Query 024962
Match_columns 260
No_of_seqs 94 out of 96
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 08:51:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024962.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024962hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13266 DUF4057: Protein of u 100.0 4E-113 9E-118 782.6 15.4 254 4-258 48-302 (302)
2 PF13266 DUF4057: Protein of u 100.0 1.2E-33 2.7E-38 259.6 6.0 144 56-238 32-179 (302)
3 PF14493 HTH_40: Helix-turn-he 24.0 39 0.00085 25.9 1.0 15 88-102 14-28 (91)
4 PRK14463 ribosomal RNA large s 15.8 79 0.0017 30.4 1.4 29 224-256 319-348 (349)
5 PF11288 DUF3089: Protein of u 15.2 88 0.0019 28.4 1.4 28 1-28 126-153 (207)
6 PF08920 SF3b1: Splicing facto 13.1 83 0.0018 27.2 0.6 19 9-30 85-103 (144)
7 PRK10040 hypothetical protein; 12.4 1.1E+02 0.0024 22.5 1.0 15 16-30 12-26 (52)
8 PF07623 PEGSRP: Protein of un 12.4 91 0.002 20.2 0.5 8 247-254 4-11 (27)
9 PF03544 TonB_C: Gram-negative 12.0 42 0.00091 23.9 -1.3 43 89-131 4-46 (79)
10 TIGR01352 tonB_Cterm TonB fami 10.1 51 0.0011 23.2 -1.4 38 93-130 2-39 (74)
No 1
>PF13266 DUF4057: Protein of unknown function (DUF4057)
Probab=100.00 E-value=4.1e-113 Score=782.59 Aligned_cols=254 Identities=76% Similarity=1.082 Sum_probs=250.2
Q ss_pred eeeeecccchhhhhhhcccCCCCcccccccccCCcccCCCCCCCCCCCCCCC-CCCCcccccccccCccceeeecCCccc
Q 024962 4 AAVITYLSSSKIVQCDEFRKPCSGYKLKEINGSGIFVANGENGASESDAGNR-NNRTSVRVYQQAMNGISQISFSAEETV 82 (260)
Q Consensus 4 ~~~~~~~~~~ee~~~l~krkpcS~~K~KEmtGsgIF~~~~e~~~~~~~~a~~-~~~t~vr~~qqa~~g~SqIsFg~~~~v 82 (260)
-||||+|||+||||+||||||||+||||||||||||++++++++++.+.+|+ ++||+||||||+++|||||||++||+|
T Consensus 48 kv~fGgQvT~EEAEsL~KRKpCS~~K~KEmTGSGIF~~~~e~~~se~~san~~~~rt~vr~yQq~~~giSqISF~~eesv 127 (302)
T PF13266_consen 48 KVVFGGQVTEEEAESLNKRKPCSGYKMKEMTGSGIFSANGEDDASESGSANPTPNRTGVRMYQQAINGISQISFSEEESV 127 (302)
T ss_pred ccccCCcCCHHHHHHHhccCcCccccceecccccccccCCCCcccccccCCCCccccccceecccccccceeeecCCCCc
Confidence 4899999999999999999999999999999999999999999999999987 789999999999999999999999999
Q ss_pred CCCCCCChhHHhhhhhcccccccchhhhhhcccchhhhhhhccCCCCCCCCCCCCchhHHhhhhccccccCCCCCCCCCc
Q 024962 83 SPKKPTSVPEVAKQRELSGSLQSESDLKTKKQISDAKFKEISGHDIFSPAPEIQPRSLAAARSLESKESKDMGEPAPRNV 162 (260)
Q Consensus 83 spkkpts~~evAkqrELsgt~ese~d~k~kKqiS~aK~KELSGsdIFapppe~~p~s~a~ar~~~~~~~~~~g~p~prn~ 162 (260)
+|||||||+|||||||||||||+|+|.+++||+|+||+|||||||||+||++++|++.+ +|.||.+|++++++|.||+.
T Consensus 128 sPKKpts~~EVAKQRELSGTlese~D~k~kkq~S~AK~KELSGhdIFapp~~~~pr~~~-~r~le~k~~~~~~e~~~~~~ 206 (302)
T PF13266_consen 128 SPKKPTSLPEVAKQRELSGTLESEADSKMKKQISNAKSKELSGHDIFAPPPEIKPRSLT-ARSLELKENKDRGEPAPRNV 206 (302)
T ss_pred CCCCccchHHHHHHhhhcCccccchhhHHHhhhhhhhhhhcccCcccCCCccCCCCcch-hhhhhhcccccccCCCCCcc
Confidence 99999999999999999999999999999999999999999999999999999999985 79999999999999999999
Q ss_pred cccccccCCCCCCCccccCCCCcccccccchhhhhhhhcCCcccCCCCCCCCCCCCcchhhhhhccCCCCCCCCcccccc
Q 024962 163 RTSVKVSNPAGGQSNILFGEEPVVKTSKKIHNQKFAELTGNDIFKGDVPPGSAEKPLSNAKLREMSGSNIFADEKVESRD 242 (260)
Q Consensus 163 ~t~v~v~~p~gG~SsIsF~ee~~vkt~Kkis~~K~aELsGn~IFk~D~~p~~~eK~lS~AKlkEmSG~dIFAdgk~~~rd 242 (260)
++++++.+++||+|+|.|++|+++||+||||++||+||+|||||++|.++.++||+||.||||||+|+|||||||+++||
T Consensus 207 ~ts~~~~n~a~~~s~~~~~~~~~~Ktakki~~~K~aeltGN~IFk~d~p~~saek~lS~AKlrEmsGsdIFaDgk~~~rd 286 (302)
T PF13266_consen 207 RTSVKVSNPAGGQSNIEFGEDSVVKTAKKISNQKFAELTGNNIFKGDVPPASAEKPLSSAKLREMSGSDIFADGKAESRD 286 (302)
T ss_pred cccccccCCcCcccccccccCcchhhhhhhhhhhhhhcccCcccCCCCCCCCcccchhhhhHhhcccccccccCCcccch
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCcccCCCCCCCcc
Q 024962 243 YFGGVRKPPGGESSIS 258 (260)
Q Consensus 243 ~~gg~rkpPGg~SsIa 258 (260)
|+|||||||||+||||
T Consensus 287 ~~gg~rkPPGG~SSIa 302 (302)
T PF13266_consen 287 YLGGVRKPPGGESSIA 302 (302)
T ss_pred hcCCccCCCCCCCcCC
Confidence 9999999999999997
No 2
>PF13266 DUF4057: Protein of unknown function (DUF4057)
Probab=99.98 E-value=1.2e-33 Score=259.65 Aligned_cols=144 Identities=33% Similarity=0.423 Sum_probs=126.5
Q ss_pred CCCCcccccccccCccceeeecCCcccCCCCCCChhHHhhhhhcccccccchhhhhhcccchhhhhhhccCCCCCCCCCC
Q 024962 56 NNRTSVRVYQQAMNGISQISFSAEETVSPKKPTSVPEVAKQRELSGSLQSESDLKTKKQISDAKFKEISGHDIFSPAPEI 135 (260)
Q Consensus 56 ~~~t~vr~~qqa~~g~SqIsFg~~~~vspkkpts~~evAkqrELsgt~ese~d~k~kKqiS~aK~KELSGsdIFapppe~ 135 (260)
+.+..+|++|++ +|||.|.||++ .|.|...+|++||+||++|||||+|++||+...+.
T Consensus 32 ~~~~a~RshQPs-~giskv~fGgQ---------------------vT~EEAEsL~KRKpCS~~K~KEmTGSGIF~~~~e~ 89 (302)
T PF13266_consen 32 TSRPARRSHQPS-DGISKVVFGGQ---------------------VTEEEAESLNKRKPCSGYKMKEMTGSGIFSANGED 89 (302)
T ss_pred CCCCCCCCCCCc-ccccccccCCc---------------------CCHHHHHHHhccCcCccccceecccccccccCCCC
Confidence 456778999866 99999999997 56665678999999999999999999999999988
Q ss_pred CCchhHHhhhhccccccCCCCCCCCCccccccccC-CCCCCCccccCCCCcccccccchhhhhh---hhcCCcccCCCCC
Q 024962 136 QPRSLAAARSLESKESKDMGEPAPRNVRTSVKVSN-PAGGQSNILFGEEPVVKTSKKIHNQKFA---ELTGNDIFKGDVP 211 (260)
Q Consensus 136 ~p~s~a~ar~~~~~~~~~~g~p~prn~~t~v~v~~-p~gG~SsIsF~ee~~vkt~Kkis~~K~a---ELsGn~IFk~D~~ 211 (260)
...+.+.+ ++...+|++|+|| +.+|+|||+|++|++|.++|+++..+|| ||||+.....|.+
T Consensus 90 ~~se~~sa--------------n~~~~rt~vr~yQq~~~giSqISF~~eesvsPKKpts~~EVAKQRELSGTlese~D~k 155 (302)
T PF13266_consen 90 DASESGSA--------------NPTPNRTGVRMYQQAINGISQISFSEEESVSPKKPTSLPEVAKQRELSGTLESEADSK 155 (302)
T ss_pred cccccccC--------------CCCccccccceecccccccceeeecCCCCcCCCCccchHHHHHHhhhcCccccchhhH
Confidence 87766532 4445699999888 5589999999999999999999999988 9999999999998
Q ss_pred CCCCCCCcchhhhhhccCCCCCCCCcc
Q 024962 212 PGSAEKPLSNAKLREMSGSNIFADEKV 238 (260)
Q Consensus 212 p~~~eK~lS~AKlkEmSG~dIFAdgk~ 238 (260)
.. |+||+||.||||||||||++..
T Consensus 156 ~k---kq~S~AK~KELSGhdIFapp~~ 179 (302)
T PF13266_consen 156 MK---KQISNAKSKELSGHDIFAPPPE 179 (302)
T ss_pred HH---hhhhhhhhhhcccCcccCCCcc
Confidence 77 9999999999999999998643
No 3
>PF14493 HTH_40: Helix-turn-helix domain
Probab=24.00 E-value=39 Score=25.87 Aligned_cols=15 Identities=47% Similarity=0.519 Sum_probs=12.9
Q ss_pred CChhHHhhhhhcccc
Q 024962 88 TSVPEVAKQRELSGS 102 (260)
Q Consensus 88 ts~~evAkqrELsgt 102 (260)
.|+.|||++|.|+-+
T Consensus 14 ~si~eIA~~R~L~~s 28 (91)
T PF14493_consen 14 LSIEEIAKIRGLKES 28 (91)
T ss_pred CCHHHHHHHcCCCHH
Confidence 589999999999744
No 4
>PRK14463 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=15.81 E-value=79 Score=30.43 Aligned_cols=29 Identities=38% Similarity=0.559 Sum_probs=18.9
Q ss_pred hhhccCCCCCCC-CcccccccCCCcccCCCCCCC
Q 024962 224 LREMSGSNIFAD-EKVESRDYFGGVRKPPGGESS 256 (260)
Q Consensus 224 lkEmSG~dIFAd-gk~~~rd~~gg~rkpPGg~Ss 256 (260)
+|.=-|.||.|- |.... -.+|-||||||-
T Consensus 319 vR~~~G~di~aaCGqL~~----~~~~~~~~~~~~ 348 (349)
T PRK14463 319 TRSSRGSDISAACGQLKG----KLDKAPPGGESC 348 (349)
T ss_pred EeCCCCcchhhccCcccc----cccCCCCCCCCC
Confidence 344468888875 33322 257999999983
No 5
>PF11288 DUF3089: Protein of unknown function (DUF3089); InterPro: IPR021440 This family of proteins has no known function.
Probab=15.21 E-value=88 Score=28.44 Aligned_cols=28 Identities=21% Similarity=0.250 Sum_probs=22.3
Q ss_pred CcceeeeecccchhhhhhhcccCCCCcc
Q 024962 1 MLAAAVITYLSSSKIVQCDEFRKPCSGY 28 (260)
Q Consensus 1 ~~~~~~~~~~~~~ee~~~l~krkpcS~~ 28 (260)
|+||-+||+.||.++......-++|-.+
T Consensus 126 LVAAYliG~~v~~~~~~~~~~lp~c~~~ 153 (207)
T PF11288_consen 126 LVAAYLIGYPVTVEDLGPFPHLPACTGP 153 (207)
T ss_pred hheeeecCccccHhhcCcCCCCCCCCCC
Confidence 6899999999999777666667788654
No 6
>PF08920 SF3b1: Splicing factor 3B subunit 1; InterPro: IPR015016 This group of proteins consists of several eukaryotic splicing factor 3B subunit 1 proteins, which associate with p14 through a C terminus beta-strand that interacts with beta-3 of the p14 RNA recognition motif (RRM) beta-sheet, which is in turn connected to an alpha-helix by a loop that makes extensive contacts with both the shorter C-terminal helix and RRM of p14. This subunit is required for 'A' splicing complex assembly (formed by the stable binding of U2 snRNP to the branchpoint sequence in pre-mRNA) and 'E' splicing complex assembly []. ; PDB: 2FHO_A 3LQV_P 2PEH_D 2F9J_P 2F9D_Q.
Probab=13.13 E-value=83 Score=27.20 Aligned_cols=19 Identities=21% Similarity=0.352 Sum_probs=12.5
Q ss_pred cccchhhhhhhcccCCCCcccc
Q 024962 9 YLSSSKIVQCDEFRKPCSGYKL 30 (260)
Q Consensus 9 ~~~~~ee~~~l~krkpcS~~K~ 30 (260)
-++||||..+|+ |..+||+
T Consensus 85 rpLTDEELD~mL---PseGYkI 103 (144)
T PF08920_consen 85 RPLTDEELDAML---PSEGYKI 103 (144)
T ss_dssp S-S-HHHHHHTS-----SSEEE
T ss_pred CcCCHHHHHHhC---CcCCcEE
Confidence 368999999998 7788885
No 7
>PRK10040 hypothetical protein; Provisional
Probab=12.44 E-value=1.1e+02 Score=22.54 Aligned_cols=15 Identities=47% Similarity=0.589 Sum_probs=11.7
Q ss_pred hhhhcccCCCCcccc
Q 024962 16 VQCDEFRKPCSGYKL 30 (260)
Q Consensus 16 ~~~l~krkpcS~~K~ 30 (260)
+.++..|.|||+.|-
T Consensus 12 ~~a~a~n~PCSG~KG 26 (52)
T PRK10040 12 FYADAGNKPCSGKKG 26 (52)
T ss_pred HHHHhcCCCCCCCCC
Confidence 346778999999983
No 8
>PF07623 PEGSRP: Protein of unknown function (DUF1584); InterPro: IPR011477 This sequence motif is highly conserved in several short hypothetical proteins from Rhodopirellula baltica. It is also associated with IPR011476 from INTERPRO in Q7UJJ9 from SWISSPROT.
Probab=12.40 E-value=91 Score=20.23 Aligned_cols=8 Identities=75% Similarity=1.244 Sum_probs=5.8
Q ss_pred cccCCCCC
Q 024962 247 VRKPPGGE 254 (260)
Q Consensus 247 ~rkpPGg~ 254 (260)
-|||||-+
T Consensus 4 ~RkppG~~ 11 (27)
T PF07623_consen 4 WRKPPGEE 11 (27)
T ss_pred cccCCCCC
Confidence 48999853
No 9
>PF03544 TonB_C: Gram-negative bacterial TonB protein C-terminal; InterPro: IPR006260 The sequences in this set all contain a conserved C-terminal domain which is characteristic of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria []. Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetitive region is found N-terminal to this domain; these low-complexity regions are highly divergent and cannot readily be aligned. The region is suggested to span the periplasm. Iron is essential for growth in both bacteria and mammals. Controlling the amount of free iron in solution is often used as a tactic by hosts to limit invasion of pathogenic microbes; binding iron tightly within protein molecules can accomplish this. Some bacteria express surface receptors to capture eukaryotic iron-binding compounds, while others have evolved siderophores to scavenge iron from iron-binding host proteins []. The absence of free iron molecules in the surrounding environment triggers transcription of gene clusters that encode both siderophore-synthesis ezymes, and receptors that recognise iron-bound siderophores []. An example of the latter is Escherichia coli fepA, which resides in the outer envelope and captures iron-bound enterobactin []. To complete transport of bound iron across the inner membrane, a second receptor complex is needed. The major component of this is tonB, a 27kDa protein that facilitates energy transfer from the proton motive force to outer receptors. B-12 and colicin receptors also make use of the tonB system to drive active transport at the outer membrane.; GO: 0008565 protein transporter activity, 0015031 protein transport, 0016020 membrane, 0030288 outer membrane-bounded periplasmic space; PDB: 1U07_B 1IHR_A 2GRX_C 2GSK_B 1QXX_A 1XX3_A 2K9K_A.
Probab=11.95 E-value=42 Score=23.92 Aligned_cols=43 Identities=26% Similarity=0.442 Sum_probs=34.2
Q ss_pred ChhHHhhhhhcccccccchhhhhhcccchhhhhhhccCCCCCC
Q 024962 89 SVPEVAKQRELSGSLQSESDLKTKKQISDAKFKEISGHDIFSP 131 (260)
Q Consensus 89 s~~evAkqrELsgt~ese~d~k~kKqiS~aK~KELSGsdIFap 131 (260)
..|+.|+++.+.|++.-+-.....-.+++.++.+=+|+.+|..
T Consensus 4 ~YP~~a~~~~~~G~v~v~~~I~~~G~v~~~~v~~s~~~~~l~~ 46 (79)
T PF03544_consen 4 VYPEEARRRGIEGTVVVEFTIDPDGRVSDVRVIQSSGPPILDE 46 (79)
T ss_dssp ---CHHHHHTEEEEEEEEEEEETTTEEEEEEEEEESSSSCSHH
T ss_pred CCCHHHHHCCCeEEEEEEEEEeCCCCEEEEEEEEccCHHHHHH
Confidence 3567899999999998777777788999999999888887763
No 10
>TIGR01352 tonB_Cterm TonB family C-terminal domain. This model represents the C-terminal of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria. Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetive region is found N-terminal to this domain; these low-complexity regions are highly divergent and cannot readily be aligned. The region is suggested to help span the periplasm.
Probab=10.07 E-value=51 Score=23.15 Aligned_cols=38 Identities=13% Similarity=0.323 Sum_probs=30.1
Q ss_pred HhhhhhcccccccchhhhhhcccchhhhhhhccCCCCC
Q 024962 93 VAKQRELSGSLQSESDLKTKKQISDAKFKEISGHDIFS 130 (260)
Q Consensus 93 vAkqrELsgt~ese~d~k~kKqiS~aK~KELSGsdIFa 130 (260)
.|+++.+.|++.=+-.......+.+.++.+-+|+.+|.
T Consensus 2 ~a~~~~~~G~v~v~~~i~~~G~v~~~~i~~ssg~~~ld 39 (74)
T TIGR01352 2 RARRRGIEGTVVVRFTVDADGRVTSVSVLKSSGDEALD 39 (74)
T ss_pred hHHHcCCceEEEEEEEECCCCCEEEEEEEEcCCChhHH
Confidence 47788889988766667777888899988888887765
Done!