Query psy8340
Match_columns 173
No_of_seqs 135 out of 209
Neff 3.6
Searched_HMMs 46136
Date Sat Aug 17 01:12:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8340.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8340hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4137|consensus 100.0 2.2E-37 4.8E-42 234.9 6.7 101 61-173 2-102 (102)
2 COG5195 Uncharacterized conser 100.0 1.9E-34 4E-39 222.5 5.4 113 47-172 5-117 (118)
3 PF08265 YL1_C: YL1 nuclear pr 99.5 1.9E-15 4.1E-20 93.3 2.0 30 122-151 1-30 (30)
4 KOG3362|consensus 99.4 4.1E-14 8.9E-19 114.8 1.7 68 81-150 80-147 (156)
5 PF04438 zf-HIT: HIT zinc fing 98.3 2.5E-07 5.4E-12 56.9 1.3 30 120-149 1-30 (30)
6 KOG2897|consensus 98.2 1.1E-06 2.4E-11 80.3 3.0 46 120-168 292-337 (390)
7 KOG4317|consensus 96.6 0.00059 1.3E-08 62.2 0.3 33 120-152 6-39 (383)
8 PF13824 zf-Mss51: Zinc-finger 91.9 0.11 2.4E-06 36.3 1.9 25 123-147 1-29 (55)
9 KOG2857|consensus 90.0 0.16 3.5E-06 41.9 1.5 34 122-155 6-40 (157)
10 cd00350 rubredoxin_like Rubred 67.7 3.4 7.4E-05 25.2 1.3 19 123-141 3-26 (33)
11 cd00730 rubredoxin Rubredoxin; 54.3 9.9 0.00022 25.7 1.8 15 127-141 29-43 (50)
12 PHA00616 hypothetical protein 47.4 8.3 0.00018 25.8 0.6 19 132-150 1-19 (44)
13 KOG2858|consensus 46.3 9.9 0.00021 35.6 1.1 28 122-149 18-46 (390)
14 cd00729 rubredoxin_SM Rubredox 45.7 14 0.0003 22.9 1.4 18 123-140 4-26 (34)
15 PRK08271 anaerobic ribonucleos 41.2 23 0.0005 34.8 2.8 55 85-152 541-598 (623)
16 PF09538 FYDLN_acid: Protein o 40.5 13 0.00029 28.6 0.9 14 131-144 8-21 (108)
17 PRK14704 anaerobic ribonucleos 38.2 27 0.00058 34.2 2.7 58 84-152 533-593 (618)
18 PRK09263 anaerobic ribonucleos 36.6 21 0.00046 35.3 1.8 31 105-141 631-668 (711)
19 PRK00432 30S ribosomal protein 36.2 15 0.00033 24.7 0.5 37 106-143 6-48 (50)
20 PLN03158 methionine aminopepti 35.8 27 0.00059 32.2 2.2 32 119-150 7-46 (396)
21 PRK07111 anaerobic ribonucleos 34.5 18 0.00039 36.0 0.9 39 105-151 670-710 (735)
22 PF13894 zf-C2H2_4: C2H2-type 34.0 26 0.00056 18.1 1.1 18 133-150 1-18 (24)
23 PF00096 zf-C2H2: Zinc finger, 32.6 21 0.00045 19.1 0.6 18 133-150 1-18 (23)
24 PRK04179 rpl37e 50S ribosomal 32.2 21 0.00046 25.7 0.7 18 115-132 26-44 (62)
25 TIGR02487 NrdD anaerobic ribon 30.3 28 0.0006 33.5 1.4 37 106-150 515-554 (579)
26 TIGR02300 FYDLN_acid conserved 30.0 25 0.00055 28.5 0.9 14 131-144 8-21 (129)
27 PRK08270 anaerobic ribonucleos 30.0 19 0.0004 35.4 0.2 52 86-150 601-654 (656)
28 PF01753 zf-MYND: MYND finger; 28.2 46 0.001 20.2 1.7 27 124-150 1-28 (37)
29 KOG1710|consensus 27.8 19 0.0004 33.6 -0.2 30 121-150 319-350 (396)
30 PRK08579 anaerobic ribonucleos 27.4 48 0.001 32.6 2.5 40 105-152 558-600 (625)
31 PHA02757 hypothetical protein; 26.9 30 0.00066 25.5 0.8 16 115-130 8-23 (75)
32 TIGR02827 RNR_anaer_Bdell anae 26.1 40 0.00086 33.0 1.7 53 85-150 507-562 (586)
33 PF01907 Ribosomal_L37e: Ribos 25.1 23 0.00049 24.9 -0.1 17 116-132 25-41 (55)
34 KOG2934|consensus 24.0 44 0.00096 28.8 1.4 39 127-165 93-132 (204)
35 PF00301 Rubredoxin: Rubredoxi 24.0 45 0.00097 22.3 1.2 16 126-141 28-43 (47)
36 PLN00206 DEAD-box ATP-dependen 24.0 64 0.0014 30.0 2.6 33 119-151 26-58 (518)
37 PF03884 DUF329: Domain of unk 22.5 51 0.0011 23.0 1.2 28 122-149 3-30 (57)
38 COG2126 RPL37A Ribosomal prote 22.3 39 0.00085 24.3 0.6 15 116-130 26-40 (61)
39 COG1592 Rubrerythrin [Energy p 22.3 55 0.0012 27.3 1.6 22 121-142 134-159 (166)
40 COG0675 Transposase and inacti 22.3 52 0.0011 26.9 1.5 27 118-144 306-334 (364)
41 PTZ00073 60S ribosomal protein 22.0 39 0.00085 26.0 0.6 19 114-132 24-42 (91)
42 PRK00420 hypothetical protein; 21.3 54 0.0012 25.7 1.3 22 122-143 24-51 (112)
No 1
>KOG4137|consensus
Probab=100.00 E-value=2.2e-37 Score=234.88 Aligned_cols=101 Identities=42% Similarity=0.592 Sum_probs=95.2
Q ss_pred CCCCchhhHhhhhcccCCCCCCCcccccHHHHHHHhhcCCCCCCCCcccccccCCCCCCCcccccccCCCccccCCCCCC
Q psy8340 61 IFKNPEYEQRKLSRRSTSSNLPTKQWKSLKQILSYEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKL 140 (173)
Q Consensus 61 ~FKnp~~~~~~~~~~~~~~~~k~R~~KnlKQLL~~E~~~~~~~d~ptY~sI~APPSlkP~kkyCdITGlpA~YtDP~TgL 140 (173)
+||+|.+.. +.++.||+||++..|+.+...+..++|++|+||||++|++||||||||||.|+||.|||
T Consensus 2 ~fk~p~~kk------------~t~~~kn~rq~~~~e~~q~l~~~k~tYfsi~appSv~PakKycDvTGLpapYtdP~t~L 69 (102)
T KOG4137|consen 2 KFQKPWYKK------------STRRGKNMRQKILKELLQRLIEKKHTYFSIEAPPSVKPAKKYCDVTGLPAPYTDPNTGL 69 (102)
T ss_pred CccCccccC------------CcccCccHHHHHhhhhhhhcccccCceEEecCCCccccchhhccccCCcccccCCCccc
Confidence 489998852 56999999999999998777788899999999999999999999999999999999999
Q ss_pred cccCHHHHHHHhcCChhHHHHHHHhhCCCCCCC
Q psy8340 141 YYYNIEEYKLIRKLPSDIVNGYLALRGALNPLA 173 (173)
Q Consensus 141 RY~n~~~y~~Ir~lp~~~~q~YL~LRga~~iv~ 173 (173)
||||+++|+.|++||+|+||+||.|||++++|+
T Consensus 70 ry~naeiY~~i~empsd~vq~ylklRg~~~~l~ 102 (102)
T KOG4137|consen 70 RYHNAEIYKLICEMPSDRVQEYLKLRGFGKVLK 102 (102)
T ss_pred eeccHHHHHHHHHCCchHhhhHHhhhccccccC
Confidence 999999999999999999999999999999986
No 2
>COG5195 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.9e-34 Score=222.54 Aligned_cols=113 Identities=35% Similarity=0.505 Sum_probs=98.4
Q ss_pred chhhhhhhccCCCCCCCCchhhHhhhhcccCCCCCCCcccccHHHHHHHhhcCCCCCCCCcccccccCCCCCCCcccccc
Q psy8340 47 NSQNQMQEKLAPKYIFKNPEYEQRKLSRRSTSSNLPTKQWKSLKQILSYEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDI 126 (173)
Q Consensus 47 ~~~~~~~~~~~~~~~FKnp~~~~~~~~~~~~~~~~k~R~~KnlKQLL~~E~~~~~~~d~ptY~sI~APPSlkP~kkyCdI 126 (173)
++.+..++.+..+|-||+++|.. +.|++|++||||..+.... .....+|++|+||||++|+++||||
T Consensus 5 nn~d~~d~~ll~rP~fk~~~Yk~------------~~rr~ktlrQli~~~~i~n-e~sk~~Y~sieappSv~P~~KyCDv 71 (118)
T COG5195 5 NNNDGGDMKLLKRPWFKKSTYKG------------KNRRFKTLRQLIPRLTIEN-ESSKHRYLSIEAPPSVKPRMKYCDV 71 (118)
T ss_pred CCCcccchhhhhcccccCccccC------------cccchhhHHHHcccccccc-ccccceeEeecCCCccccccccccc
Confidence 33444566666666799999953 5699999999999875443 2335799999999999999999999
Q ss_pred cCCCccccCCCCCCcccCHHHHHHHhcCChhHHHHHHHhhCCCCCC
Q psy8340 127 SRFECNYKDPQTKLYYYNIEEYKLIRKLPSDIVNGYLALRGALNPL 172 (173)
Q Consensus 127 TGlpA~YtDP~TgLRY~n~~~y~~Ir~lp~~~~q~YL~LRga~~iv 172 (173)
|||||.||||.|||||||+++|+.|+.||+|.+|+||.||+++.||
T Consensus 72 TGL~a~Yt~P~t~lrYhn~eiY~lI~elpsg~dQeylkLR~~~~vL 117 (118)
T COG5195 72 TGLPAPYTCPNTGLRYHNSEIYKLICELPSGRDQEYLKLREFGKVL 117 (118)
T ss_pred cCCcccccCCCcCceeccHHHHHHhhcCCCchhHHHHHhhhcCccc
Confidence 9999999999999999999999999999999999999999999987
No 3
>PF08265 YL1_C: YL1 nuclear protein C-terminal domain; InterPro: IPR013272 This domain is found at the C terminus in proteins of the YL1 family []. These proteins have been shown to be DNA-binding and may be transcription factors []. This domain is also found in proteins that do not belong to the YL1 family.
Probab=99.54 E-value=1.9e-15 Score=93.32 Aligned_cols=30 Identities=50% Similarity=0.868 Sum_probs=28.8
Q ss_pred ccccccCCCccccCCCCCCcccCHHHHHHH
Q psy8340 122 KYSDISRFECNYKDPQTKLYYYNIEEYKLI 151 (173)
Q Consensus 122 kyCdITGlpA~YtDP~TgLRY~n~~~y~~I 151 (173)
|+|||||+||+|+||+|||+|+|.++|++|
T Consensus 1 k~C~iTglpA~Y~DP~T~l~Y~n~~ayk~i 30 (30)
T PF08265_consen 1 KYCDITGLPARYRDPKTGLPYANSEAYKII 30 (30)
T ss_pred CcccccCCCccccCCCCCCcccCHHHhhcC
Confidence 689999999999999999999999999976
No 4
>KOG3362|consensus
Probab=99.42 E-value=4.1e-14 Score=114.76 Aligned_cols=68 Identities=19% Similarity=0.294 Sum_probs=60.1
Q ss_pred CCCcccccHHHHHHHhhcCCCCCCCCcccccccCCCCCCCcccccccCCCccccCCCCCCcccCHHHHHH
Q psy8340 81 LPTKQWKSLKQILSYEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEYKL 150 (173)
Q Consensus 81 ~k~R~~KnlKQLL~~E~~~~~~~d~ptY~sI~APPSlkP~kkyCdITGlpA~YtDP~TgLRY~n~~~y~~ 150 (173)
.+.+++|||+++|++.... +. ..++|.++-||||.+|.++||.|||++++|.|..||.+||++.|+++
T Consensus 80 ~~~~~RKnf~~~Ldea~~~-~~-k~~~Y~~~~a~p~~KP~r~fCaVCG~~S~ysC~~CG~kyCsv~C~~~ 147 (156)
T KOG3362|consen 80 FKLRFRKNFQALLDEALLN-LM-KNPNYHTAYAKPSFKPLRKFCAVCGYDSKYSCVNCGTKYCSVRCLKT 147 (156)
T ss_pred hhhhHHHHHHHHHHccchh-hh-hccchhhcccCCCCCCcchhhhhcCCCchhHHHhcCCceeechhhhh
Confidence 3578899999999865432 22 67999999999999999999999999999999999999999999986
No 5
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=98.30 E-value=2.5e-07 Score=56.88 Aligned_cols=30 Identities=20% Similarity=0.365 Sum_probs=23.9
Q ss_pred CcccccccCCCccccCCCCCCcccCHHHHH
Q psy8340 120 SLKYSDISRFECNYKDPQTKLYYYNIEEYK 149 (173)
Q Consensus 120 ~kkyCdITGlpA~YtDP~TgLRY~n~~~y~ 149 (173)
++++|.|+|.+|+|+||+|+++|++.++|+
T Consensus 1 ~~~~C~vC~~~~kY~Cp~C~~~~CSl~C~k 30 (30)
T PF04438_consen 1 PRKLCSVCGNPAKYRCPRCGARYCSLACYK 30 (30)
T ss_dssp --EEETSSSSEESEE-TTT--EESSHHHHH
T ss_pred CcCCCccCcCCCEEECCCcCCceeCcEeEC
Confidence 367999999999999999999999999985
No 6
>KOG2897|consensus
Probab=98.17 E-value=1.1e-06 Score=80.28 Aligned_cols=46 Identities=26% Similarity=0.360 Sum_probs=38.6
Q ss_pred CcccccccCCCccccCCCCCCcccCHHHHHHHhcCChhHHHHHHHhhCC
Q psy8340 120 SLKYSDISRFECNYKDPQTKLYYYNIEEYKLIRKLPSDIVNGYLALRGA 168 (173)
Q Consensus 120 ~kkyCdITGlpA~YtDP~TgLRY~n~~~y~~Ir~lp~~~~q~YL~LRga 168 (173)
.+-.|.|||+||+|.||.|||+|+++.+|++||. ..-+.|+.+||-
T Consensus 292 ~~~~C~iTg~PA~Y~DPVT~lPy~ta~AFKviRe---~y~~~~~~~~~~ 337 (390)
T KOG2897|consen 292 ERVVCVITGRPARYLDPVTGLPYSTAQAFKVIRE---RYKKHLRSIRGN 337 (390)
T ss_pred ccccccccCCcccccCcccCCcchhHHHHHHHHH---HHHHHhhhcccc
Confidence 5569999999999999999999999999999994 344556666653
No 7
>KOG4317|consensus
Probab=96.60 E-value=0.00059 Score=62.15 Aligned_cols=33 Identities=21% Similarity=0.390 Sum_probs=28.7
Q ss_pred CcccccccCC-CccccCCCCCCcccCHHHHHHHh
Q psy8340 120 SLKYSDISRF-ECNYKDPQTKLYYYNIEEYKLIR 152 (173)
Q Consensus 120 ~kkyCdITGl-pA~YtDP~TgLRY~n~~~y~~Ir 152 (173)
+.-+|.|||. ++.||||+|.++||+..||..=.
T Consensus 6 ~~~~C~ic~vq~~~YtCPRCn~~YCsl~CYr~h~ 39 (383)
T KOG4317|consen 6 SFLACGICGVQKREYTCPRCNLLYCSLKCYRNHK 39 (383)
T ss_pred ceeeccccccccccccCCCCCccceeeeeecCCC
Confidence 3568999996 78999999999999999998644
No 8
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=91.86 E-value=0.11 Score=36.26 Aligned_cols=25 Identities=16% Similarity=0.207 Sum_probs=21.5
Q ss_pred cccccCC----CccccCCCCCCcccCHHH
Q psy8340 123 YSDISRF----ECNYKDPQTKLYYYNIEE 147 (173)
Q Consensus 123 yCdITGl----pA~YtDP~TgLRY~n~~~ 147 (173)
+|.+|+- ..+|+||.||++++.++.
T Consensus 1 ~Cpv~~~~~~~~v~~~Cp~cGipthcS~e 29 (55)
T PF13824_consen 1 LCPVCKKDLPAHVNFECPDCGIPTHCSEE 29 (55)
T ss_pred CCCCCccccccccCCcCCCCCCcCccCHH
Confidence 5899998 999999999999876554
No 9
>KOG2857|consensus
Probab=90.01 E-value=0.16 Score=41.94 Aligned_cols=34 Identities=24% Similarity=0.368 Sum_probs=28.7
Q ss_pred ccccccCC-CccccCCCCCCcccCHHHHHHHhcCC
Q psy8340 122 KYSDISRF-ECNYKDPQTKLYYYNIEEYKLIRKLP 155 (173)
Q Consensus 122 kyCdITGl-pA~YtDP~TgLRY~n~~~y~~Ir~lp 155 (173)
..|.||-- +.+|+||+|..+||+.-||++=+.-|
T Consensus 6 ~tC~ic~e~~~KYKCpkC~vPYCSl~CfKiHk~tP 40 (157)
T KOG2857|consen 6 TTCVICLESEIKYKCPKCSVPYCSLPCFKIHKSTP 40 (157)
T ss_pred eeehhhhcchhhccCCCCCCccccchhhhhccCCc
Confidence 46888865 66999999999999999999877633
No 10
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=67.66 E-value=3.4 Score=25.23 Aligned_cols=19 Identities=5% Similarity=0.036 Sum_probs=15.6
Q ss_pred cccccCCC-----ccccCCCCCCc
Q psy8340 123 YSDISRFE-----CNYKDPQTKLY 141 (173)
Q Consensus 123 yCdITGlp-----A~YtDP~TgLR 141 (173)
.|.+||+. ++++||.||.+
T Consensus 3 ~C~~CGy~y~~~~~~~~CP~Cg~~ 26 (33)
T cd00350 3 VCPVCGYIYDGEEAPWVCPVCGAP 26 (33)
T ss_pred ECCCCCCEECCCcCCCcCcCCCCc
Confidence 58888887 78999999874
No 11
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=54.32 E-value=9.9 Score=25.72 Aligned_cols=15 Identities=7% Similarity=-0.022 Sum_probs=11.7
Q ss_pred cCCCccccCCCCCCc
Q psy8340 127 SRFECNYKDPQTKLY 141 (173)
Q Consensus 127 TGlpA~YtDP~TgLR 141 (173)
.-||..|+||.||..
T Consensus 29 ~~Lp~~w~CP~C~a~ 43 (50)
T cd00730 29 EDLPDDWVCPVCGAG 43 (50)
T ss_pred hHCCCCCCCCCCCCc
Confidence 347889999999864
No 12
>PHA00616 hypothetical protein
Probab=47.36 E-value=8.3 Score=25.80 Aligned_cols=19 Identities=11% Similarity=-0.047 Sum_probs=16.9
Q ss_pred cccCCCCCCcccCHHHHHH
Q psy8340 132 NYKDPQTKLYYYNIEEYKL 150 (173)
Q Consensus 132 ~YtDP~TgLRY~n~~~y~~ 150 (173)
+|.||+||..|.+...+..
T Consensus 1 pYqC~~CG~~F~~~s~l~~ 19 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIE 19 (44)
T ss_pred CCccchhhHHHhhHHHHHH
Confidence 5999999999999988765
No 13
>KOG2858|consensus
Probab=46.34 E-value=9.9 Score=35.61 Aligned_cols=28 Identities=18% Similarity=0.114 Sum_probs=24.3
Q ss_pred ccccccCCCc-cccCCCCCCcccCHHHHH
Q psy8340 122 KYSDISRFEC-NYKDPQTKLYYYNIEEYK 149 (173)
Q Consensus 122 kyCdITGlpA-~YtDP~TgLRY~n~~~y~ 149 (173)
..|-||+-++ +|+||+|-.|+|+.+|=.
T Consensus 18 vlCgVClknE~KYkCPRCl~rtCsLeCsk 46 (390)
T KOG2858|consen 18 VLCGVCLKNEPKYKCPRCLARTCSLECSK 46 (390)
T ss_pred hhhhhcccCcccccCcchhhhheeccccc
Confidence 3799999876 699999999999988744
No 14
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=45.69 E-value=14 Score=22.93 Aligned_cols=18 Identities=11% Similarity=0.052 Sum_probs=12.9
Q ss_pred cccccCCC-----ccccCCCCCC
Q psy8340 123 YSDISRFE-----CNYKDPQTKL 140 (173)
Q Consensus 123 yCdITGlp-----A~YtDP~TgL 140 (173)
.|.+||+. ++..||.||.
T Consensus 4 ~C~~CG~i~~g~~~p~~CP~Cg~ 26 (34)
T cd00729 4 VCPVCGYIHEGEEAPEKCPICGA 26 (34)
T ss_pred ECCCCCCEeECCcCCCcCcCCCC
Confidence 47777776 5677888776
No 15
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=41.22 E-value=23 Score=34.79 Aligned_cols=55 Identities=11% Similarity=0.107 Sum_probs=35.6
Q ss_pred ccccHHHHHHHhhcCCCCCCCCcccccccCCCCCCCcccccccCCC---ccccCCCCCCcccCHHHHHHHh
Q psy8340 85 QWKSLKQILSYEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFE---CNYKDPQTKLYYYNIEEYKLIR 152 (173)
Q Consensus 85 ~~KnlKQLL~~E~~~~~~~d~ptY~sI~APPSlkP~kkyCdITGlp---A~YtDP~TgLRY~n~~~y~~Ir 152 (173)
-.+.+++|+.-- .. ....|++|.-| -.+|..||+. -.++||.||- .+.+++..|-
T Consensus 541 n~eal~~lv~~~----~~-~~i~Yf~in~~------~~iC~~CG~~~~g~~~~CP~CGs--~~~ev~~RV~ 598 (623)
T PRK08271 541 SEEGYRKLLNIA----AK-TGCNYFAFNVK------ITICNDCHHIDKRTGKRCPICGS--ENIDYYTRVI 598 (623)
T ss_pred CHHHHHHHHHHH----HH-cCCceEEeCCC------CccCCCCCCcCCCCCcCCcCCCC--cchhHHHHHh
Confidence 455566655421 11 24678887754 4489999985 4789999997 3556666543
No 16
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=40.54 E-value=13 Score=28.64 Aligned_cols=14 Identities=14% Similarity=0.320 Sum_probs=8.8
Q ss_pred ccccCCCCCCcccC
Q psy8340 131 CNYKDPQTKLYYYN 144 (173)
Q Consensus 131 A~YtDP~TgLRY~n 144 (173)
.+-+||.||.|||+
T Consensus 8 tKR~Cp~CG~kFYD 21 (108)
T PF09538_consen 8 TKRTCPSCGAKFYD 21 (108)
T ss_pred CcccCCCCcchhcc
Confidence 34566777777665
No 17
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=38.25 E-value=27 Score=34.22 Aligned_cols=58 Identities=26% Similarity=0.248 Sum_probs=36.4
Q ss_pred cccccHHHHHHHhhcCCCCCCCCcccccccCCCCCCCcccccccCCCcc--ccCCCCCCcc-cCHHHHHHHh
Q psy8340 84 KQWKSLKQILSYEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFECN--YKDPQTKLYY-YNIEEYKLIR 152 (173)
Q Consensus 84 R~~KnlKQLL~~E~~~~~~~d~ptY~sI~APPSlkP~kkyCdITGlpA~--YtDP~TgLRY-~n~~~y~~Ir 152 (173)
.-.+.+++|+.-- -....-|++|.-|. .+|..||+.+- ++||.||-+= ++.+++..|-
T Consensus 533 ~n~~Al~~lvk~~-----~~~~i~Y~sin~~~------~~C~~CGy~g~~~~~CP~CG~~d~~~~~v~~Ri~ 593 (618)
T PRK14704 533 HNKKALKQIVQAM-----AEHGVGYGSINHPV------DRCKCCSYHGVIGNECPSCGNEDEANIERIRRIT 593 (618)
T ss_pred CCHHHHHHHHHHH-----HhcCCceEEeCCCC------eecCCCCCCCCcCccCcCCCCCCcchhHHHHHHH
Confidence 3456666665531 11246788877554 48888888655 7999999732 2366776543
No 18
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=36.56 E-value=21 Score=35.35 Aligned_cols=31 Identities=13% Similarity=0.126 Sum_probs=23.1
Q ss_pred CCcccccccCCCCCCCcccccccCCCc-------cccCCCCCCc
Q psy8340 105 TIHYSSIVAPPSFKPSLKYSDISRFEC-------NYKDPQTKLY 141 (173)
Q Consensus 105 ~ptY~sI~APPSlkP~kkyCdITGlpA-------~YtDP~TgLR 141 (173)
..-|++|.-|. .+|..||+.+ .+.||.||-+
T Consensus 631 ~i~Y~~in~~~------~~C~~CG~~Ge~~~~~~~~~CP~CG~~ 668 (711)
T PRK09263 631 RVGYLGTNTPI------DECYECGFTGEFECTEKGFTCPKCGNH 668 (711)
T ss_pred CCCeEEeCCCC------cccCCCCCCccccCCCCCCcCcCCCCC
Confidence 37788887554 4899999853 2699999953
No 19
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=36.19 E-value=15 Score=24.69 Aligned_cols=37 Identities=8% Similarity=-0.007 Sum_probs=26.3
Q ss_pred CcccccccCCCCCCCcccccccCC------CccccCCCCCCccc
Q psy8340 106 IHYSSIVAPPSFKPSLKYSDISRF------ECNYKDPQTKLYYY 143 (173)
Q Consensus 106 ptY~sI~APPSlkP~kkyCdITGl------pA~YtDP~TgLRY~ 143 (173)
-.|..|+.- .+.+.++||+-||- ..++.|.+||..|.
T Consensus 6 ~~~y~v~~~-~v~~~~~fCP~Cg~~~m~~~~~r~~C~~Cgyt~~ 48 (50)
T PRK00432 6 REYYEVDGG-KVKRKNKFCPRCGSGFMAEHLDRWHCGKCGYTEF 48 (50)
T ss_pred eeeEEECCC-EEEEccCcCcCCCcchheccCCcEECCCcCCEEe
Confidence 356677655 56677889999984 23788888887764
No 20
>PLN03158 methionine aminopeptidase; Provisional
Probab=35.79 E-value=27 Score=32.20 Aligned_cols=32 Identities=9% Similarity=0.044 Sum_probs=26.3
Q ss_pred CCcccccccCCCccccCCCC--------CCcccCHHHHHH
Q psy8340 119 PSLKYSDISRFECNYKDPQT--------KLYYYNIEEYKL 150 (173)
Q Consensus 119 P~kkyCdITGlpA~YtDP~T--------gLRY~n~~~y~~ 150 (173)
|...-|.=||-+|.-.||.| +.-||+.+||+.
T Consensus 7 ~~~~~c~~c~~~a~l~Cp~C~k~~~~~~~s~fCsq~CFk~ 46 (396)
T PLN03158 7 TSPLACARCSKPAHLQCPKCLELKLPREGASFCSQDCFKA 46 (396)
T ss_pred CCcccccCCCCcccccCccchhcCCCCCCceeECHHHHHH
Confidence 44556988999999999995 467999999974
No 21
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=34.51 E-value=18 Score=36.01 Aligned_cols=39 Identities=23% Similarity=0.278 Sum_probs=26.3
Q ss_pred CCcccccccCCCCCCCcccccccCCCc--cccCCCCCCcccCHHHHHHH
Q psy8340 105 TIHYSSIVAPPSFKPSLKYSDISRFEC--NYKDPQTKLYYYNIEEYKLI 151 (173)
Q Consensus 105 ~ptY~sI~APPSlkP~kkyCdITGlpA--~YtDP~TgLRY~n~~~y~~I 151 (173)
..-|++|. |+-.+|..||+-. .++||.||- .+.++|..|
T Consensus 670 ~i~Y~sin------~~~~~C~~CG~~~~~~~~CP~CG~--~~~~~~~Ri 710 (735)
T PRK07111 670 NIGYGSIN------HPVDRCPVCGYLGVIEDKCPKCGS--TNIQRIRRI 710 (735)
T ss_pred CCceEEeC------CCCeecCCCCCCCCcCccCcCCCC--ccceeeehh
Confidence 35677765 4455888888744 489999997 355555543
No 22
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=33.98 E-value=26 Score=18.06 Aligned_cols=18 Identities=11% Similarity=0.196 Sum_probs=12.5
Q ss_pred ccCCCCCCcccCHHHHHH
Q psy8340 133 YKDPQTKLYYYNIEEYKL 150 (173)
Q Consensus 133 YtDP~TgLRY~n~~~y~~ 150 (173)
|.|+.|+..|.+...+..
T Consensus 1 ~~C~~C~~~~~~~~~l~~ 18 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQ 18 (24)
T ss_dssp EE-SSTS-EESSHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHH
Confidence 678888888888877764
No 23
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=32.63 E-value=21 Score=19.11 Aligned_cols=18 Identities=22% Similarity=0.224 Sum_probs=15.1
Q ss_pred ccCCCCCCcccCHHHHHH
Q psy8340 133 YKDPQTKLYYYNIEEYKL 150 (173)
Q Consensus 133 YtDP~TgLRY~n~~~y~~ 150 (173)
|+|+.|+-.|.+...+..
T Consensus 1 y~C~~C~~~f~~~~~l~~ 18 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKR 18 (23)
T ss_dssp EEETTTTEEESSHHHHHH
T ss_pred CCCCCCCCccCCHHHHHH
Confidence 789999999999887764
No 24
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=32.15 E-value=21 Score=25.67 Aligned_cols=18 Identities=22% Similarity=0.377 Sum_probs=14.2
Q ss_pred CCCCCCcccccccCC-Ccc
Q psy8340 115 PSFKPSLKYSDISRF-ECN 132 (173)
Q Consensus 115 PSlkP~kkyCdITGl-pA~ 132 (173)
-|+.-++++|.-||| |+.
T Consensus 26 ~syh~qK~~CasCGygps~ 44 (62)
T PRK04179 26 HSYNVRKKYCAACGFGRSK 44 (62)
T ss_pred ccccccccchhhcCCCccc
Confidence 355678999999999 764
No 25
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=30.33 E-value=28 Score=33.55 Aligned_cols=37 Identities=22% Similarity=0.196 Sum_probs=26.8
Q ss_pred CcccccccCCCCCCCcccccccCCCccc---cCCCCCCcccCHHHHHH
Q psy8340 106 IHYSSIVAPPSFKPSLKYSDISRFECNY---KDPQTKLYYYNIEEYKL 150 (173)
Q Consensus 106 ptY~sI~APPSlkP~kkyCdITGlpA~Y---tDP~TgLRY~n~~~y~~ 150 (173)
..|++|.-|.+ +|.-||+.+.. +||.||-+ +.+++..
T Consensus 515 i~Y~~~n~~~~------~C~~CG~~g~~~~~~CP~Cgs~--~~~~~~R 554 (579)
T TIGR02487 515 IGYFGINPPVD------VCEDCGYTGEGLNDKCPKCGSH--DIEVISR 554 (579)
T ss_pred CceEEeccCCc------cCCCCCCCCCCCCCcCcCCCCc--cceehhh
Confidence 67888775544 78888887765 79999975 3555544
No 26
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=30.02 E-value=25 Score=28.46 Aligned_cols=14 Identities=21% Similarity=0.330 Sum_probs=8.1
Q ss_pred ccccCCCCCCcccC
Q psy8340 131 CNYKDPQTKLYYYN 144 (173)
Q Consensus 131 A~YtDP~TgLRY~n 144 (173)
.+.+||.||.|||+
T Consensus 8 tKr~Cp~cg~kFYD 21 (129)
T TIGR02300 8 TKRICPNTGSKFYD 21 (129)
T ss_pred ccccCCCcCccccc
Confidence 34556666666654
No 27
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=30.02 E-value=19 Score=35.42 Aligned_cols=52 Identities=13% Similarity=0.078 Sum_probs=31.3
Q ss_pred cccHHHHHHHhhcCCCCCCCCcccccccCCCCCCCcccccccCCCc--cccCCCCCCcccCHHHHHH
Q psy8340 86 WKSLKQILSYEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFEC--NYKDPQTKLYYYNIEEYKL 150 (173)
Q Consensus 86 ~KnlKQLL~~E~~~~~~~d~ptY~sI~APPSlkP~kkyCdITGlpA--~YtDP~TgLRY~n~~~y~~ 150 (173)
++.++.|+.-- .......|++|.-|.+ +|..||+.. .+.||.||-. .++|..
T Consensus 601 ~~a~~~lv~~~----~~~~~i~Y~~in~~~~------~C~~CG~~~g~~~~CP~CG~~---~~v~sR 654 (656)
T PRK08270 601 AEACKKLVKKA----LENYRLPYITITPTFS------ICPKHGYLSGEHEFCPKCGEE---TEVYSR 654 (656)
T ss_pred HHHHHHHHHHH----HHhCCCceEEeCCCCc------ccCCCCCcCCCCCCCcCCcCc---cceEEe
Confidence 45555555421 1112467888875555 777777633 5899999944 555543
No 28
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=28.17 E-value=46 Score=20.23 Aligned_cols=27 Identities=11% Similarity=0.127 Sum_probs=19.5
Q ss_pred ccccCCCccccCCCC-CCcccCHHHHHH
Q psy8340 124 SDISRFECNYKDPQT-KLYYYNIEEYKL 150 (173)
Q Consensus 124 CdITGlpA~YtDP~T-gLRY~n~~~y~~ 150 (173)
|+++|-++.-+|+.+ ...|++.++...
T Consensus 1 C~~C~~~~~~~C~~C~~~~YCs~~Cq~~ 28 (37)
T PF01753_consen 1 CAVCGKPALKRCSRCKSVYYCSEECQRA 28 (37)
T ss_dssp -TTTSSCSSEEETTTSSSEESSHHHHHH
T ss_pred CcCCCCCcCCcCCCCCCEEecCHHHHHH
Confidence 667777776688888 567888877654
No 29
>KOG1710|consensus
Probab=27.76 E-value=19 Score=33.57 Aligned_cols=30 Identities=17% Similarity=0.190 Sum_probs=25.7
Q ss_pred cccccccCCCc-cccCCCCC-CcccCHHHHHH
Q psy8340 121 LKYSDISRFEC-NYKDPQTK-LYYYNIEEYKL 150 (173)
Q Consensus 121 kkyCdITGlpA-~YtDP~Tg-LRY~n~~~y~~ 150 (173)
-.||..||-|+ .=+|.+|+ +.||+.+|-+.
T Consensus 319 ~~fCstCG~~ga~KrCs~CKav~YCdqeCQk~ 350 (396)
T KOG1710|consen 319 CQFCSTCGHPGAKKRCSQCKAVAYCDQECQKF 350 (396)
T ss_pred cccccccCCCCccchhhhhHHHHHHHHHHHHh
Confidence 56999999986 56799999 99999999764
No 30
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=27.40 E-value=48 Score=32.58 Aligned_cols=40 Identities=15% Similarity=0.174 Sum_probs=27.7
Q ss_pred CCcccccccCCCCCCCcccccccCC---CccccCCCCCCcccCHHHHHHHh
Q psy8340 105 TIHYSSIVAPPSFKPSLKYSDISRF---ECNYKDPQTKLYYYNIEEYKLIR 152 (173)
Q Consensus 105 ~ptY~sI~APPSlkP~kkyCdITGl---pA~YtDP~TgLRY~n~~~y~~Ir 152 (173)
..-|++|. |+-.+|..||. --.+.||.||-+ +.+++..|-
T Consensus 558 ~i~Y~~in------p~~~~C~~CG~~~~g~~~~CP~CGs~--~~~v~~Rv~ 600 (625)
T PRK08579 558 KLVYWSYT------PAITVCNKCGRSTTGLYTRCPRCGSE--DVEVWSRII 600 (625)
T ss_pred CCceEEeC------CCCccCCCCCCccCCCCCcCcCCCCc--hhHHHHHHH
Confidence 36677765 45568888886 235799999984 567776543
No 31
>PHA02757 hypothetical protein; Provisional
Probab=26.90 E-value=30 Score=25.53 Aligned_cols=16 Identities=25% Similarity=0.100 Sum_probs=12.6
Q ss_pred CCCCCCcccccccCCC
Q psy8340 115 PSFKPSLKYSDISRFE 130 (173)
Q Consensus 115 PSlkP~kkyCdITGlp 130 (173)
-|.+|++.||.||--+
T Consensus 8 GSskPprnvCViTPsg 23 (75)
T PHA02757 8 GSSKPPRNVCVITPSG 23 (75)
T ss_pred CCCCCCCCEEEEeCCC
Confidence 3678999999998543
No 32
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=26.08 E-value=40 Score=32.99 Aligned_cols=53 Identities=9% Similarity=-0.017 Sum_probs=33.0
Q ss_pred ccccHHHHHHHhhcCCCCCCCCcccccccCCCCCCCcccccccCCCcc---ccCCCCCCcccCHHHHHH
Q psy8340 85 QWKSLKQILSYEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFECN---YKDPQTKLYYYNIEEYKL 150 (173)
Q Consensus 85 ~~KnlKQLL~~E~~~~~~~d~ptY~sI~APPSlkP~kkyCdITGlpA~---YtDP~TgLRY~n~~~y~~ 150 (173)
-.+.+++|+.--- . ....|++|.-|. .+|..||.... ++||.||-. +.+++..
T Consensus 507 n~ea~~~lv~~~~----~-~~i~Y~tin~~~------siC~~CGy~~g~~~~~CP~CGs~--~~ev~sR 562 (586)
T TIGR02827 507 SEDGYRKLLRVAA----D-TGCNYFCFNIKI------TICNDCHHIDKRTLHRCPVCGSA--NIDYGTR 562 (586)
T ss_pred CHHHHHHHHHHHH----h-cCCceEEeCCCC------eecCCCCCcCCCcCCcCcCCCCc--cceEEEe
Confidence 3455666554221 1 246788887544 48999998532 899999963 4444443
No 33
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=25.13 E-value=23 Score=24.92 Aligned_cols=17 Identities=12% Similarity=0.131 Sum_probs=14.2
Q ss_pred CCCCCcccccccCCCcc
Q psy8340 116 SFKPSLKYSDISRFECN 132 (173)
Q Consensus 116 SlkP~kkyCdITGlpA~ 132 (173)
|+..+++.|.-||+|+.
T Consensus 25 syH~qK~~CasCGyp~~ 41 (55)
T PF01907_consen 25 SYHIQKKTCASCGYPAA 41 (55)
T ss_dssp EEETTTTEETTTBTTTS
T ss_pred eeecCCCcccccCCCcc
Confidence 45578999999999985
No 34
>KOG2934|consensus
Probab=24.01 E-value=44 Score=28.83 Aligned_cols=39 Identities=23% Similarity=0.399 Sum_probs=33.1
Q ss_pred cCCCccccCCCCCCcccCH-HHHHHHhcCChhHHHHHHHh
Q psy8340 127 SRFECNYKDPQTKLYYYNI-EEYKLIRKLPSDIVNGYLAL 165 (173)
Q Consensus 127 TGlpA~YtDP~TgLRY~n~-~~y~~Ir~lp~~~~q~YL~L 165 (173)
||+.|-+-|-++-.--... .+|+.|.+||....-+||.|
T Consensus 93 ~gl~avw~dRrrd~~~l~L~~v~gfIlnlp~~~slG~L~L 132 (204)
T KOG2934|consen 93 CGLEAVWLDRRRDVTALALSVVFGFILNLPCKFSLGYLRL 132 (204)
T ss_pred cCceeeeccccCCcchhhhHHHHHHHHcCCchhccccccc
Confidence 9999999998887665553 78999999999999998765
No 35
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=23.98 E-value=45 Score=22.30 Aligned_cols=16 Identities=6% Similarity=0.019 Sum_probs=10.1
Q ss_pred ccCCCccccCCCCCCc
Q psy8340 126 ISRFECNYKDPQTKLY 141 (173)
Q Consensus 126 ITGlpA~YtDP~TgLR 141 (173)
+..||..|+||.|+..
T Consensus 28 F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 28 FEDLPDDWVCPVCGAP 43 (47)
T ss_dssp GGGS-TT-B-TTTSSB
T ss_pred HHHCCCCCcCcCCCCc
Confidence 4568999999999875
No 36
>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional
Probab=23.97 E-value=64 Score=30.04 Aligned_cols=33 Identities=12% Similarity=-0.011 Sum_probs=28.8
Q ss_pred CCcccccccCCCccccCCCCCCcccCHHHHHHH
Q psy8340 119 PSLKYSDISRFECNYKDPQTKLYYYNIEEYKLI 151 (173)
Q Consensus 119 P~kkyCdITGlpA~YtDP~TgLRY~n~~~y~~I 151 (173)
|.--.|.+||-.+-|.|-+|.-.-|+.||-+.+
T Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 (518)
T PLN00206 26 PGEPKCVVCGRYGEYICDETDDDICSLECKQAL 58 (518)
T ss_pred CCCceEEEecCccceeccCCCCccccHHHHHHH
Confidence 334459999999999999999999999999863
No 37
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=22.48 E-value=51 Score=23.05 Aligned_cols=28 Identities=4% Similarity=-0.152 Sum_probs=18.0
Q ss_pred ccccccCCCccccCCCCCCcccCHHHHH
Q psy8340 122 KYSDISRFECNYKDPQTKLYYYNIEEYK 149 (173)
Q Consensus 122 kyCdITGlpA~YtDP~TgLRY~n~~~y~ 149 (173)
.-|.+||-+..+..-..--+||+.+|-.
T Consensus 3 v~CP~C~k~~~~~~~n~~rPFCS~RCk~ 30 (57)
T PF03884_consen 3 VKCPICGKPVEWSPENPFRPFCSERCKL 30 (57)
T ss_dssp EE-TTT--EEE-SSSSS--SSSSHHHHH
T ss_pred ccCCCCCCeecccCCCCcCCcccHhhcc
Confidence 4599999999998777777899999864
No 38
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=22.30 E-value=39 Score=24.28 Aligned_cols=15 Identities=27% Similarity=0.425 Sum_probs=12.6
Q ss_pred CCCCCcccccccCCC
Q psy8340 116 SFKPSLKYSDISRFE 130 (173)
Q Consensus 116 SlkP~kkyCdITGlp 130 (173)
|+.-.+++|.-||||
T Consensus 26 syhv~k~~CaaCGfg 40 (61)
T COG2126 26 SYHVRKKYCAACGFG 40 (61)
T ss_pred heeeccceecccCCC
Confidence 445679999999999
No 39
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=22.27 E-value=55 Score=27.27 Aligned_cols=22 Identities=9% Similarity=-0.040 Sum_probs=17.6
Q ss_pred cccccccCC----CccccCCCCCCcc
Q psy8340 121 LKYSDISRF----ECNYKDPQTKLYY 142 (173)
Q Consensus 121 kkyCdITGl----pA~YtDP~TgLRY 142 (173)
--.|.+||+ .++-.||.||.+.
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCga~k 159 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICGAPK 159 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCCChH
Confidence 446999987 4789999999764
No 40
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.26 E-value=52 Score=26.93 Aligned_cols=27 Identities=11% Similarity=-0.076 Sum_probs=21.1
Q ss_pred CCCcccccccCCC--ccccCCCCCCcccC
Q psy8340 118 KPSLKYSDISRFE--CNYKDPQTKLYYYN 144 (173)
Q Consensus 118 kP~kkyCdITGlp--A~YtDP~TgLRY~n 144 (173)
.+.-+.|..||.. ..|.||.||...+-
T Consensus 306 ~~tS~~C~~cg~~~~r~~~C~~cg~~~~r 334 (364)
T COG0675 306 YYTSKTCPCCGHLSGRLFKCPRCGFVHDR 334 (364)
T ss_pred CCCcccccccCCccceeEECCCCCCeehh
Confidence 4667899999974 35899999987653
No 41
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=21.99 E-value=39 Score=25.96 Aligned_cols=19 Identities=16% Similarity=0.134 Sum_probs=14.7
Q ss_pred CCCCCCCcccccccCCCcc
Q psy8340 114 PPSFKPSLKYSDISRFECN 132 (173)
Q Consensus 114 PPSlkP~kkyCdITGlpA~ 132 (173)
--|+.-+++.|.-||+|+.
T Consensus 24 ~~syH~qK~~CasCGypsa 42 (91)
T PTZ00073 24 KRSFHVQKKRCASCGYPSA 42 (91)
T ss_pred ccccccccccchhcCCchh
Confidence 3455678999999999764
No 42
>PRK00420 hypothetical protein; Validated
Probab=21.26 E-value=54 Score=25.71 Aligned_cols=22 Identities=14% Similarity=0.087 Sum_probs=15.6
Q ss_pred ccccccCCC------ccccCCCCCCccc
Q psy8340 122 KYSDISRFE------CNYKDPQTKLYYY 143 (173)
Q Consensus 122 kyCdITGlp------A~YtDP~TgLRY~ 143 (173)
..|++||.| +...||.||-.+-
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCeee
Confidence 468888875 4567888887665
Done!