dependence, and overal protein protein length.
Probab=100.00 E-value=4.7e-79 Score=616.52 Aligned_cols=301 Identities=38% Similarity=0.701 Sum_probs=277.4
Q ss_pred cccHHHHHHHHhCCCeE-EEEeCccchHHHHHHhCCChHH-HHHHHHHHHHHcCCcEEEechhHHHHhHHHHHHHHHHHH
Q 015642 4 KQSLDEFLSNINKGKAV-IISLSPQSRASLAEHFGISPLQ-VFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIARY 81 (403)
Q Consensus 4 ~qs~~~~~~~l~~~k~~-Vv~iaPq~r~sl~~~f~~~~~~-~~~kl~~~lk~LGf~~V~dt~~gadi~~~e~~~E~~~~~ 81 (403)
+.+++++++.|++++.+ ++++||++++|+++.|+.+++. ..++|..+||+|||++|+||++|+|+++.|++.||++|+
T Consensus 70 ~~~~~~v~~~l~~~~~~~v~~~ap~~~~s~ge~~~~~~~~~~~~~l~~~lk~lGf~~v~et~~~ad~~~~e~~~e~i~~~ 149 (374)
T TIGR02512 70 KDHVDRVLKALADPKKVVVVQIAPAVRVALGEEFGMPIGTDVTGKMVAALRKLGFDYVFDTNFAADLTIMEEGTELLERL 149 (374)
T ss_pred hccHHHHHHHhccccceEEEEeChHHHHHHHHHhCCCccchHHHHHHHHHHHcCCCEEEECcHHHHHHHHHHHHHHHHHh
Confidence 35678999999887655 9999999999999999998644 468999999999999999999999999999999999987
Q ss_pred hhcccCcccccCCCCCceecCChHHHHHHHHhcCCCCCCCCCCCCCHHHHHHHHHHHHHhHhhCCCCCCeEEEEEEccch
Q 015642 82 KQSQESDDERSNSSLPMLSSACPGWICYAEKQLGSYILPYISSVKSPQQTIGATIKHHICQKLGFRPDEIYHVTVMPCYD 161 (403)
Q Consensus 82 ~~~~~~~~~~~~~~~P~isS~CPgwV~yiEk~~~P~lip~Ls~vkSPq~i~g~liK~~~~~~~~~~~~~i~~V~I~PC~a 161 (403)
++ +.++|||||||||||+||||+| |+|+|||||++|||+|+|+++|+++++.++++|++|+|||||||+|
T Consensus 150 ~~---------~~~~p~itS~CP~~v~~iek~~-P~li~~ls~v~SP~~~~g~~iK~~~~~~~~~~~~~i~~v~i~PC~a 219 (374)
T TIGR02512 150 KN---------GGKLPMFTSCCPGWVNYAEKYY-PELLPNLSSCKSPQQMLGAVIKTYWAKKMGIDPEDVYVVSIMPCTA 219 (374)
T ss_pred hc---------CCCCCeEecCCHHHHHHHHHHC-hhhhccccCCCChHHHHHHHHHHHhHHHcCCCcccEEEEEEECccc
Confidence 53 3457999999999999999999 9999999999999999999999999999999999999999999999
Q ss_pred hhHhhhcchhhcccccchhccccCCCCCCCceEEEcHHHHHHHHHhcCCCCCCCCCCcccccCCCCCCCCccccccCCCc
Q 015642 162 KKLEAAREDFVFQLDSQEETYRDEGLEIPEVDSVLTTGEVLDLIQLKAVNFEALEESPLDKMLTNVDDEGHLYGVAGSSG 241 (403)
Q Consensus 162 KK~Ea~r~~~~~~~~~~~~~~~~~~~~~~~VD~VLTt~El~~~l~~~~i~~~~l~~~~~d~~~~~~s~~~~~~~~~~~SG 241 (403)
||+||.|+++... +.++||+||||+||.+||++.+|++.++++.++|.++...++.+++|+. ||
T Consensus 220 KK~Ea~r~~~~~~-------------~~~~vD~vlT~~El~~~~~~~~i~~~~~~~~~~d~~~~~~~~~~~~f~~---sG 283 (374)
T TIGR02512 220 KKDEAQRPELKSD-------------GYRDVDAVLTTRELARMIKEAGIDFAKLPDSQFDSPFGEYSGAGAIFGA---TG 283 (374)
T ss_pred chhhhcCchhccc-------------CCCcccEEeeHHHHHHHHHHcCCChhhCCCcccccccccCCccccccCC---cc
Confidence 9999999987322 2479999999999999999999999999999999988777888999998 99
Q ss_pred cHHHHHHHHHHHHhhccccccccceeeecCC-CcEEEEEEeCCeeeEEEEEEechHHHHHHHHHHhcCCCCCcEEEecCC
Q 015642 242 GYAETVFRHAAKTLFGKVIEGHLEFKTIRNS-DFREVALEVEGKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVEVMAC 320 (403)
Q Consensus 242 G~~e~i~~~~~~~l~~~~~~~~~~~~~~rn~-d~~e~~l~~~g~~~~~~a~v~G~~ni~~~l~~lk~gk~~~~fIEvmAC 320 (403)
||+++++|++++.++|.+. ..++|+.+||. |++|+++..+|. .+++++||||+|+|++|+++++|+.+|+|||+|||
T Consensus 284 G~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~e~~~~~~~~-~~~~~~~~G~~~~~~~l~~~~~g~~~~~fiE~maC 361 (374)
T TIGR02512 284 GVMEAALRTAYEIVTGKEL-ELIEFKAVRGLDGVKEATVDIGGT-KVKVAVAHGLGNARKLLDDVKAGEADYHFIEVMAC 361 (374)
T ss_pred cHHHHHHHHHHHHhcCCCC-cccceeeecCCCCeEEEEEEECCE-EEEEEEEeCHHHHHHHHHHHHcCCCCccEEEECCC
Confidence 9999999999999999876 57889999985 899999999984 47999999999999999999999999999999999
Q ss_pred cccccCCCCCcC
Q 015642 321 PSGCLNGGGQIK 332 (403)
Q Consensus 321 pgGCinGgGq~~ 332 (403)
||||+|||||++
T Consensus 362 ~gGCi~G~g~~~ 373 (374)
T TIGR02512 362 PGGCVNGGGQPK 373 (374)
T ss_pred CccccCCCCccC
Confidence 999999999986
No 5
>PF02256 Fe_hyd_SSU: Iron hydrogenase small subunit; InterPro: IPR003149 Many microorganisms, such as methanogenic, acetogenic, nitrogen-fixing, photosynthetic, or sulphate-reducing bacteria, metabolise hydrogen. Hydrogen activation is mediated by a family of enzymes, termed hydrogenases, which either provide these organisms with reducing power from hydrogen oxidation, or act as electron sinks. There are two hydrogenases families that differ functionally from each other: NiFe hydrogenases tend to be more involved in hydrogen oxidation, while Iron-only FeFe (Fe only) hydrogenases in hydrogen production. Fe only hydrogenases (1.12.7.2 from EC) show a common core structure, which contains a moiety, deeply buried inside the protein, with an Fe-Fe dinuclear centre, nonproteic bridging, terminal CO and CN- ligands attached to each of the iron atoms, and a dithio moiety, which also bridges the two iron atoms and has been tentatively assigned as a di(thiomethyl)amine. This common core also harbours three [4Fe-4S] iron-sulphur clusters []. In FeFe hydrogenases, as in NiFe hydrogenases, the set of iron-sulphur clusters is dispersed regularly between the dinuclear Fe-Fe centre and the molecular surface. These clusters are distant by about 1.2 nm from each other but the [4Fe-4S] cluster closest to the dinuclear centre is covalently bound to one of the iron atoms though a thiolate bridging ligand. The moiety including the dinuclear centre, the thiolate bridging ligand, and the proximal [4Fe-4S] cluster is known as the H-cluster. A channel, lined with hydrophobic amino acid side chains, nearly connects the dinuclear centre and the molecular surface. Furthermore hydrogen-bonded water molecule sites have been identified at the interior and at the surface of the protein. The small subunit is comprised of alternating random coil and alpha helical structures that encompass the large subunit in a novel protein fold [].; PDB: 3LX4_A 1C4C_A 1FEH_A 3C8Y_A 1C4A_A 1HFE_S 1GX7_D 1E08_D.
Probab=99.33 E-value=4.1e-13 Score=101.01 Aligned_cols=54 Identities=39% Similarity=0.580 Sum_probs=42.7
Q ss_pred hhHHHHHHHHHHhhcc--cCCCCCCChHHHHHHHHHhcCCCChhhhcceeeeeccc
Q 015642 339 PKELIKTLETIYLENV--MLADPFKNPLVRSLYDEWLEQPGSEKAKKHVHTEYHPV 392 (403)
Q Consensus 339 ~~~~~~~~~~~y~~~~--~~~~~~~n~~v~~ly~~~l~~~~~~~~~~llht~y~~~ 392 (403)
.+.+..|++.+|..+. .++.|++||.|++||++||++|+++++|+||||+|+++
T Consensus 4 ~~~~~~R~~~LY~~d~~~~~r~s~eNp~v~~lY~~~lg~p~s~~ah~lLHT~Y~~r 59 (60)
T PF02256_consen 4 KEIRLKRAEGLYNIDKSSPLRKSHENPEVQELYKEFLGGPGSEKAHELLHTHYHDR 59 (60)
T ss_dssp CCHHHHHHHHHHHHHHHTSB-SGGG-HHHHHHHHHTTSSTTSHHHHHHHB----T-
T ss_pred HHHHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHHHhCCCCchHHHHHhCcCccCC
Confidence 3678889999998654 67999999999999999999999999999999999987
No 6
>PRK12809 putative oxidoreductase Fe-S binding subunit; Reviewed
Probab=74.80 E-value=1.8 Score=47.38 Aligned_cols=47 Identities=11% Similarity=-0.041 Sum_probs=40.2
Q ss_pred CCeEEEEeCccchHHHHHHhCCChHHHH-HHHHHHHHHcCCcEEEech
Q 015642 17 GKAVIISLSPQSRASLAEHFGISPLQVF-KKLTTFLKSLGVKSIFDTS 63 (403)
Q Consensus 17 ~k~~Vv~iaPq~r~sl~~~f~~~~~~~~-~kl~~~lk~LGf~~V~dt~ 63 (403)
.+.+++++||++|+++++.|++.++... .++....|.++|++|++.-
T Consensus 151 ~~~~~~~~~p~~r~~~~~~~~~~~~r~~~~~~~~~~R~~~f~Ev~~~~ 198 (639)
T PRK12809 151 RKTAAGKASSDAQPSRSAALLPVNSRKGADKISASERKTHFGEIYCGL 198 (639)
T ss_pred hhhcccccCcccccchHHHhCCCccccCcccCCHHHHhcCHHHhhccC
Confidence 4678999999999999999998765544 8899999999999998743
No 7
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=61.50 E-value=11 Score=34.90 Aligned_cols=50 Identities=26% Similarity=0.470 Sum_probs=35.7
Q ss_pred cHHHHHHHHhCCCeEEEEeCccchHHHHHHhCCChHHHHHHHHHHHHHcCCcEEEec
Q 015642 6 SLDEFLSNINKGKAVIISLSPQSRASLAEHFGISPLQVFKKLTTFLKSLGVKSIFDT 62 (403)
Q Consensus 6 s~~~~~~~l~~~k~~Vv~iaPq~r~sl~~~f~~~~~~~~~kl~~~lk~LGf~~V~dt 62 (403)
.+.+|++.|+..|.| .|. -||++||++..++..+|-.++..=-..-|+|-
T Consensus 100 lL~~Fi~yIK~~Kvv--~le-----dla~~f~l~t~~~i~ri~~L~~~g~ltGv~Dd 149 (188)
T PF09756_consen 100 LLQEFINYIKEHKVV--NLE-----DLAAEFGLRTQDVINRIQELEAEGRLTGVIDD 149 (188)
T ss_dssp HHHHHHHHHHH-SEE---HH-----HHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-T
T ss_pred HHHHHHHHHHHccee--eHH-----HHHHHcCCCHHHHHHHHHHHHHCCCceeeEcC
Confidence 588999999987754 333 59999999999899999888887666677776
No 8
>PF06574 FAD_syn: FAD synthetase; InterPro: IPR015864 Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (2.7.1.26 from EC), which converts it into FMN, and FAD synthetase (2.7.7.2 from EC), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme [], the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family []. The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases []. This entry represents prokaryotic-type FAD synthetase, which occurs primarily as part of a bifunctional enzyme.; GO: 0003919 FMN adenylyltransferase activity, 0009231 riboflavin biosynthetic process; PDB: 2X0K_B 3OP1_B 1T6Z_A 2I1L_A 1T6Y_B 1T6X_B 1S4M_A 1MRZ_A.
Probab=50.45 E-value=12 Score=33.31 Aligned_cols=60 Identities=18% Similarity=0.412 Sum_probs=39.5
Q ss_pred CeEEEEeCccchHHHH-HHhC--CChHHHHHHHHHHHHHcCCcEEEechhHHHHhHHHHHHHHHHHH
Q 015642 18 KAVIISLSPQSRASLA-EHFG--ISPLQVFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIARY 81 (403)
Q Consensus 18 k~~Vv~iaPq~r~sl~-~~f~--~~~~~~~~kl~~~lk~LGf~~V~dt~~gadi~~~e~~~E~~~~~ 81 (403)
+.+|++..|..+..+. .... +.. ..+=...|+++|+++|+-..|..++.- -++++|++.+
T Consensus 38 ~~~v~tF~~~P~~~~~~~~~~~~l~s---~~ek~~~l~~~Gvd~~~~~~F~~~~~~-ls~~~Fi~~i 100 (157)
T PF06574_consen 38 KSVVLTFDPHPKEVLNPDKPPKLLTS---LEEKLELLESLGVDYVIVIPFTEEFAN-LSPEDFIEKI 100 (157)
T ss_dssp EEEEEEESS-CHHHHSCTCCGGBSS----HHHHHHHHHHTTESEEEEE-CCCHHCC-S-HHHHHHHH
T ss_pred ceEEEEcccCHHHHhcCCCcccCCCC---HHHHHHHHHHcCCCEEEEecchHHHHc-CCHHHHHHHH
Confidence 4678899987665555 1111 221 245667899999999999888777663 3488999874
No 9
>PF04914 DltD_C: DltD C-terminal region; InterPro: IPR006998 The dlt operon (dltA to dltD) of Lactobacillus rhamnosus 7469 encodes four proteins responsible for the esterification of lipoteichoic acid (LTA) by D-alanine. These esters play an important role in controlling the net anionic charge of the poly (GroP) moiety of LTA. DltA and DltC encode the D-alanine-D-alanyl carrier protein ligase (Dcl) and D-alanyl carrier protein (Dcp), respectively. Whereas the functions of DltA and DltC are defined, the functions of DltB and DltD are unknown. In vitro assays showed that DltD bound Dcp for ligation with D-alanine by Dcl in the presence of ATP. In contrast, the homologue of Dcp, the Escherichia coli acyl carrier protein (ACP), involved in fatty acid biosynthesis, was not bound to DltD and thus was not ligated with D-alanine. DltD also catalyzed the hydrolysis of the mischarged D-alanyl-ACP. The hydrophobic N-terminal sequence of DltD was required for anchoring the protein in the membrane. It is hypothesized that this membrane-associated DltD facilitates the binding of Dcp and Dcl for ligation of Dcp with D-alanine and that the resulting D-alanyl-Dcp is translocated to the primary site of D-alanylation []. These sequences contain the C-terminal region of DltD.; PDB: 3BMA_C.
Probab=44.94 E-value=60 Score=28.18 Aligned_cols=58 Identities=21% Similarity=0.194 Sum_probs=34.0
Q ss_pred ccHHHHHHHHhCCCeEEEEeCccchHHHHHHhCCChHHH---HHHHHHHHHHcCCcEEEech
Q 015642 5 QSLDEFLSNINKGKAVIISLSPQSRASLAEHFGISPLQV---FKKLTTFLKSLGVKSIFDTS 63 (403)
Q Consensus 5 qs~~~~~~~l~~~k~~Vv~iaPq~r~sl~~~f~~~~~~~---~~kl~~~lk~LGf~~V~dt~ 63 (403)
.+.+-+|+.+++...-|..|.|.+=--.+.+-|++.+.- ..+|...+++-|| .|.|.+
T Consensus 36 ~Dl~l~L~~~k~~g~~~lfVi~PvNg~wydytG~~~~~r~~~y~kI~~~~~~~gf-~v~D~s 96 (130)
T PF04914_consen 36 DDLQLLLDVCKELGIDVLFVIQPVNGKWYDYTGLSKEMRQEYYKKIKYQLKSQGF-NVADFS 96 (130)
T ss_dssp HHHHHHHHHHHHTT-EEEEEE----HHHHHHTT--HHHHHHHHHHHHHHHHTTT---EEE-T
T ss_pred HHHHHHHHHHHHcCCceEEEecCCcHHHHHHhCCCHHHHHHHHHHHHHHHHHCCC-EEEecc
Confidence 356678888877654444444445555667778887543 3899999999999 788876
No 10
>PRK13011 formyltetrahydrofolate deformylase; Reviewed
Probab=42.16 E-value=1.3e+02 Score=29.50 Aligned_cols=73 Identities=16% Similarity=0.212 Sum_probs=52.0
Q ss_pred ccHHHHHHHHhCCC---eEEEEeCcc-chHHHHHHhCCChH----------HHHHHHHHHHHHcCCcEEEechhHHHHhH
Q 015642 5 QSLDEFLSNINKGK---AVIISLSPQ-SRASLAEHFGISPL----------QVFKKLTTFLKSLGVKSIFDTSCSRDLTL 70 (403)
Q Consensus 5 qs~~~~~~~l~~~k---~~Vv~iaPq-~r~sl~~~f~~~~~----------~~~~kl~~~lk~LGf~~V~dt~~gadi~~ 70 (403)
.+...++++++++. .+++.||-+ -...+|..+|++.- +....+...|+++++|.|+=..|++=+.
T Consensus 101 ~nl~al~~~~~~~~~~~~i~~visn~~~~~~lA~~~gIp~~~~~~~~~~~~~~~~~~~~~l~~~~~Dlivlagy~~il~- 179 (286)
T PRK13011 101 HCLNDLLYRWRIGELPMDIVGVVSNHPDLEPLAAWHGIPFHHFPITPDTKPQQEAQVLDVVEESGAELVVLARYMQVLS- 179 (286)
T ss_pred ccHHHHHHHHHcCCCCcEEEEEEECCccHHHHHHHhCCCEEEeCCCcCchhhhHHHHHHHHHHhCcCEEEEeChhhhCC-
Confidence 35677888887764 466666633 35567999987642 1225688899999999999999998774
Q ss_pred HHHHHHHHHHHh
Q 015642 71 IEACNEFIARYK 82 (403)
Q Consensus 71 ~e~~~E~~~~~~ 82 (403)
.+|+++++
T Consensus 180 ----~~~l~~~~ 187 (286)
T PRK13011 180 ----PELCRKLA 187 (286)
T ss_pred ----HHHHhhcc
Confidence 57887654
No 11
>cd01965 Nitrogenase_MoFe_beta_like Nitrogenase_MoFe_beta_like: Nitrogenase MoFe protein, beta subunit_like. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen (N2) to ammonia. This group contains the beta subunits of component 1 of the three known genetically distinct types of nitrogenase systems: a molybdenum-dependent nitrogenase (Mo-nitrogenase), a vanadium-dependent nitrogenase (V-nitrogenase), and an iron-only nitrogenase (Fe-nitrogenase). These nitrogenase systems consist of component 1 (MoFe protein, VFe protein or, FeFe protein respectively) and, component 2 (Fe protein). The most widespread and best characterized of these systems is the Mo-nitrogenase. MoFe is an alpha2beta2 tetramer, the alternative nitrogenases are alpha2beta2delta2 hexamers having alpha and beta subunits similar to the alpha and beta subunits of MoFe. For MoFe, each alphabeta pair contains one P-cluster (at the alphabeta interface) and, one molecule of iron molybdenum cofactor (Fe
Probab=41.77 E-value=87 Score=32.38 Aligned_cols=20 Identities=10% Similarity=0.094 Sum_probs=16.3
Q ss_pred cHHHHHHHHHhcCCCCCCCC
Q 015642 197 TTGEVLDLIQLKAVNFEALE 216 (403)
Q Consensus 197 Tt~El~~~l~~~~i~~~~l~ 216 (403)
...||.++|++.|++...+.
T Consensus 170 d~~el~~lL~~~Gl~v~~~~ 189 (428)
T cd01965 170 DVREIKRILEAFGLEPIILP 189 (428)
T ss_pred CHHHHHHHHHHcCCCEEEec
Confidence 46899999999999876554
No 12
>cd01966 Nitrogenase_NifN_1 Nitrogenase_nifN1: A subgroup of the NifN subunit of the NifEN complex: NifN forms an alpha2beta2 tetramer with NifE. NifN and nifE are structurally homologous to nitrogenase MoFe protein beta and alpha subunits respectively. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of the MoFe protein. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it is further processed to FeMoco. The nifEN bound precursor of FeMoco has been identified as a molybdenum-free, iron- and sulfur- containing analog of FeMoco. It has been suggested that this nifEN bound precursor also acts as a cofactor precursor in nitrogenase systems which require a cofactor other than FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron only cofactor (FeFeco).
Probab=40.72 E-value=1.3e+02 Score=31.19 Aligned_cols=89 Identities=17% Similarity=0.078 Sum_probs=48.4
Q ss_pred CeEEEEeCccchHHHHHHh-----CCChHHHHHHHHHHHHHcCCcEEEechhHHHHhHHHHHHHHHHHHhhcccCccccc
Q 015642 18 KAVIISLSPQSRASLAEHF-----GISPLQVFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIARYKQSQESDDERS 92 (403)
Q Consensus 18 k~~Vv~iaPq~r~sl~~~f-----~~~~~~~~~kl~~~lk~LGf~~V~dt~~gadi~~~e~~~E~~~~~~~~~~~~~~~~ 92 (403)
.-+++.-+||-|+++...+ .-+. .-.++.|.+ -|+-||.+=-+.+..++..++|+
T Consensus 22 ~~~~ivHgp~GC~~~~~~~~~r~~~~~~----~~~sT~l~E------~d~VfGg~~~L~~~i~~~~~~~~---------- 81 (417)
T cd01966 22 GCMPLFHGAQGCTSFAKVLLVRHFKEPI----PLQTTAMDE------VSTILGGGENLEEALDTLAERAK---------- 81 (417)
T ss_pred CceEeccCchhHHhHHHHHHhcccCCCc----cccccccCC------CcEEECCHHHHHHHHHHHHHhcC----------
Confidence 5578889999999876543 2111 111222221 13346677777787878777653
Q ss_pred CCCC-CceecCChH--------HHHHHHHhcCCCC-CCCCCCCCCH
Q 015642 93 NSSL-PMLSSACPG--------WICYAEKQLGSYI-LPYISSVKSP 128 (403)
Q Consensus 93 ~~~~-P~isS~CPg--------wV~yiEk~~~P~l-ip~Ls~vkSP 128 (403)
++. -++|||.|+ +++-+++.+ |+. -..+.++.+|
T Consensus 82 -p~~I~V~ttc~~eiIGdDi~~v~~~~~~~~-p~~~~~~vi~v~t~ 125 (417)
T cd01966 82 -PKVIGLLSTGLTETRGEDIAGALKQFRAEH-PELADVPVVYVSTP 125 (417)
T ss_pred -CCEEEEECCCcccccccCHHHHHHHHHhhc-cccCCCeEEEecCC
Confidence 222 345555544 556666666 652 2224445555
No 13
>PRK07114 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=40.40 E-value=2.9e+02 Score=26.18 Aligned_cols=129 Identities=16% Similarity=0.174 Sum_probs=79.4
Q ss_pred HHHHHHHHhCCCeEEEEeCccchHHHHHHhCCChHHHHHHHHHHHHHcCCcEEEechhHHHHhHHHHHHHHHHHHhhccc
Q 015642 7 LDEFLSNINKGKAVIISLSPQSRASLAEHFGISPLQVFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIARYKQSQE 86 (403)
Q Consensus 7 ~~~~~~~l~~~k~~Vv~iaPq~r~sl~~~f~~~~~~~~~kl~~~lk~LGf~~V~dt~~gadi~~~e~~~E~~~~~~~~~~ 86 (403)
..++++.|.+.+.+.+.-.. ++ +....+..+|.+-|++ ++|+++-..-. .+..+++.+.+
T Consensus 5 ~~~~~~~l~~~~vi~Vvr~~------------~~-~~a~~~~~al~~gGi~-~iEiT~~tp~a-~~~i~~l~~~~----- 64 (222)
T PRK07114 5 RIAVLTAMKATGMVPVFYHA------------DV-EVAKKVIKACYDGGAR-VFEFTNRGDFA-HEVFAELVKYA----- 64 (222)
T ss_pred HHHHHHHHHhCCEEEEEEcC------------CH-HHHHHHHHHHHHCCCC-EEEEeCCCCcH-HHHHHHHHHHH-----
Confidence 45677888876655333222 22 3346788899999998 88888722111 12122222222
Q ss_pred CcccccCCCCCceecCChHHHHHHHHhcCCCCCCCCCCCCCHHHHHHHHHHHHHhHhhCCCCCCeEEEEEEccchhhHhh
Q 015642 87 SDDERSNSSLPMLSSACPGWICYAEKQLGSYILPYISSVKSPQQTIGATIKHHICQKLGFRPDEIYHVTVMPCYDKKLEA 166 (403)
Q Consensus 87 ~~~~~~~~~~P~isS~CPgwV~yiEk~~~P~lip~Ls~vkSPq~i~g~liK~~~~~~~~~~~~~i~~V~I~PC~aKK~Ea 166 (403)
.+.| |+++==--||.+|.|+...+- .| -.+.|+||+++.+=.
T Consensus 65 ------------------------~~~~-p~~~vGaGTVl~~e~a~~a~~-------aG------A~FiVsP~~~~~v~~ 106 (222)
T PRK07114 65 ------------------------AKEL-PGMILGVGSIVDAATAALYIQ-------LG------ANFIVTPLFNPDIAK 106 (222)
T ss_pred ------------------------HhhC-CCeEEeeEeCcCHHHHHHHHH-------cC------CCEEECCCCCHHHHH
Confidence 2245 777777789999999765431 11 127899999985432
Q ss_pred -hcchhhcccccchhccccCCCCCCCceEEEcHHHHHHHHHhcCCC
Q 015642 167 -AREDFVFQLDSQEETYRDEGLEIPEVDSVLTTGEVLDLIQLKAVN 211 (403)
Q Consensus 167 -~r~~~~~~~~~~~~~~~~~~~~~~~VD~VLTt~El~~~l~~~~i~ 211 (403)
.+. .+...+=.|+|..|+.+-++. |.+
T Consensus 107 ~~~~-----------------~~i~~iPG~~TpsEi~~A~~~-Ga~ 134 (222)
T PRK07114 107 VCNR-----------------RKVPYSPGCGSLSEIGYAEEL-GCE 134 (222)
T ss_pred HHHH-----------------cCCCEeCCCCCHHHHHHHHHC-CCC
Confidence 232 146778889999999987775 443
No 14
>PF02236 Viral_DNA_bi: Viral DNA-binding protein, all alpha domain; InterPro: IPR003176 This domain represents the N-terminal domain of the viral DNA-binding protein, a multi functional protein involved in DNA replication and transcription control.; GO: 0003677 DNA binding, 0006260 DNA replication, 0006351 transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ADU_A 1ADV_B 2WB0_X 2WAZ_X 1ANV_A.
Probab=33.31 E-value=36 Score=27.48 Aligned_cols=41 Identities=17% Similarity=0.238 Sum_probs=28.8
Q ss_pred HHHHhcCCCCCCCCCCCCCHHHHHHHHHHHHHhHhhCCCCCC
Q 015642 109 YAEKQLGSYILPYISSVKSPQQTIGATIKHHICQKLGFRPDE 150 (403)
Q Consensus 109 yiEk~~~P~lip~Ls~vkSPq~i~g~liK~~~~~~~~~~~~~ 150 (403)
|+-+.+ +.+-.-.|+-||=+.++|+++-.+..+.-|+.|.+
T Consensus 44 ~l~~~k-~~~~LTFSS~KSf~~~mGRfL~~~v~~~agl~~~~ 84 (86)
T PF02236_consen 44 WLNEEK-RGLQLTFSSQKSFTHMMGRFLAAFVYKYAGLAPKN 84 (86)
T ss_dssp HHHHHH-TT---SS--HHHHHHHHHHHHHHHHHHHHT---TT
T ss_pred HHHhcC-cCCCcceechHHHHHHHHHHHHHHHHHHcCCCCCC
Confidence 566777 88888899999999999999999999888887753
No 15
>PF13592 HTH_33: Winged helix-turn helix
Probab=33.13 E-value=30 Score=25.51 Aligned_cols=36 Identities=22% Similarity=0.226 Sum_probs=25.4
Q ss_pred cchHHHHHHhCCChHHHHHHHHHHHHHcCCcEEEechh
Q 015642 27 QSRASLAEHFGISPLQVFKKLTTFLKSLGVKSIFDTSC 64 (403)
Q Consensus 27 q~r~sl~~~f~~~~~~~~~kl~~~lk~LGf~~V~dt~~ 64 (403)
..+.-+...||+.. ....+..+|++|||.+.--...
T Consensus 9 ~i~~~I~~~fgv~y--s~~~v~~lL~r~G~s~~kp~~~ 44 (60)
T PF13592_consen 9 EIAAYIEEEFGVKY--SPSGVYRLLKRLGFSYQKPRPR 44 (60)
T ss_pred HHHHHHHHHHCCEE--cHHHHHHHHHHcCCccccCCCC
Confidence 34556788899554 2357888999999987655443
No 16
>TIGR00083 ribF riboflavin kinase/FMN adenylyltransferase. multifunctional enzyme: riboflavin kinase (EC 2.7.1.26) (flavokinase) / FMN adenylyltransferase (EC 2.7.7.2) (FAD pyrophosphorylase) (FAD synthetase).
Probab=31.49 E-value=1.2e+02 Score=30.03 Aligned_cols=63 Identities=10% Similarity=0.142 Sum_probs=41.8
Q ss_pred CeEEEEeCccchHHHHHHhCCChHHHHHHHHHHHHHcCCcEEEechhHHHHhHHHHHHHHHHHHh
Q 015642 18 KAVIISLSPQSRASLAEHFGISPLQVFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIARYK 82 (403)
Q Consensus 18 k~~Vv~iaPq~r~sl~~~f~~~~~~~~~kl~~~lk~LGf~~V~dt~~gadi~~~e~~~E~~~~~~ 82 (403)
+.+|++..|..+.-|........ .+...=...|.++|+++|+-..|-.++.- -++++|++.+-
T Consensus 31 ~~~V~tF~phP~~~~~~~~~~~l-~~~~~k~~~l~~~Gvd~~~~~~F~~~~a~-ls~e~Fi~~~l 93 (288)
T TIGR00083 31 PPAVLLFEPHPSEQFNWLTAPAL-TPLEDKARQLQIKGVEQLLVVVFDEEFAN-LSALQFIDQLI 93 (288)
T ss_pred CEEEEEeCCChHHHhCccCCCCC-CCHHHHHHHHHHcCCCEEEEeCCCHHHHc-CCHHHHHHHHH
Confidence 57899999977665543211111 11234456888999999999998877763 35788987653
No 17
>KOG1611 consensus Predicted short chain-type dehydrogenase [General function prediction only]
Probab=30.97 E-value=11 Score=36.04 Aligned_cols=33 Identities=27% Similarity=0.424 Sum_probs=20.3
Q ss_pred CccchHHHHHHhC---CChHHHHHHHHHHHHHcCCc
Q 015642 25 SPQSRASLAEHFG---ISPLQVFKKLTTFLKSLGVK 57 (403)
Q Consensus 25 aPq~r~sl~~~f~---~~~~~~~~kl~~~lk~LGf~ 57 (403)
...+|..+..+|. +++--+.+.+.-.||+-.-+
T Consensus 102 ~~~~r~~~~~~~~tN~v~~il~~Q~~lPLLkkaas~ 137 (249)
T KOG1611|consen 102 LKPSRAVLLEQYETNAVGPILLTQAFLPLLKKAASK 137 (249)
T ss_pred cCCcHHHHHHHhhhcchhHHHHHHHHHHHHHHHhhc
Confidence 3445788888886 44444446777777764433
No 18
>cd01977 Nitrogenase_VFe_alpha Nitrogenase_VFe_alpha -like: Nitrogenase VFe protein, alpha subunit like. This group contains proteins similar to the alpha subunits of, the VFe protein of the vanadium-dependent (V-) nitrogenase and the FeFe protein of the iron only (Fe-) nitrogenase Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen (N2) to ammonia. In addition to V- and Fe- nitrogenases there is a molybdenum (Mo)-dependent nitrogenase which is the most widespread and best characterized of these systems. These systems consist of component 1 (VFe protein, FeFe protein or, MoFe protein respectively) and, component 2 (Fe protein). MoFe is an alpha2beta2 tetramer, V-and Fe- nitrogenases are alpha2beta2delta2 hexamers. The alpha and beta subunits of VFe and FeFe are similar to the alpha and beta subunits of MoFe. For MoFe each alphabeta pair contains one P-cluster (at the alphabeta interface) and, one molecule of iron molybdenum cofactor (FeMoco) contained within the alpha sub
Probab=27.64 E-value=4.9e+02 Score=26.76 Aligned_cols=46 Identities=7% Similarity=0.051 Sum_probs=27.6
Q ss_pred echhHHHHhHHHHHHHHHHHHhhcccCcccccCCC-CCceecCChH--------HHHHHHHhcCCC
Q 015642 61 DTSCSRDLTLIEACNEFIARYKQSQESDDERSNSS-LPMLSSACPG--------WICYAEKQLGSY 117 (403)
Q Consensus 61 dt~~gadi~~~e~~~E~~~~~~~~~~~~~~~~~~~-~P~isS~CPg--------wV~yiEk~~~P~ 117 (403)
|+-+|.+=-+.+..++..+++. +++ .-+++||.|+ +++-+++.+ |+
T Consensus 66 d~VfGg~~~L~~aI~~~~~~~p----------~p~~i~V~~tc~~~liGdDi~~v~~~~~~~~-~~ 120 (415)
T cd01977 66 HVVFGGEKKLKKNIIEAFKEFP----------DIKRMTVYTTCTTALIGDDIKAVAKEVMEEL-PD 120 (415)
T ss_pred ceeeccHHHHHHHHHHHHHhCC----------CCcEEEEECCCchhhhcCCHHHHHHHHHHhc-CC
Confidence 3446777777888888777642 122 2345666665 456667777 53
No 19
>COG1105 FruK Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]
Probab=26.75 E-value=1.8e+02 Score=29.19 Aligned_cols=56 Identities=30% Similarity=0.592 Sum_probs=37.1
Q ss_pred cccccHHHHHHHHhC----CCeEEEEeCccchHHHHHHhCCChHHHHHHHHHHHHHcCCcEEEechhHH
Q 015642 2 LEKQSLDEFLSNINK----GKAVIISLSPQSRASLAEHFGISPLQVFKKLTTFLKSLGVKSIFDTSCSR 66 (403)
Q Consensus 2 ~~~qs~~~~~~~l~~----~k~~Vv~iaPq~r~sl~~~f~~~~~~~~~kl~~~lk~LGf~~V~dt~~ga 66 (403)
|+.++.++|++.++. ...+|+ |= |+.. |+++ +.+.+|...+|+.|..-|+|++=.+
T Consensus 111 is~~~~~~~l~~~~~~l~~~d~Vvl--sG----SlP~--g~~~-d~y~~li~~~~~~g~~vilD~Sg~~ 170 (310)
T COG1105 111 ISEAELEQFLEQLKALLESDDIVVL--SG----SLPP--GVPP-DAYAELIRILRQQGAKVILDTSGEA 170 (310)
T ss_pred CCHHHHHHHHHHHHHhcccCCEEEE--eC----CCCC--CCCH-HHHHHHHHHHHhcCCeEEEECChHH
Confidence 456677777777665 344443 32 2222 3433 4568999999999999999998544
No 20
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=25.54 E-value=1.2e+02 Score=20.61 Aligned_cols=30 Identities=37% Similarity=0.600 Sum_probs=24.9
Q ss_pred hHHHHHHhCCChHHHHHHHHHHHHHcCCcE
Q 015642 29 RASLAEHFGISPLQVFKKLTTFLKSLGVKS 58 (403)
Q Consensus 29 r~sl~~~f~~~~~~~~~kl~~~lk~LGf~~ 58 (403)
..-++..++++...+...+..++++||++.
T Consensus 21 ~~eia~~l~is~~tv~~~~~~~~~kl~~~~ 50 (58)
T smart00421 21 NKEIAERLGISEKTVKTHLSNIMRKLGVRS 50 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
Confidence 347899999999888888888899999763
No 21
>PF03096 Ndr: Ndr family; InterPro: IPR004142 This family consists of proteins from different gene families: Ndr1/RTP/Drg1, Ndr2, and Ndr3. Their similarity was previously noted []. The precise molecular and cellular function of members of this family is still unknown, yet they are known to be involved in cellular differentiation events. The Ndr1 group was the first to be discovered. Their expression is repressed by the proto-oncogenes N-myc and c-myc, and in line with this observation, Ndr1 protein expression is down-regulated in neoplastic cells, and is reactivated when differentiation is induced by chemicals such as retinoic acid. Ndr2 and Ndr3 expression is not under the control of N-myc or c-myc. Ndr1 expression is also activated by several chemicals: tunicamycin and homocysteine induce Ndr1 in human umbilical endothelial cells; nickel induces Ndr1 in several cell types. Members of this family are found in wide variety of multicellular eukaryotes, including an Ndr1 type protein in Helianthus annuus (Common sunflower), known as Sf21. Interestingly, the highest scoring matches in the noise are all alpha/beta hydrolases (IPR000073 from INTERPRO), suggesting that this family may have an enzymatic function.; PDB: 2QMQ_A 2XMR_B 2XMQ_B 2XMS_A.
Probab=25.22 E-value=89 Score=30.83 Aligned_cols=98 Identities=16% Similarity=0.233 Sum_probs=44.0
Q ss_pred HHHHHhCC-ChHHHHHHHHHHHHHcCCcEEEechhHHHHhHHHHHHHHHHHHhhcccCcccccCCCCCce--ecCChHHH
Q 015642 31 SLAEHFGI-SPLQVFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIARYKQSQESDDERSNSSLPML--SSACPGWI 107 (403)
Q Consensus 31 sl~~~f~~-~~~~~~~kl~~~lk~LGf~~V~dt~~gadi~~~e~~~E~~~~~~~~~~~~~~~~~~~~P~i--sS~CPgwV 107 (403)
.|..-|.. +..+...+|...|..+|+++|.-...||-.-++- .|.-.+.+. -..+-+| +++.|||.
T Consensus 72 ~~p~~y~yPsmd~LAe~l~~Vl~~f~lk~vIg~GvGAGAnIL~---rfAl~~p~~--------V~GLiLvn~~~~~~gw~ 140 (283)
T PF03096_consen 72 TLPEGYQYPSMDQLAEMLPEVLDHFGLKSVIGFGVGAGANILA---RFALKHPER--------VLGLILVNPTCTAAGWM 140 (283)
T ss_dssp ---TT-----HHHHHCTHHHHHHHHT---EEEEEETHHHHHHH---HHHHHSGGG--------EEEEEEES---S---HH
T ss_pred cccccccccCHHHHHHHHHHHHHhCCccEEEEEeeccchhhhh---hccccCccc--------eeEEEEEecCCCCccHH
Confidence 45555553 3455568899999999999998887766444321 233222210 0112233 66789999
Q ss_pred HHHHHhcCCCCCCCCCCCCCHHHHHHHHHHHHHhH
Q 015642 108 CYAEKQLGSYILPYISSVKSPQQTIGATIKHHICQ 142 (403)
Q Consensus 108 ~yiEk~~~P~lip~Ls~vkSPq~i~g~liK~~~~~ 142 (403)
.++..+. ...+|....-.+.+--.++..+|++
T Consensus 141 Ew~~~K~---~~~~L~~~gmt~~~~d~Ll~h~Fg~ 172 (283)
T PF03096_consen 141 EWFYQKL---SSWLLYSYGMTSSVKDYLLWHYFGK 172 (283)
T ss_dssp HHHHHHH---H-------CTTS-HHHHHHHHHS-H
T ss_pred HHHHHHH---hcccccccccccchHHhhhhccccc
Confidence 9888776 3344444444555555666666664
No 22
>KOG2931 consensus Differentiation-related gene 1 protein (NDR1 protein), related proteins [Function unknown]
Probab=24.05 E-value=1.3e+02 Score=30.05 Aligned_cols=73 Identities=21% Similarity=0.375 Sum_probs=44.8
Q ss_pred HHHHHhCCC-hHHHHHHHHHHHHHcCCcEEEechhHHHHhHHHHHHHHHHHHhhcccCcccccCCCCCce--ecCChHHH
Q 015642 31 SLAEHFGIS-PLQVFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIARYKQSQESDDERSNSSLPML--SSACPGWI 107 (403)
Q Consensus 31 sl~~~f~~~-~~~~~~kl~~~lk~LGf~~V~dt~~gadi~~~e~~~E~~~~~~~~~~~~~~~~~~~~P~i--sS~CPgwV 107 (403)
+|..-|..| .++...+|...|..+|+++|.-...||-.- .+.||.-+.- + .-..+-+| +++=|||+
T Consensus 95 ~~p~~y~yPsmd~LAd~l~~VL~~f~lk~vIg~GvGAGAy-------IL~rFAl~hp---~-rV~GLvLIn~~~~a~gwi 163 (326)
T KOG2931|consen 95 SFPEGYPYPSMDDLADMLPEVLDHFGLKSVIGMGVGAGAY-------ILARFALNHP---E-RVLGLVLINCDPCAKGWI 163 (326)
T ss_pred cCCCCCCCCCHHHHHHHHHHHHHhcCcceEEEecccccHH-------HHHHHHhcCh---h-heeEEEEEecCCCCchHH
Confidence 577766654 445569999999999999999888766433 3444421000 0 00112233 44557899
Q ss_pred HHHHHhc
Q 015642 108 CYAEKQL 114 (403)
Q Consensus 108 ~yiEk~~ 114 (403)
.++-.++
T Consensus 164 ew~~~K~ 170 (326)
T KOG2931|consen 164 EWAYNKV 170 (326)
T ss_pred HHHHHHH
Confidence 9887766
No 23
>PF11576 DUF3236: Protein of unknown function (DUF3236); InterPro: IPR012019 This family of proteins with unknown function appears to be restricted to Methanobacteria. ; PDB: 3BRC_B.
Probab=24.03 E-value=73 Score=28.20 Aligned_cols=36 Identities=31% Similarity=0.460 Sum_probs=21.1
Q ss_pred CCeEEEEeCccchHHHHHHhCCChHHHH-HHHHHHHHHcCCc
Q 015642 17 GKAVIISLSPQSRASLAEHFGISPLQVF-KKLTTFLKSLGVK 57 (403)
Q Consensus 17 ~k~~Vv~iaPq~r~sl~~~f~~~~~~~~-~kl~~~lk~LGf~ 57 (403)
++...+++||+ ++.-. .+.++.. ..+..||+++||+
T Consensus 118 GRiLtaslSPs---~~iHk--~~ie~~v~~E~~~AL~RiG~k 154 (154)
T PF11576_consen 118 GRILTASLSPS---HVIHK--KSIEDAVKKEMIEALKRIGIK 154 (154)
T ss_dssp S-EEEEEEE-----TTTS-----HHHHHHHHHHHHHHTTT--
T ss_pred CcEEeeccCch---hhhcc--ccHHHHHHHHHHHHHHHhCCC
Confidence 46778999997 34433 3455554 7899999999985
No 24
>PF04343 DUF488: Protein of unknown function, DUF488; InterPro: IPR007438 This family includes several proteins of uncharacterised function.
Probab=22.00 E-value=1.5e+02 Score=24.89 Aligned_cols=55 Identities=24% Similarity=0.461 Sum_probs=37.3
Q ss_pred cHHHHHHHHhCCCe-EEE--EeCccchHHHHHHhCCChHHHHHHHHHHHHHcCCcEEEechhHHHHh
Q 015642 6 SLDEFLSNINKGKA-VII--SLSPQSRASLAEHFGISPLQVFKKLTTFLKSLGVKSIFDTSCSRDLT 69 (403)
Q Consensus 6 s~~~~~~~l~~~k~-~Vv--~iaPq~r~sl~~~f~~~~~~~~~kl~~~lk~LGf~~V~dt~~gadi~ 69 (403)
++++|++.|++.+. ++| =.-|.|| ...| +- ..|..+|...|..||+--.+|---.
T Consensus 1 ~~e~f~~~l~~~~i~~lVDVR~~P~S~---~~~~--~k----~~l~~~l~~~gi~Y~~~~~Lg~~~~ 58 (122)
T PF04343_consen 1 SIERFYDLLKKNGIRVLVDVRLWPRSR---KPGF--NK----EDLASFLEEAGIEYVWLPELGPSRE 58 (122)
T ss_pred CHHHHHHHHHHCCCeEEEEECCCCCCC---CCCC--CH----HHHHHHHHHCCceEeechhhcCccc
Confidence 57899998887654 333 3567543 2223 33 4788899999999999888777443
No 25
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=21.54 E-value=1.1e+02 Score=26.74 Aligned_cols=21 Identities=19% Similarity=0.561 Sum_probs=17.9
Q ss_pred HHHHHHHHHHcCCcEEEechh
Q 015642 44 FKKLTTFLKSLGVKSIFDTSC 64 (403)
Q Consensus 44 ~~kl~~~lk~LGf~~V~dt~~ 64 (403)
.++|+..||.+|||-++.-..
T Consensus 9 L~~Lar~LR~lG~Dt~~~~~~ 29 (147)
T PF01927_consen 9 LGRLARWLRLLGYDTLYSRDI 29 (147)
T ss_pred HHHHHHHHHHCCCcEEEeCCC
Confidence 369999999999998877755
No 26
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=21.08 E-value=1.9e+02 Score=18.88 Aligned_cols=28 Identities=18% Similarity=0.464 Sum_probs=19.1
Q ss_pred chHHHHHHhCCChHHHHHHHHHHHHHcCC
Q 015642 28 SRASLAEHFGISPLQVFKKLTTFLKSLGV 56 (403)
Q Consensus 28 ~r~sl~~~f~~~~~~~~~kl~~~lk~LGf 56 (403)
+|.-+|.+.|+++ ++..++.+-|++-|.
T Consensus 4 tr~diA~~lG~t~-ETVSR~l~~l~~~gl 31 (32)
T PF00325_consen 4 TRQDIADYLGLTR-ETVSRILKKLERQGL 31 (32)
T ss_dssp -HHHHHHHHTS-H-HHHHHHHHHHHHTTS
T ss_pred CHHHHHHHhCCcH-HHHHHHHHHHHHcCC
Confidence 4567899999998 466667777776653
No 27
>cd01979 Pchlide_reductase_N Pchlide_reductase_N: N protein of the NB protein complex of Protochlorophyllide (Pchlide)_reductase. Pchlide reductase catalyzes the reductive formation of chlorophyllide (chlide) from protochlorophyllide (pchlide) during biosynthesis of chlorophylls and bacteriochlorophylls. This group contains both the light-independent Pchlide reductase (DPOR) and light-dependent Pchlide reductase (LPOR). Angiosperms contain only LPOR, cyanobacteria, algae and gymnosperms contain both DPOR and LPOR, primitive anoxygenic photosynthetic bacteria contain only DPOR. NB is structurally similar to the FeMo protein of nitrogenase, forming an N2B2 heterotetramer. N and B are homologous to the FeMo alpha and beta subunits respectively. Also in common with nitrogenase in vitro DPOR activity requires ATP hydrolysis and dithoionite or ferredoxin as electron donor. The NB protein complex may serve as a catalytic site for Pchlide reduction similar to MoFe for nitrogen reduction.
Probab=21.03 E-value=8.9e+02 Score=24.63 Aligned_cols=16 Identities=0% Similarity=0.001 Sum_probs=14.2
Q ss_pred HHHHHHHHHhcCCCCC
Q 015642 198 TGEVLDLIQLKAVNFE 213 (403)
Q Consensus 198 t~El~~~l~~~~i~~~ 213 (403)
..||.++|++.|+...
T Consensus 169 ~~el~~lL~~~Gi~v~ 184 (396)
T cd01979 169 EDQLRRELEQLGIPVV 184 (396)
T ss_pred HHHHHHHHHHcCCeEE
Confidence 6899999999999874
No 28
>cd07025 Peptidase_S66 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein. LD-carboxypeptidase (Muramoyltetrapeptide carboxypeptidase; EC 3.4.17.13; Merops family S66; initially described as Carboxypeptidase II) family also includes the microcin c7 self-immunity protein (MccF) as well as uncharacterized proteins including hypothetical proteins. LD-carboxypeptidase hydrolyzes the amide bond that links the dibasic amino acids to C-terminal D-amino acids. The physiological substrates of LD-carboxypeptidase are tetrapeptide fragments (such as UDP-MurNAc-tetrapeptides) that are produced when bacterial cell walls are degraded; they contain an L-configured residue (L-lysine or meso-diaminopimelic acid residue) as the penultimate residue and D-alanine as the ultimate residue. A possible role of LD-carboxypeptidase is in peptidoglycan recycling whereby the resulting tripeptide (precursor for murein synthesis) can be reconverted into peptidoglycan by attachment o
Probab=20.80 E-value=2e+02 Score=28.00 Aligned_cols=54 Identities=19% Similarity=0.190 Sum_probs=35.4
Q ss_pred EEEeCccchHHHHHHhCCChHHHHHHHHHHHHHcCCcEEEechhHHH-----HhHHHHHHHHHHHHh
Q 015642 21 IISLSPQSRASLAEHFGISPLQVFKKLTTFLKSLGVKSIFDTSCSRD-----LTLIEACNEFIARYK 82 (403)
Q Consensus 21 Vv~iaPq~r~sl~~~f~~~~~~~~~kl~~~lk~LGf~~V~dt~~gad-----i~~~e~~~E~~~~~~ 82 (403)
|+.|||++.+ +..+...+....|+++||.-++.-+...+ -+..+.++||.+.+.
T Consensus 1 I~iiapSs~~--------~~~~~~~~~~~~L~~~G~~v~~~~~~~~~~~~~a~s~~~Ra~dL~~a~~ 59 (282)
T cd07025 1 IGIVAPSSPI--------DEEERLERAIARLESLGLEVVVGPHVLARDGYLAGTDEERAADLNAAFA 59 (282)
T ss_pred CEEEeCCCCC--------CcHHHHHHHHHHHHhCCCEEEeccchhhhcCccCCCHHHHHHHHHHHhh
Confidence 4678886422 22144568888999999987666654443 345667778777765
No 29
>cd00068 GGL G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G-protein complex; involved in signal transduction via G-protein-coupled receptors
Probab=20.57 E-value=51 Score=24.25 Aligned_cols=23 Identities=17% Similarity=0.208 Sum_probs=17.4
Q ss_pred eecCChHHHHHHHHh--cCCCCCCC
Q 015642 99 LSSACPGWICYAEKQ--LGSYILPY 121 (403)
Q Consensus 99 isS~CPgwV~yiEk~--~~P~lip~ 121 (403)
+|-+|..++.|+|.+ +||-|.+-
T Consensus 22 vS~a~~~l~~y~e~~~~~Dpll~g~ 46 (57)
T cd00068 22 VSKAAAELLKYCEQNAENDPLLTGP 46 (57)
T ss_pred HHHHHHHHHHHHHhcCCCCCCCCCC
Confidence 466899999999998 76655443
No 30
>PRK05569 flavodoxin; Provisional
Probab=20.08 E-value=3.7e+02 Score=22.59 Aligned_cols=65 Identities=18% Similarity=0.263 Sum_probs=37.3
Q ss_pred cHHHHHHHHhC----CCeEEEEeCccchHHHHHHhCCChHHHHHHHHHHHHHcCCcEEEechh--HHHHhHHHHHHHHHH
Q 015642 6 SLDEFLSNINK----GKAVIISLSPQSRASLAEHFGISPLQVFKKLTTFLKSLGVKSIFDTSC--SRDLTLIEACNEFIA 79 (403)
Q Consensus 6 s~~~~~~~l~~----~k~~Vv~iaPq~r~sl~~~f~~~~~~~~~kl~~~lk~LGf~~V~dt~~--gadi~~~e~~~E~~~ 79 (403)
....+++.+.. +|+ |+.++- ||.+.......+...|+++||..+-.+.+ .-|-...+.++||-+
T Consensus 68 ~~~~~~~~l~~~~~~~K~-v~~f~t---------~g~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~p~~~~~~~~~~~g~ 137 (141)
T PRK05569 68 EMAPFLDQFKLTPNENKK-CILFGS---------YGWDNGEFMKLWKDRMKDYGFNVIGDLAVNESPNKEELNSAKELGK 137 (141)
T ss_pred HHHHHHHHhhccCcCCCE-EEEEeC---------CCCCCCcHHHHHHHHHHHCCCeEeeeEEEccCCCHHHHHHHHHHHH
Confidence 45667776642 344 444443 34443344567778888899987665553 234444566666655
Q ss_pred H
Q 015642 80 R 80 (403)
Q Consensus 80 ~ 80 (403)
+
T Consensus 138 ~ 138 (141)
T PRK05569 138 K 138 (141)
T ss_pred H
Confidence 4
No 31
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=20.07 E-value=1.3e+02 Score=23.24 Aligned_cols=25 Identities=40% Similarity=0.626 Sum_probs=19.5
Q ss_pred hHHHHHHhCCChHHHHHHHHHHHHHcCCc
Q 015642 29 RASLAEHFGISPLQVFKKLTTFLKSLGVK 57 (403)
Q Consensus 29 r~sl~~~f~~~~~~~~~kl~~~lk~LGf~ 57 (403)
...+|..-+.|+. -|..|.|+|||+
T Consensus 37 i~elA~~~~vS~s----ti~Rf~kkLG~~ 61 (77)
T PF01418_consen 37 ISELAEKAGVSPS----TIVRFCKKLGFS 61 (77)
T ss_dssp HHHHHHHCTS-HH----HHHHHHHHCTTT
T ss_pred HHHHHHHcCCCHH----HHHHHHHHhCCC
Confidence 3478999999886 666699999997
Done!