Query 023461
Match_columns 282
No_of_seqs 16 out of 18
Neff 2.1
Searched_HMMs 46136
Date Fri Mar 29 04:12:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023461.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023461hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03120 nucleic acid binding 89.3 0.43 9.3E-06 44.5 3.8 52 66-117 140-191 (260)
2 PF08271 TF_Zn_Ribbon: TFIIB z 81.3 0.84 1.8E-05 30.9 1.2 32 182-218 1-32 (43)
3 PF14257 DUF4349: Domain of un 80.1 3.5 7.5E-05 36.4 5.0 31 34-64 105-135 (262)
4 PF09538 FYDLN_acid: Protein o 71.4 1.4 3E-05 36.1 0.2 32 180-218 8-39 (108)
5 TIGR02098 MJ0042_CXXC MJ0042 f 68.7 2.7 5.7E-05 27.4 1.0 32 182-215 3-36 (38)
6 PF11833 DUF3353: Protein of u 67.7 20 0.00042 31.9 6.5 88 59-152 5-108 (194)
7 TIGR03518 ABC_perm_GldF glidin 67.6 15 0.00032 32.3 5.8 35 119-153 2-36 (240)
8 PF09832 DUF2059: Uncharacteri 67.4 1.7 3.6E-05 30.9 -0.1 20 123-142 22-41 (64)
9 COG3809 Uncharacterized protei 64.9 3.7 8E-05 33.5 1.4 37 182-222 2-38 (88)
10 TIGR02300 FYDLN_acid conserved 64.7 2.6 5.6E-05 36.3 0.5 32 180-218 8-39 (129)
11 PF05957 DUF883: Bacterial pro 57.1 85 0.0019 23.9 9.1 28 125-153 64-91 (94)
12 PF04956 TrbC: TrbC/VIRB2 fami 54.5 26 0.00056 26.5 4.3 35 117-151 36-70 (99)
13 TIGR01206 lysW lysine biosynth 44.4 14 0.0003 27.3 1.4 29 182-213 3-31 (54)
14 PLN03121 nucleic acid binding 43.7 29 0.00063 32.5 3.7 46 68-117 155-200 (243)
15 PF13717 zinc_ribbon_4: zinc-r 42.7 15 0.00032 24.7 1.2 29 183-213 4-34 (36)
16 PRK00398 rpoP DNA-directed RNA 40.2 13 0.00027 25.4 0.6 36 180-220 2-38 (46)
17 PRK15035 cytochrome bd-II oxid 39.7 62 0.0014 33.2 5.6 53 114-166 76-136 (514)
18 PF13913 zf-C2HC_2: zinc-finge 39.6 13 0.00027 23.2 0.5 9 183-191 4-12 (25)
19 PF08507 COPI_assoc: COPI asso 38.0 88 0.0019 25.5 5.3 28 123-150 57-84 (136)
20 PF14570 zf-RING_4: RING/Ubox 37.8 13 0.00027 27.2 0.3 12 180-191 36-47 (48)
21 PF04423 Rad50_zn_hook: Rad50 36.8 14 0.0003 25.9 0.4 13 179-191 18-30 (54)
22 COG2991 Uncharacterized protei 35.8 28 0.00061 28.0 2.0 22 165-186 14-35 (77)
23 PF08209 Sgf11: Sgf11 (transcr 35.3 17 0.00038 24.6 0.7 14 182-198 5-18 (33)
24 PRK00420 hypothetical protein; 34.3 34 0.00074 28.6 2.4 31 179-215 21-51 (112)
25 PF13719 zinc_ribbon_5: zinc-r 33.3 18 0.00039 24.2 0.5 29 183-213 4-34 (37)
26 PRK10697 DNA-binding transcrip 33.2 47 0.001 27.9 3.0 40 144-183 27-66 (118)
27 PF13693 HTH_35: Winged helix- 32.2 46 0.00099 26.2 2.7 40 93-134 16-55 (78)
28 PF14257 DUF4349: Domain of un 31.4 1.7E+02 0.0037 25.9 6.4 41 132-172 216-256 (262)
29 PF12648 TcpE: TcpE family 31.0 65 0.0014 25.4 3.4 64 118-182 7-81 (108)
30 TIGR02978 phageshock_pspC phag 30.7 75 0.0016 26.6 3.9 39 145-183 23-61 (121)
31 smart00531 TFIIE Transcription 30.7 16 0.00036 30.2 -0.0 33 182-214 100-133 (147)
32 cd04511 Nudix_Hydrolase_4 Memb 30.3 49 0.0011 25.5 2.6 25 184-211 1-33 (130)
33 COG2835 Uncharacterized conser 30.2 34 0.00075 26.2 1.6 26 181-211 8-33 (60)
34 PRK15097 cytochrome d terminal 29.8 1.1E+02 0.0024 31.5 5.6 53 114-166 76-136 (522)
35 PRK11827 hypothetical protein; 29.5 33 0.00071 26.0 1.4 29 178-211 5-33 (60)
36 PF05957 DUF883: Bacterial pro 28.9 2.6E+02 0.0057 21.3 7.0 7 35-41 13-19 (94)
37 PF14353 CpXC: CpXC protein 28.8 22 0.00048 28.3 0.4 13 181-193 1-13 (128)
38 PF14787 zf-CCHC_5: GAG-polypr 28.7 23 0.00049 25.0 0.4 11 181-191 2-12 (36)
39 PF11793 FANCL_C: FANCL C-term 28.5 19 0.0004 26.9 -0.0 13 179-191 53-65 (70)
40 TIGR00630 uvra excinuclease AB 28.0 39 0.00084 36.4 2.1 46 172-218 728-773 (924)
41 smart00834 CxxC_CXXC_SSSS Puta 27.3 29 0.00062 22.3 0.7 30 181-212 5-34 (41)
42 PRK06996 hypothetical protein; 27.1 4.6E+02 0.0099 24.0 8.5 75 54-131 309-393 (398)
43 PRK10344 DNA-binding transcrip 26.6 57 0.0012 27.0 2.4 47 87-135 16-62 (92)
44 PRK02935 hypothetical protein; 26.5 69 0.0015 27.3 2.9 41 166-214 56-96 (110)
45 PRK13454 F0F1 ATP synthase sub 26.5 1.2E+02 0.0026 26.1 4.4 23 155-177 40-63 (181)
46 KOG3966 p53-mediated apoptosis 26.4 3.3E+02 0.0071 27.1 7.8 52 61-113 18-69 (360)
47 PLN03120 nucleic acid binding 26.3 75 0.0016 30.0 3.5 30 67-96 165-194 (260)
48 PF11023 DUF2614: Protein of u 26.1 55 0.0012 27.9 2.3 53 168-242 57-109 (114)
49 PF04216 FdhE: Protein involve 25.8 47 0.001 30.1 2.0 56 179-242 170-228 (290)
50 PRK12366 replication factor A; 25.6 10 0.00022 38.6 -2.4 35 180-223 531-565 (637)
51 PF13134 DUF3948: Protein of u 24.7 69 0.0015 22.6 2.2 21 127-147 12-32 (35)
52 PLN03121 nucleic acid binding 24.6 71 0.0015 30.0 2.9 58 66-132 136-193 (243)
53 KOG3096 Spliceosome-associated 24.3 3E+02 0.0066 26.0 6.9 53 51-103 127-180 (225)
54 PRK05759 F0F1 ATP synthase sub 24.3 1.3E+02 0.0028 24.3 4.1 25 153-177 11-36 (156)
55 COG3162 Predicted membrane pro 24.1 74 0.0016 26.8 2.7 27 235-261 11-37 (102)
56 KOG2173 Integral membrane prot 24.0 1E+02 0.0022 33.6 4.2 27 136-162 215-241 (849)
57 TIGR01144 ATP_synt_b ATP synth 23.9 93 0.002 25.0 3.2 22 156-177 5-27 (147)
58 PF03348 Serinc: Serine incorp 23.4 77 0.0017 31.2 3.1 20 150-169 111-131 (429)
59 PF12732 YtxH: YtxH-like prote 23.2 3.1E+02 0.0067 20.2 6.9 19 80-98 53-71 (74)
60 smart00661 RPOL9 RNA polymeras 23.1 46 0.001 22.4 1.1 27 184-213 3-29 (52)
61 PF02773 S-AdoMet_synt_C: S-ad 22.7 55 0.0012 28.6 1.7 35 171-205 47-81 (138)
62 PRK14471 F0F1 ATP synthase sub 22.5 1.8E+02 0.004 24.0 4.7 27 151-177 13-40 (164)
63 PF11241 DUF3043: Protein of u 22.1 5.8E+02 0.012 22.9 10.8 91 91-181 28-132 (170)
64 PF06847 Arc_PepC_II: Archaeal 21.8 50 0.0011 26.4 1.2 17 160-176 70-86 (93)
65 PRK00349 uvrA excinuclease ABC 21.8 43 0.00094 36.2 1.1 39 181-219 738-776 (943)
66 PRK14472 F0F1 ATP synthase sub 21.5 1.1E+02 0.0024 25.7 3.3 28 150-177 22-50 (175)
67 PF00096 zf-C2H2: Zinc finger, 21.2 38 0.00082 19.3 0.3 9 183-191 2-10 (23)
68 PRK06266 transcription initiat 21.0 27 0.00057 30.4 -0.5 39 172-214 103-146 (178)
69 PF13453 zf-TFIIB: Transcripti 20.5 62 0.0013 21.7 1.3 30 183-218 1-32 (41)
70 COG5005 Mu-like prophage prote 20.3 1.5E+02 0.0033 26.2 3.9 36 66-101 15-50 (140)
71 PF09723 Zn-ribbon_8: Zinc rib 20.2 46 0.001 22.7 0.6 30 181-212 5-34 (42)
No 1
>PLN03120 nucleic acid binding protein; Provisional
Probab=89.29 E-value=0.43 Score=44.48 Aligned_cols=52 Identities=15% Similarity=0.319 Sum_probs=44.4
Q ss_pred HHHHHHHhhhhhhhhhhhHHHHHHHHHHHHHHhhhhhhhhHhHHhhhhhhhh
Q 023461 66 DAKKTAERIDRQYSVSRRLNSAARTAAVRARELDREFAISVRWRSFRMDFSR 117 (282)
Q Consensus 66 EARktA~rlDr~YsVSrR~A~Aar~A~erArEIDrefgIrrR~R~fs~Df~R 117 (282)
.|......+|++|-+|.|++.-.-.+.|++++||++|+|.-+..++..=..+
T Consensus 140 ~a~a~v~~~d~k~gltek~~~g~~~v~~~~k~vDeky~vs~kt~sa~~~~~~ 191 (260)
T PLN03120 140 TASAKVASLDKKIGLSEKLSAGTAVVNEKVKEVDQKYQVSEKTKSALAAAEQ 191 (260)
T ss_pred HHHHHHHhhhhhcCcccccccchHHHHHHHHhhhhhhchhHHHHHHHHHHHH
Confidence 3455677899999999999988889999999999999999999886655443
No 2
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=81.35 E-value=0.84 Score=30.90 Aligned_cols=32 Identities=19% Similarity=0.039 Sum_probs=21.0
Q ss_pred hcccccccceeeeecceeccceEEEEeeecccccccc
Q 023461 182 MAFSVLTVGIYCLIGMDVLLNEWVLVRLVRGSLLVPR 218 (282)
Q Consensus 182 gaCP~ck~~~~~~ig~~~~~~q~v~~r~~rg~v~~pr 218 (282)
|.||+|+... |=-|---|+. +|..| |.|+.-.
T Consensus 1 m~Cp~Cg~~~---~~~D~~~g~~-vC~~C-G~Vl~e~ 32 (43)
T PF08271_consen 1 MKCPNCGSKE---IVFDPERGEL-VCPNC-GLVLEEN 32 (43)
T ss_dssp ESBTTTSSSE---EEEETTTTEE-EETTT--BBEE-T
T ss_pred CCCcCCcCCc---eEEcCCCCeE-ECCCC-CCEeecc
Confidence 5799999987 2223333666 89999 8877643
No 3
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=80.11 E-value=3.5 Score=36.38 Aligned_cols=31 Identities=19% Similarity=0.199 Sum_probs=15.5
Q ss_pred cchhHHHHhhhcchHHHHHHHHHhHHHHHhH
Q 023461 34 SDFDRFARRMTSGEAWRDAWRTANNGFEQLV 64 (282)
Q Consensus 34 ~d~D~~a~r~~sg~awR~AwRsAN~gfEq~~ 64 (282)
..||.|...+.+...=..-.-++.|..|++.
T Consensus 105 ~~~~~~l~~l~~~g~v~~~~~~~~DvT~~y~ 135 (262)
T PF14257_consen 105 DKFDSFLDELSELGKVTSRNISSEDVTEQYV 135 (262)
T ss_pred HHHHHHHHHHhccCceeeeeccccchHHHHH
Confidence 5677777776432221222234455555554
No 4
>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=71.42 E-value=1.4 Score=36.08 Aligned_cols=32 Identities=16% Similarity=0.181 Sum_probs=23.6
Q ss_pred HhhcccccccceeeeecceeccceEEEEeeecccccccc
Q 023461 180 IKMAFSVLTVGIYCLIGMDVLLNEWVLVRLVRGSLLVPR 218 (282)
Q Consensus 180 iEgaCP~ck~~~~~~ig~~~~~~q~v~~r~~rg~v~~pr 218 (282)
.|-.||.|+++||=|= -.-|+|--| |..|+|-
T Consensus 8 tKR~Cp~CG~kFYDLn------k~PivCP~C-G~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLN------KDPIVCPKC-GTEFPPE 39 (108)
T ss_pred CcccCCCCcchhccCC------CCCccCCCC-CCccCcc
Confidence 3668999999998652 356889988 4556654
No 5
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=68.66 E-value=2.7 Score=27.38 Aligned_cols=32 Identities=6% Similarity=-0.149 Sum_probs=21.8
Q ss_pred hcccccccceeeeecceecc--ceEEEEeeeccccc
Q 023461 182 MAFSVLTVGIYCLIGMDVLL--NEWVLVRLVRGSLL 215 (282)
Q Consensus 182 gaCP~ck~~~~~~ig~~~~~--~q~v~~r~~rg~v~ 215 (282)
-.||+|+..|+.- .+.+. +..|.|-.|..++.
T Consensus 3 ~~CP~C~~~~~v~--~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVV--DSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeC--HHHcCCCCCEEECCCCCCEEE
Confidence 3699999999643 22221 44789999987654
No 6
>PF11833 DUF3353: Protein of unknown function (DUF3353); InterPro: IPR021788 This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 205 to 258 amino acids in length.
Probab=67.71 E-value=20 Score=31.89 Aligned_cols=88 Identities=20% Similarity=0.214 Sum_probs=56.7
Q ss_pred HHHHhHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHHHHHhhhhhh--------hhHhHHhhhh--------hhhhcchhh
Q 023461 59 GFEQLVFDAKKTAERIDRQYSVSRRLNSAARTAAVRARELDREFA--------ISVRWRSFRM--------DFSRNWPRY 122 (282)
Q Consensus 59 gfEq~~fEARktA~rlDr~YsVSrR~A~Aar~A~erArEIDrefg--------IrrR~R~fs~--------Df~RnWP~Y 122 (282)
.||+.+ ++-+++-.+|.=-.+.-+..++|-|.- +=+.+. +..+.|..-. .-..+=|.|
T Consensus 5 SfeEIq----~Arn~ll~~y~gd~~~~~~IEaAYD~I--LM~rL~~Rq~Gki~v~~~ir~ad~~~~~~~~~~~~~~~p~w 78 (194)
T PF11833_consen 5 SFEEIQ----AARNRLLAQYAGDEKSREAIEAAYDAI--LMERLRQRQKGKIKVPERIRYADREEPKPPNPKPSNPSPPW 78 (194)
T ss_pred CHHHHH----HHHHHHHHHhcCCHHHHHHHHHHHHHH--HHHHHHHHHcCCCCccHHHHHhhhccccccCCCCCCccchH
Confidence 455444 555677778866666666666665532 112222 3344443322 334577889
Q ss_pred HHhhhHhhCCCCchHHHHHHHHHHHHHHHH
Q 023461 123 RKQLNDFLNTPLGRSFATIFFLWFALSGWL 152 (282)
Q Consensus 123 RRQL~dFl~TPlGks~~TiFF~WfalSGWl 152 (282)
-+++-..++||-+..+..=.+++.++++|.
T Consensus 79 l~~~~~~~~~P~~~~l~~~~~~f~~L~~~~ 108 (194)
T PF11833_consen 79 LQRLLPSFDTPSSQDLLIRAAAFGALGLWS 108 (194)
T ss_pred HHhcccceeCCCcchHHHHHHHHHHHHHHH
Confidence 999888899999998887778888888884
No 7
>TIGR03518 ABC_perm_GldF gliding motility-associated ABC transporter permease protein GldF. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldF is believed to be a ABC transporter permease protein (along with ATP-binding subunit, GldA and a sunstrate-binding subunit, GldG) and is linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldF abolish the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.
Probab=67.57 E-value=15 Score=32.30 Aligned_cols=35 Identities=29% Similarity=0.643 Sum_probs=28.8
Q ss_pred chhhHHhhhHhhCCCCchHHHHHHHHHHHHHHHHH
Q 023461 119 WPRYRKQLNDFLNTPLGRSFATIFFLWFALSGWLF 153 (282)
Q Consensus 119 WP~YRRQL~dFl~TPlGks~~TiFF~WfalSGWlF 153 (282)
++-+||++..+..||.+=.+..+|.+...+..|.+
T Consensus 2 ~~i~~kEl~~~f~sp~~yv~~~~~~~~~g~~~~~~ 36 (240)
T TIGR03518 2 KAIFKKEFNSFFSSPIGYLVIAVFLLANGLFLWVF 36 (240)
T ss_pred HHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHH
Confidence 57799999999999999988888877666655644
No 8
>PF09832 DUF2059: Uncharacterized protein conserved in bacteria (DUF2059); InterPro: IPR018637 This entry contains proteins that have no known function. ; PDB: 2X3O_B 3OAO_A.
Probab=67.44 E-value=1.7 Score=30.86 Aligned_cols=20 Identities=20% Similarity=0.376 Sum_probs=16.3
Q ss_pred HHhhhHhhCCCCchHHHHHH
Q 023461 123 RKQLNDFLNTPLGRSFATIF 142 (282)
Q Consensus 123 RRQL~dFl~TPlGks~~TiF 142 (282)
-+++.+|.+||+|+.++...
T Consensus 22 l~~i~~FY~Sp~Gqk~~~~~ 41 (64)
T PF09832_consen 22 LDAILAFYESPLGQKIVAKE 41 (64)
T ss_dssp HHHHHHHHHSHHHHHHHHHH
T ss_pred HHHHHHHHCCHHhHHHHHHh
Confidence 46788999999999887543
No 9
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.93 E-value=3.7 Score=33.52 Aligned_cols=37 Identities=16% Similarity=0.121 Sum_probs=25.4
Q ss_pred hcccccccceeeeecceeccceEEEEeeeccccccccchhh
Q 023461 182 MAFSVLTVGIYCLIGMDVLLNEWVLVRLVRGSLLVPRARLF 222 (282)
Q Consensus 182 gaCP~ck~~~~~~ig~~~~~~q~v~~r~~rg~v~~pr~~~~ 222 (282)
+-||+|.....-..-++ =|.=.|.+|||| |--|--|=
T Consensus 2 llCP~C~v~l~~~~rs~---vEiD~CPrCrGV-WLDrGELd 38 (88)
T COG3809 2 LLCPICGVELVMSVRSG---VEIDYCPRCRGV-WLDRGELD 38 (88)
T ss_pred cccCcCCceeeeeeecC---ceeeeCCccccE-eecchhHH
Confidence 35999998873333333 466689999995 76666553
No 10
>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=64.67 E-value=2.6 Score=36.31 Aligned_cols=32 Identities=13% Similarity=0.024 Sum_probs=24.0
Q ss_pred HhhcccccccceeeeecceeccceEEEEeeecccccccc
Q 023461 180 IKMAFSVLTVGIYCLIGMDVLLNEWVLVRLVRGSLLVPR 218 (282)
Q Consensus 180 iEgaCP~ck~~~~~~ig~~~~~~q~v~~r~~rg~v~~pr 218 (282)
.|-.||.|+++||=|- ..-|+|..|-.+ |.|-
T Consensus 8 tKr~Cp~cg~kFYDLn------k~p~vcP~cg~~-~~~~ 39 (129)
T TIGR02300 8 TKRICPNTGSKFYDLN------RRPAVSPYTGEQ-FPPE 39 (129)
T ss_pred ccccCCCcCccccccC------CCCccCCCcCCc-cCcc
Confidence 3668999999998653 356899999655 6554
No 11
>PF05957 DUF883: Bacterial protein of unknown function (DUF883); InterPro: IPR010279 This family consists of several bacterial proteins of unknown function that include the Escherichia coli genes for ElaB, YgaM and YqjD.
Probab=57.11 E-value=85 Score=23.95 Aligned_cols=28 Identities=25% Similarity=0.250 Sum_probs=15.7
Q ss_pred hhhHhhCCCCchHHHHHHHHHHHHHHHHH
Q 023461 125 QLNDFLNTPLGRSFATIFFLWFALSGWLF 153 (282)
Q Consensus 125 QL~dFl~TPlGks~~TiFF~WfalSGWlF 153 (282)
+.++|..--+.+++...+-+=| |.|+|+
T Consensus 64 ~~~~~V~e~P~~svgiAagvG~-llG~Ll 91 (94)
T PF05957_consen 64 QTEDYVRENPWQSVGIAAGVGF-LLGLLL 91 (94)
T ss_pred HHHHHHHHChHHHHHHHHHHHH-HHHHHH
Confidence 3444444455667666666555 556654
No 12
>PF04956 TrbC: TrbC/VIRB2 family; InterPro: IPR007039 Conjugal transfer protein, TrbC has been identified as a subunit of the pilus precursor in bacteria. The protein undergoes three processing steps before gaining its mature cyclic structure[]. This family also contains several VirB2 type IV secretion proteins. The virB2 gene encodes a putative type IV secretion system and is known to be a pathogenicity factor in Bartonella species [].
Probab=54.50 E-value=26 Score=26.47 Aligned_cols=35 Identities=20% Similarity=0.456 Sum_probs=29.7
Q ss_pred hcchhhHHhhhHhhCCCCchHHHHHHHHHHHHHHH
Q 023461 117 RNWPRYRKQLNDFLNTPLGRSFATIFFLWFALSGW 151 (282)
Q Consensus 117 RnWP~YRRQL~dFl~TPlGks~~TiFF~WfalSGW 151 (282)
-+|=..=.++.+++.+|+|+.++++.+++.++..+
T Consensus 36 ~~~~~~l~~i~~~l~gp~~~~i~~i~ii~~g~~~~ 70 (99)
T PF04956_consen 36 DPWTSFLCKIIDWLTGPIGKAIAIIAIIVAGIMMM 70 (99)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55666677889999999999999999999988743
No 13
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=44.44 E-value=14 Score=27.30 Aligned_cols=29 Identities=14% Similarity=0.043 Sum_probs=21.9
Q ss_pred hcccccccceeeeecceeccceEEEEeeeccc
Q 023461 182 MAFSVLTVGIYCLIGMDVLLNEWVLVRLVRGS 213 (282)
Q Consensus 182 gaCP~ck~~~~~~ig~~~~~~q~v~~r~~rg~ 213 (282)
..||.|+..+ -+-...+ |+.|.|-.|.-.
T Consensus 3 ~~CP~CG~~i--ev~~~~~-GeiV~Cp~CGae 31 (54)
T TIGR01206 3 FECPDCGAEI--ELENPEL-GELVICDECGAE 31 (54)
T ss_pred cCCCCCCCEE--ecCCCcc-CCEEeCCCCCCE
Confidence 4899999988 3444444 999999988654
No 14
>PLN03121 nucleic acid binding protein; Provisional
Probab=43.73 E-value=29 Score=32.51 Aligned_cols=46 Identities=11% Similarity=0.211 Sum_probs=34.1
Q ss_pred HHHHHhhhhhhhhhhhHHHHHHHHHHHHHHhhhhhhhhHhHHhhhhhhhh
Q 023461 68 KKTAERIDRQYSVSRRLNSAARTAAVRARELDREFAISVRWRSFRMDFSR 117 (282)
Q Consensus 68 RktA~rlDr~YsVSrR~A~Aar~A~erArEIDrefgIrrR~R~fs~Df~R 117 (282)
.....+||++.-+|.|++.-. +..+++|++|.+.-+-+++....-+
T Consensus 155 ~a~v~~~d~~iglt~k~~~g~----~~vk~vDeky~vs~~tksA~~aa~~ 200 (243)
T PLN03121 155 AAKVAELSKRIGLTDKIFAGM----EAVRSVDEKYHVSEFTKSAATATGR 200 (243)
T ss_pred hhhhhhhhhhccchhhhhhhH----HHHHhhhhhhhhHHHHHHHHHHHHH
Confidence 344456777777777777655 6679999999999999887766554
No 15
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=42.68 E-value=15 Score=24.69 Aligned_cols=29 Identities=7% Similarity=-0.141 Sum_probs=18.2
Q ss_pred cccccccceeeeecceecc--ceEEEEeeeccc
Q 023461 183 AFSVLTVGIYCLIGMDVLL--NEWVLVRLVRGS 213 (282)
Q Consensus 183 aCP~ck~~~~~~ig~~~~~--~q~v~~r~~rg~ 213 (282)
.||+|+.+|- |-.+.+. |-.|.|..|..+
T Consensus 4 ~Cp~C~~~y~--i~d~~ip~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 4 TCPNCQAKYE--IDDEKIPPKGRKVRCSKCGHV 34 (36)
T ss_pred ECCCCCCEEe--CCHHHCCCCCcEEECCCCCCE
Confidence 6999999993 2222111 456778777643
No 16
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=40.20 E-value=13 Score=25.43 Aligned_cols=36 Identities=8% Similarity=-0.086 Sum_probs=22.8
Q ss_pred HhhcccccccceeeeecceeccceEEEEeeeccc-cccccch
Q 023461 180 IKMAFSVLTVGIYCLIGMDVLLNEWVLVRLVRGS-LLVPRAR 220 (282)
Q Consensus 180 iEgaCP~ck~~~~~~ig~~~~~~q~v~~r~~rg~-v~~pr~~ 220 (282)
.+-.||+|+..+ .+... .+.+.|..|.+- +...|..
T Consensus 2 ~~y~C~~CG~~~--~~~~~---~~~~~Cp~CG~~~~~~~~~~ 38 (46)
T PRK00398 2 AEYKCARCGREV--ELDEY---GTGVRCPYCGYRILFKERPP 38 (46)
T ss_pred CEEECCCCCCEE--EECCC---CCceECCCCCCeEEEccCCC
Confidence 356799999988 23333 337899999773 3344433
No 17
>PRK15035 cytochrome bd-II oxidase subunit 1; Provisional
Probab=39.67 E-value=62 Score=33.15 Aligned_cols=53 Identities=28% Similarity=0.640 Sum_probs=41.4
Q ss_pred hhhhcchhhHHhhhHhhCCCCchHHHHHHHHHHHHHH-HHH-------HHHHHHHHHHHhH
Q 023461 114 DFSRNWPRYRKQLNDFLNTPLGRSFATIFFLWFALSG-WLF-------RILILATWVLPIA 166 (282)
Q Consensus 114 Df~RnWP~YRRQL~dFl~TPlGks~~TiFF~WfalSG-WlF-------Ri~i~~tWVLP~A 166 (282)
-|..|||.|-+-.-|..+.|++=-..+.||+.-..-| |+| ++=++++|...+-
T Consensus 76 qFG~nWs~ys~~vGdvfG~pLa~E~l~AFFlEstFlGl~lFGw~rl~~~~H~~~~~lVaiG 136 (514)
T PRK15035 76 QFGTNWSFYSNYVGDIFGAPLAMEALMAFFLESTFVGLFFFGWQRLNKYQHLLVTWLVAFG 136 (514)
T ss_pred hhhcchHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhhhhcchHHHHHHHHHHHHH
Confidence 4668999999999999999999999999998765543 344 3456677776643
No 18
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=39.58 E-value=13 Score=23.23 Aligned_cols=9 Identities=0% Similarity=-0.060 Sum_probs=8.4
Q ss_pred cccccccce
Q 023461 183 AFSVLTVGI 191 (282)
Q Consensus 183 aCP~ck~~~ 191 (282)
.||.|++.|
T Consensus 4 ~C~~CgR~F 12 (25)
T PF13913_consen 4 PCPICGRKF 12 (25)
T ss_pred cCCCCCCEE
Confidence 599999999
No 19
>PF08507 COPI_assoc: COPI associated protein; InterPro: IPR013714 Proteins in this family co-localise with COPI vesicle coat proteins []. In yeast it is a Golgi membrane protein involved in vesicular trafficking, interacting with TVP18 [].
Probab=37.99 E-value=88 Score=25.48 Aligned_cols=28 Identities=25% Similarity=0.360 Sum_probs=23.6
Q ss_pred HHhhhHhhCCCCchHHHHHHHHHHHHHH
Q 023461 123 RKQLNDFLNTPLGRSFATIFFLWFALSG 150 (282)
Q Consensus 123 RRQL~dFl~TPlGks~~TiFF~WfalSG 150 (282)
=++.-.|+.++.||.+.-+|.--++++.
T Consensus 57 i~~~~~FL~~~~GRGlfyif~G~l~~~~ 84 (136)
T PF08507_consen 57 IRKYFGFLYSYIGRGLFYIFLGTLCLGQ 84 (136)
T ss_pred HHHhHhHHHhHHHHHHHHHHHHHHHHhh
Confidence 5566789999999999988888887774
No 20
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=37.83 E-value=13 Score=27.21 Aligned_cols=12 Identities=0% Similarity=-0.482 Sum_probs=6.1
Q ss_pred Hhhcccccccce
Q 023461 180 IKMAFSVLTVGI 191 (282)
Q Consensus 180 iEgaCP~ck~~~ 191 (282)
.+|.||+|++.|
T Consensus 36 ~~g~CPgCr~~Y 47 (48)
T PF14570_consen 36 EGGRCPGCREPY 47 (48)
T ss_dssp S-SB-TTT--B-
T ss_pred cCCCCCCCCCCC
Confidence 479999999987
No 21
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=36.82 E-value=14 Score=25.92 Aligned_cols=13 Identities=8% Similarity=-0.113 Sum_probs=7.2
Q ss_pred HHhhcccccccce
Q 023461 179 VIKMAFSVLTVGI 191 (282)
Q Consensus 179 viEgaCP~ck~~~ 191 (282)
-.++.||.|++.|
T Consensus 18 ~~~~~CPlC~r~l 30 (54)
T PF04423_consen 18 EAKGCCPLCGRPL 30 (54)
T ss_dssp T-SEE-TTT--EE
T ss_pred cCCCcCCCCCCCC
Confidence 3556999999987
No 22
>COG2991 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.85 E-value=28 Score=28.00 Aligned_cols=22 Identities=23% Similarity=0.172 Sum_probs=18.7
Q ss_pred hHHHHHHHHHHhHHHHhhcccc
Q 023461 165 IAAPLLIGTVANNFVIKMAFSV 186 (282)
Q Consensus 165 ~A~PlLIGtian~~viEgaCP~ 186 (282)
+++-|.||+|.+|=.|+|.|-.
T Consensus 14 vi~gMsiG~I~krk~I~GSCGG 35 (77)
T COG2991 14 VIAGMSIGYIFKRKSIKGSCGG 35 (77)
T ss_pred HHHHHhHhhheecccccccccc
Confidence 4456899999999999999964
No 23
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=35.31 E-value=17 Score=24.62 Aligned_cols=14 Identities=0% Similarity=-0.142 Sum_probs=10.0
Q ss_pred hcccccccceeeeecce
Q 023461 182 MAFSVLTVGIYCLIGMD 198 (282)
Q Consensus 182 gaCP~ck~~~~~~ig~~ 198 (282)
-.||+|++.+ .++|
T Consensus 5 ~~C~nC~R~v---~a~R 18 (33)
T PF08209_consen 5 VECPNCGRPV---AASR 18 (33)
T ss_dssp EE-TTTSSEE---EGGG
T ss_pred EECCCCcCCc---chhh
Confidence 4699999988 5555
No 24
>PRK00420 hypothetical protein; Validated
Probab=34.31 E-value=34 Score=28.57 Aligned_cols=31 Identities=10% Similarity=0.065 Sum_probs=22.0
Q ss_pred HHhhcccccccceeeeecceeccceEEEEeeeccccc
Q 023461 179 VIKMAFSVLTVGIYCLIGMDVLLNEWVLVRLVRGSLL 215 (282)
Q Consensus 179 viEgaCP~ck~~~~~~ig~~~~~~q~v~~r~~rg~v~ 215 (282)
+....||.|+..++.+-.+ -+.|..|-.++-
T Consensus 21 ml~~~CP~Cg~pLf~lk~g------~~~Cp~Cg~~~~ 51 (112)
T PRK00420 21 MLSKHCPVCGLPLFELKDG------EVVCPVHGKVYI 51 (112)
T ss_pred HccCCCCCCCCcceecCCC------ceECCCCCCeee
Confidence 3668999999998555333 478888866543
No 25
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=33.35 E-value=18 Score=24.17 Aligned_cols=29 Identities=7% Similarity=-0.196 Sum_probs=19.4
Q ss_pred cccccccceeeeeccee--ccceEEEEeeeccc
Q 023461 183 AFSVLTVGIYCLIGMDV--LLNEWVLVRLVRGS 213 (282)
Q Consensus 183 aCP~ck~~~~~~ig~~~--~~~q~v~~r~~rg~ 213 (282)
.||+|+..|- |..+- --|..|-|-.|..+
T Consensus 4 ~CP~C~~~f~--v~~~~l~~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 4 TCPNCQTRFR--VPDDKLPAGGRKVRCPKCGHV 34 (37)
T ss_pred ECCCCCceEE--cCHHHcccCCcEEECCCCCcE
Confidence 6999999993 32221 12568888888754
No 26
>PRK10697 DNA-binding transcriptional activator PspC; Provisional
Probab=33.22 E-value=47 Score=27.94 Aligned_cols=40 Identities=15% Similarity=0.272 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhHHHHhhc
Q 023461 144 LWFALSGWLFRILILATWVLPIAAPLLIGTVANNFVIKMA 183 (282)
Q Consensus 144 ~WfalSGWlFRi~i~~tWVLP~A~PlLIGtian~~viEga 183 (282)
-.|.+.-|+.|+++++.-++++.+|.+|.||.--++++-.
T Consensus 27 ~y~gi~~~~VRl~~vl~~~~~~~~~~~~~Yi~l~~~lp~~ 66 (118)
T PRK10697 27 HYFDVPVKLVRIIVVLSIFFGLFVFTLVAYIILSFALDPM 66 (118)
T ss_pred HHHCCCHHHHHHHHHHHHHHhhchHHHHHHHHHHHhccCC
Confidence 4555667888888777666666678888888888887654
No 27
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=32.25 E-value=46 Score=26.24 Aligned_cols=40 Identities=28% Similarity=0.504 Sum_probs=30.0
Q ss_pred HHHHHhhhhhhhhHhHHhhhhhhhhcchhhHHhhhHhhCCCC
Q 023461 93 VRARELDREFAISVRWRSFRMDFSRNWPRYRKQLNDFLNTPL 134 (282)
Q Consensus 93 erArEIDrefgIrrR~R~fs~Df~RnWP~YRRQL~dFl~TPl 134 (282)
-...+|.+++|+.. .+++.=+.+.||.+.+-+.++++++.
T Consensus 16 ~sL~~lsr~~Gl~~--~tl~nal~r~~pk~E~~IA~aLgv~P 55 (78)
T PF13693_consen 16 TSLAALSREAGLSS--STLRNALRRPWPKGERIIADALGVPP 55 (78)
T ss_dssp --HHHHHHHHSS-H--HHHHHTTTSS-HHHHHHHHHHTTS-H
T ss_pred CCHHHHHHHcCCCH--HHHHHHHcCCChHHHHHHHHHHCcCH
Confidence 34567888899987 56777789999999999999999875
No 28
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=31.37 E-value=1.7e+02 Score=25.87 Aligned_cols=41 Identities=10% Similarity=-0.010 Sum_probs=17.0
Q ss_pred CCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 023461 132 TPLGRSFATIFFLWFALSGWLFRILILATWVLPIAAPLLIG 172 (282)
Q Consensus 132 TPlGks~~TiFF~WfalSGWlFRi~i~~tWVLP~A~PlLIG 172 (282)
+|++..+...+-.+.....|+.-+++++.-++|+++|.+++
T Consensus 216 ~~~~~al~~~~~~~~~~~~~lv~~l~~l~p~~~~~~~~~~~ 256 (262)
T PF14257_consen 216 SRFRDALKNGWNALVSFLSGLVVFLVGLLPWLPLILIIGLL 256 (262)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444333333333344444444444444444444443
No 29
>PF12648 TcpE: TcpE family
Probab=31.01 E-value=65 Score=25.35 Aligned_cols=64 Identities=17% Similarity=0.273 Sum_probs=34.7
Q ss_pred cchhhHHhhhHhhCCCCchHHHHH--HHHHHHHHHHHHHHHHHH--------HHHHHhH-HHHHHHHHHhHHHHhh
Q 023461 118 NWPRYRKQLNDFLNTPLGRSFATI--FFLWFALSGWLFRILILA--------TWVLPIA-APLLIGTVANNFVIKM 182 (282)
Q Consensus 118 nWP~YRRQL~dFl~TPlGks~~Ti--FF~WfalSGWlFRi~i~~--------tWVLP~A-~PlLIGtian~~viEg 182 (282)
|-|.+-.+++| ..-|.+-++.++ |.+++...-.++.++-.. .|++-.+ .|..++.+..+.-.+|
T Consensus 7 ~~p~~I~~i~~-~~Lp~~i~~~~l~~fvv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~iP~~l~~~~~~~k~DG 81 (108)
T PF12648_consen 7 KQPYWIYEIKD-FRLPFPITLSQLGYFVVSFIVFYLLLRLLPPVFWIFPFINGWLLLYFVIPYGLAWFLSKKKPDG 81 (108)
T ss_pred CCceEEEEEcc-ccCccceeHHHHHHHHHHHHHHHHHHHHhHHhhhcCcccchHHHHHHhHHHHHHHHHhhcCcCC
Confidence 55677777888 777877544443 333332222344444323 3433333 6677777766666655
No 30
>TIGR02978 phageshock_pspC phage shock protein C. All members of this protein family are the phage shock protein PspC. These proteins contain a PspC domain, as do other members of the larger family of proteins described by Pfam model pfam04024. The phage shock regulon is restricted to the Proteobacteria and somewhat sparsely distributed there. It is expressed, under positive control of a sigma-54-dependent transcription factor, PspF, which binds and is modulated by PspA. Stresses that induce the psp regulon include phage secretin overexpression, ethanol, heat shock, and protein export defects.
Probab=30.71 E-value=75 Score=26.58 Aligned_cols=39 Identities=21% Similarity=0.437 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhHHHHhhc
Q 023461 145 WFALSGWLFRILILATWVLPIAAPLLIGTVANNFVIKMA 183 (282)
Q Consensus 145 WfalSGWlFRi~i~~tWVLP~A~PlLIGtian~~viEga 183 (282)
.|.++-|+.|+++++.-++....|.+|.|+.--++++-.
T Consensus 23 y~gi~~~~VRl~~vl~~~~~~~~~~ll~Y~i~w~~lp~~ 61 (121)
T TIGR02978 23 YFGVEVWLVRILVVSALLFGGGFFVLVAYIALWLLLDKK 61 (121)
T ss_pred HHCcCHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhcC
Confidence 455677888987777655555556677788888888765
No 31
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=30.67 E-value=16 Score=30.23 Aligned_cols=33 Identities=9% Similarity=-0.049 Sum_probs=19.8
Q ss_pred hcccccccceeeeecceec-cceEEEEeeecccc
Q 023461 182 MAFSVLTVGIYCLIGMDVL-LNEWVLVRLVRGSL 214 (282)
Q Consensus 182 gaCP~ck~~~~~~ig~~~~-~~q~v~~r~~rg~v 214 (282)
--||+|+.+|.-+=-+... -..-.+|..|.+.+
T Consensus 100 Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 100 YKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEEL 133 (147)
T ss_pred EECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEE
Confidence 3599999999542111100 01128999998765
No 32
>cd04511 Nudix_Hydrolase_4 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, U=I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specifici
Probab=30.28 E-value=49 Score=25.54 Aligned_cols=25 Identities=12% Similarity=-0.023 Sum_probs=16.9
Q ss_pred cccccccee-----e---eecceeccceEEEEeeec
Q 023461 184 FSVLTVGIY-----C---LIGMDVLLNEWVLVRLVR 211 (282)
Q Consensus 184 CP~ck~~~~-----~---~ig~~~~~~q~v~~r~~r 211 (282)
||+|+..+| + +|-.+ ++++++++-+
T Consensus 1 c~~~~~~~~~~~~~~v~~ii~~~---~~vLL~kr~~ 33 (130)
T cd04511 1 CPDCGYIHYQNPKIIVGCVPEWE---GKVLLCRRAI 33 (130)
T ss_pred CCCCccccCCCCcEEEEEEEecC---CEEEEEEecC
Confidence 999998876 2 22333 7788888643
No 33
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=30.24 E-value=34 Score=26.24 Aligned_cols=26 Identities=8% Similarity=0.054 Sum_probs=17.2
Q ss_pred hhcccccccceeeeecceeccceEEEEeeec
Q 023461 181 KMAFSVLTVGIYCLIGMDVLLNEWVLVRLVR 211 (282)
Q Consensus 181 EgaCP~ck~~~~~~ig~~~~~~q~v~~r~~r 211 (282)
--+||.||-..+ .-.. +|..+|+.|+
T Consensus 8 iLaCP~~kg~L~--~~~~---~~~L~c~~~~ 33 (60)
T COG2835 8 ILACPVCKGPLV--YDEE---KQELICPRCK 33 (60)
T ss_pred eeeccCcCCcce--Eecc---CCEEEecccC
Confidence 358999988752 2222 5678888776
No 34
>PRK15097 cytochrome d terminal oxidase subunit 1; Provisional
Probab=29.78 E-value=1.1e+02 Score=31.47 Aligned_cols=53 Identities=26% Similarity=0.599 Sum_probs=40.6
Q ss_pred hhhhcchhhHHhhhHhhCCCCchHHHHHHHHHHHHHH-HHH-------HHHHHHHHHHHhH
Q 023461 114 DFSRNWPRYRKQLNDFLNTPLGRSFATIFFLWFALSG-WLF-------RILILATWVLPIA 166 (282)
Q Consensus 114 Df~RnWP~YRRQL~dFl~TPlGks~~TiFF~WfalSG-WlF-------Ri~i~~tWVLP~A 166 (282)
-|..|||.|-+-.-|....|++=...+.||+.-..-| |+| ++=++++|...+-
T Consensus 76 qFG~nWs~ys~~vGdifG~pLa~E~l~AFFlEstFlGl~~FGW~rl~~~~H~~~~~lVaiG 136 (522)
T PRK15097 76 QFGTNWSYYSHYVGDIFGAPLAIEGLMAFFLESTFVGLFFFGWDRLGKVQHMCVTWLVALG 136 (522)
T ss_pred ecccccHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhhhhcchHHHHHHHHHHHHH
Confidence 4678999999999999999999999999998765443 344 3356667766543
No 35
>PRK11827 hypothetical protein; Provisional
Probab=29.53 E-value=33 Score=26.00 Aligned_cols=29 Identities=10% Similarity=0.157 Sum_probs=19.2
Q ss_pred HHHhhcccccccceeeeecceeccceEEEEeeec
Q 023461 178 FVIKMAFSVLTVGIYCLIGMDVLLNEWVLVRLVR 211 (282)
Q Consensus 178 ~viEgaCP~ck~~~~~~ig~~~~~~q~v~~r~~r 211 (282)
+..--+||.||.....- .. .+..+|..|+
T Consensus 5 LLeILaCP~ckg~L~~~--~~---~~~Lic~~~~ 33 (60)
T PRK11827 5 LLEIIACPVCNGKLWYN--QE---KQELICKLDN 33 (60)
T ss_pred HHhheECCCCCCcCeEc--CC---CCeEECCccC
Confidence 33445899999887321 12 4677898884
No 36
>PF05957 DUF883: Bacterial protein of unknown function (DUF883); InterPro: IPR010279 This family consists of several bacterial proteins of unknown function that include the Escherichia coli genes for ElaB, YgaM and YqjD.
Probab=28.90 E-value=2.6e+02 Score=21.27 Aligned_cols=7 Identities=43% Similarity=0.866 Sum_probs=2.8
Q ss_pred chhHHHH
Q 023461 35 DFDRFAR 41 (282)
Q Consensus 35 d~D~~a~ 41 (282)
|.+.+++
T Consensus 13 d~~~l~~ 19 (94)
T PF05957_consen 13 DLEDLAR 19 (94)
T ss_pred HHHHHHH
Confidence 3444443
No 37
>PF14353 CpXC: CpXC protein
Probab=28.76 E-value=22 Score=28.29 Aligned_cols=13 Identities=0% Similarity=-0.151 Sum_probs=8.7
Q ss_pred hhcccccccceee
Q 023461 181 KMAFSVLTVGIYC 193 (282)
Q Consensus 181 EgaCP~ck~~~~~ 193 (282)
|.+||+|+..|..
T Consensus 1 ~itCP~C~~~~~~ 13 (128)
T PF14353_consen 1 EITCPHCGHEFEF 13 (128)
T ss_pred CcCCCCCCCeeEE
Confidence 3578888877643
No 38
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=28.75 E-value=23 Score=24.97 Aligned_cols=11 Identities=9% Similarity=-0.130 Sum_probs=7.6
Q ss_pred hhcccccccce
Q 023461 181 KMAFSVLTVGI 191 (282)
Q Consensus 181 EgaCP~ck~~~ 191 (282)
++.||.|+++|
T Consensus 2 ~~~CprC~kg~ 12 (36)
T PF14787_consen 2 PGLCPRCGKGF 12 (36)
T ss_dssp --C-TTTSSSC
T ss_pred CccCcccCCCc
Confidence 47899999998
No 39
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=28.49 E-value=19 Score=26.90 Aligned_cols=13 Identities=15% Similarity=-0.118 Sum_probs=8.2
Q ss_pred HHhhcccccccce
Q 023461 179 VIKMAFSVLTVGI 191 (282)
Q Consensus 179 viEgaCP~ck~~~ 191 (282)
.|.|.||.|+..+
T Consensus 53 ~~~G~CP~C~~~i 65 (70)
T PF11793_consen 53 PIFGECPYCSSPI 65 (70)
T ss_dssp --EEE-TTT-SEE
T ss_pred ccccCCcCCCCee
Confidence 6789999999887
No 40
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.96 E-value=39 Score=36.42 Aligned_cols=46 Identities=15% Similarity=0.070 Sum_probs=37.7
Q ss_pred HHHHhHHHHhhcccccccceeeeecceeccceEEEEeeecccccccc
Q 023461 172 GTVANNFVIKMAFSVLTVGIYCLIGMDVLLNEWVLVRLVRGSLLVPR 218 (282)
Q Consensus 172 Gtian~~viEgaCP~ck~~~~~~ig~~~~~~q~v~~r~~rg~v~~pr 218 (282)
++|+-|.- +|+||+|+=.=|..+.|..+..-.+.|-.|.|.-..|-
T Consensus 728 ~~FSfN~~-~G~C~~C~G~G~~~~~~~f~~~~~~~C~~C~G~R~~~e 773 (924)
T TIGR00630 728 GRFSFNVK-GGRCEACQGDGVIKIEMHFLPDVYVPCEVCKGKRYNRE 773 (924)
T ss_pred hhcCCCCC-CCCCCCCccceEEEEEccCCCCcccCCCCcCCceeChH
Confidence 44544433 79999999887788899988888999999999988875
No 41
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=27.32 E-value=29 Score=22.30 Aligned_cols=30 Identities=7% Similarity=-0.083 Sum_probs=22.7
Q ss_pred hhcccccccceeeeecceeccceEEEEeeecc
Q 023461 181 KMAFSVLTVGIYCLIGMDVLLNEWVLVRLVRG 212 (282)
Q Consensus 181 EgaCP~ck~~~~~~ig~~~~~~q~v~~r~~rg 212 (282)
+-.||.|+..|.-+.++.. ++.+.|-.|.+
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~--~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISD--DPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEecCC--CCCCCCCCCCC
Confidence 4479999999976666543 67888888876
No 42
>PRK06996 hypothetical protein; Provisional
Probab=27.08 E-value=4.6e+02 Score=24.05 Aligned_cols=75 Identities=16% Similarity=0.151 Sum_probs=43.9
Q ss_pred HHHhHHHHHhHHHHHHHHH------hhhhhhhhhhhHHHHHHHHHHHHHHhhhhhh----hhHhHHhhhhhhhhcchhhH
Q 023461 54 RTANNGFEQLVFDAKKTAE------RIDRQYSVSRRLNSAARTAAVRARELDREFA----ISVRWRSFRMDFSRNWPRYR 123 (282)
Q Consensus 54 RsAN~gfEq~~fEARktA~------rlDr~YsVSrR~A~Aar~A~erArEIDrefg----IrrR~R~fs~Df~RnWP~YR 123 (282)
+++|.|+|++..=|.+.+. -+| +|.-.|+. .++......+.+-+-|. ..+..|.+.+...-+.|..|
T Consensus 309 QG~n~ai~Da~~La~~L~~~~~~~~~L~-~Y~~~R~~--~~~~~~~~s~~l~~~~~~~~~~~~~~R~~~l~~~~~~~~~k 385 (398)
T PRK06996 309 QGLNLGLRDAHTLADALSDHGATPLALA-TFAARRAL--DRRVTIGATDLLPRLFTVDSRPLAHLRGAALTALEFVPPLK 385 (398)
T ss_pred hhHHHHHHHHHHHHHHHHhcCCcHHHHH-HHHHHHHH--HHHHHHHHHHHHHHHHcCCchHHHHHHhHHHHHHhhCHHHH
Confidence 4677777777655554432 122 45544432 12333333344444444 56778888888888899988
Q ss_pred HhhhHhhC
Q 023461 124 KQLNDFLN 131 (282)
Q Consensus 124 RQL~dFl~ 131 (282)
+.+-..+-
T Consensus 386 ~~~~~~~~ 393 (398)
T PRK06996 386 HALARQMM 393 (398)
T ss_pred HHHHHHHc
Confidence 88776543
No 43
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=26.56 E-value=57 Score=26.96 Aligned_cols=47 Identities=19% Similarity=0.238 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHhhhhhhhhHhHHhhhhhhhhcchhhHHhhhHhhCCCCc
Q 023461 87 AARTAAVRARELDREFAISVRWRSFRMDFSRNWPRYRKQLNDFLNTPLG 135 (282)
Q Consensus 87 Aar~A~erArEIDrefgIrrR~R~fs~Df~RnWP~YRRQL~dFl~TPlG 135 (282)
|-+..+-..++|.++.|+.. .+...=+.|.||++-|-+.++++++.-
T Consensus 16 aL~KrG~sLa~lsr~~Gls~--~TL~nAL~rp~PKgEriIA~aLGv~P~ 62 (92)
T PRK10344 16 GLRKKGTSMAAESRRNGLSS--STLANALSRPWPKGEMIIAKALGTDPW 62 (92)
T ss_pred HHHHcCCcHHHHHHHcCCCh--HHHHHHHcCCCchHHHHHHHHHCcCHH
Confidence 33444455678899999977 677788999999999999999998753
No 44
>PRK02935 hypothetical protein; Provisional
Probab=26.51 E-value=69 Score=27.27 Aligned_cols=41 Identities=12% Similarity=0.043 Sum_probs=29.0
Q ss_pred HHHHHHHHHHhHHHHhhcccccccceeeeecceeccceEEEEeeecccc
Q 023461 166 AAPLLIGTVANNFVIKMAFSVLTVGIYCLIGMDVLLNEWVLVRLVRGSL 214 (282)
Q Consensus 166 A~PlLIGtian~~viEgaCP~ck~~~~~~ig~~~~~~q~v~~r~~rg~v 214 (282)
+.=+-||.++-+++. -.||+|.+.- -.||.+=.|-.|.--+
T Consensus 56 vvYFwiGmlStkavq-V~CP~C~K~T-------KmLGrvD~CM~C~~PL 96 (110)
T PRK02935 56 VVYFWIGMLSTKAVQ-VICPSCEKPT-------KMLGRVDACMHCNQPL 96 (110)
T ss_pred HHHHHHhhhccccee-eECCCCCchh-------hhccceeecCcCCCcC
Confidence 344568888877654 4899999876 2346777888887543
No 45
>PRK13454 F0F1 ATP synthase subunit B'; Provisional
Probab=26.46 E-value=1.2e+02 Score=26.11 Aligned_cols=23 Identities=26% Similarity=0.387 Sum_probs=18.0
Q ss_pred HHHHHHHHH-HhHHHHHHHHHHhH
Q 023461 155 ILILATWVL-PIAAPLLIGTVANN 177 (282)
Q Consensus 155 i~i~~tWVL-P~A~PlLIGtian~ 177 (282)
.|+++.|+| -|+-|++.+.+.+|
T Consensus 40 ~F~iL~~ll~k~l~~PI~~~l~~R 63 (181)
T PRK13454 40 TLVAIYFVLTRVALPRIGAVLAER 63 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466777776 77889999999876
No 46
>KOG3966 consensus p53-mediated apoptosis protein EI24/PIG8 [Signal transduction mechanisms; Defense mechanisms]
Probab=26.41 E-value=3.3e+02 Score=27.11 Aligned_cols=52 Identities=15% Similarity=0.068 Sum_probs=29.6
Q ss_pred HHhHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHHHHHhhhhhhhhHhHHhhhh
Q 023461 61 EQLVFDAKKTAERIDRQYSVSRRLNSAARTAAVRARELDREFAISVRWRSFRM 113 (282)
Q Consensus 61 Eq~~fEARktA~rlDr~YsVSrR~A~Aar~A~erArEIDrefgIrrR~R~fs~ 113 (282)
|+...+.+..++..-|.+-=|-+...+++.-.|.|.+...|= =+|+.|+..+
T Consensus 18 qe~~~~~~~~~~D~arg~~ds~~gi~~v~iree~akq~~ee~-~~r~~~~vL~ 69 (360)
T KOG3966|consen 18 QEHMVKFQIIARDFARGFIDSFKGITFVRIREEEAKQVKEEP-PKRVERTVLM 69 (360)
T ss_pred HHHHHHHHHHHHHHhhcCCccccchhhhhhhHHHHHHhhhcC-CchHHHHHHh
Confidence 455555666666666666556666666666666666655442 2444444443
No 47
>PLN03120 nucleic acid binding protein; Provisional
Probab=26.32 E-value=75 Score=29.98 Aligned_cols=30 Identities=23% Similarity=0.421 Sum_probs=23.9
Q ss_pred HHHHHHhhhhhhhhhhhHHHHHHHHHHHHH
Q 023461 67 AKKTAERIDRQYSVSRRLNSAARTAAVRAR 96 (282)
Q Consensus 67 ARktA~rlDr~YsVSrR~A~Aar~A~erAr 96 (282)
++..+..+|.+|.||.|...|.-.|...+-
T Consensus 165 v~~~~k~vDeky~vs~kt~sa~~~~~~~~~ 194 (260)
T PLN03120 165 VNEKVKEVDQKYQVSEKTKSALAAAEQKVS 194 (260)
T ss_pred HHHHHHhhhhhhchhHHHHHHHHHHHHHHH
Confidence 346788999999999999888877766553
No 48
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=26.07 E-value=55 Score=27.94 Aligned_cols=53 Identities=17% Similarity=0.159 Sum_probs=34.6
Q ss_pred HHHHHHHHhHHHHhhcccccccceeeeecceeccceEEEEeeeccccccccchhhHHHHHHhHhcCCCCchhHHh
Q 023461 168 PLLIGTVANNFVIKMAFSVLTVGIYCLIGMDVLLNEWVLVRLVRGSLLVPRARLFVVQAVETLCGNQKGTSFQEM 242 (282)
Q Consensus 168 PlLIGtian~~viEgaCP~ck~~~~~~ig~~~~~~q~v~~r~~rg~v~~pr~~~~~~~~~~~~~~~~~~~~~~~~ 242 (282)
=+.||..+-+++ --.||+|.+.. . .||++=.|--|+--+- |=-++.|..|.|-
T Consensus 57 YfwIGmlStkav-~V~CP~C~K~T--K-----mLGr~D~CM~C~~pLT--------------Ld~~legkef~~~ 109 (114)
T PF11023_consen 57 YFWIGMLSTKAV-QVECPNCGKQT--K-----MLGRVDACMHCKEPLT--------------LDPSLEGKEFDEK 109 (114)
T ss_pred HHHhhhhcccce-eeECCCCCChH--h-----hhchhhccCcCCCcCc--------------cCchhhcchhhHh
Confidence 345777776653 34599999987 2 3355568999986553 3345566667663
No 49
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=25.81 E-value=47 Score=30.14 Aligned_cols=56 Identities=14% Similarity=0.113 Sum_probs=21.7
Q ss_pred HHhhccccccccee--eeecceeccc-eEEEEeeeccccccccchhhHHHHHHhHhcCCCCchhHHh
Q 023461 179 VIKMAFSVLTVGIY--CLIGMDVLLN-EWVLVRLVRGSLLVPRARLFVVQAVETLCGNQKGTSFQEM 242 (282)
Q Consensus 179 viEgaCP~ck~~~~--~~ig~~~~~~-q~v~~r~~rg~v~~pr~~~~~~~~~~~~~~~~~~~~~~~~ 242 (282)
--+|.||.|+..-. -+.|..- -| -...|-.|...-=.+|-. =..|||.+..++...
T Consensus 170 w~~g~CPvCGs~P~~s~l~~~~~-~G~R~L~Cs~C~t~W~~~R~~-------Cp~Cg~~~~~~l~~~ 228 (290)
T PF04216_consen 170 WQRGYCPVCGSPPVLSVLRGGER-EGKRYLHCSLCGTEWRFVRIK-------CPYCGNTDHEKLEYF 228 (290)
T ss_dssp TT-SS-TTT---EEEEEEE-------EEEEEETTT--EEE--TTS--------TTT---SS-EEE--
T ss_pred ccCCcCCCCCCcCceEEEecCCC-CccEEEEcCCCCCeeeecCCC-------CcCCCCCCCcceeeE
Confidence 34699999998641 1222210 01 477888886544344433 357999998876544
No 50
>PRK12366 replication factor A; Reviewed
Probab=25.58 E-value=10 Score=38.58 Aligned_cols=35 Identities=14% Similarity=0.203 Sum_probs=25.3
Q ss_pred HhhcccccccceeeeecceeccceEEEEeeeccccccccchhhH
Q 023461 180 IKMAFSVLTVGIYCLIGMDVLLNEWVLVRLVRGSLLVPRARLFV 223 (282)
Q Consensus 180 iEgaCP~ck~~~~~~ig~~~~~~q~v~~r~~rg~v~~pr~~~~~ 223 (282)
.--+||.|++.. +..+ |+| .|..|--+ .|..++.+
T Consensus 531 ~y~aCp~CnkKv---~~~~---g~~-~C~~c~~~--~p~~~~~l 565 (637)
T PRK12366 531 ILYLCPNCRKRV---EEVD---GEY-ICEFCGEV--EPNELLML 565 (637)
T ss_pred EEecccccCeEe---EcCC---CcE-ECCCCCCC--CCcEEEEE
Confidence 347999999987 4333 444 69889777 89888753
No 51
>PF13134 DUF3948: Protein of unknown function (DUF3948)
Probab=24.65 E-value=69 Score=22.59 Aligned_cols=21 Identities=33% Similarity=0.621 Sum_probs=18.7
Q ss_pred hHhhCCCCchHHHHHHHHHHH
Q 023461 127 NDFLNTPLGRSFATIFFLWFA 147 (282)
Q Consensus 127 ~dFl~TPlGks~~TiFF~Wfa 147 (282)
.||+++--|..+.|.|.++++
T Consensus 12 ~D~lgsasga~~LTafI~fLa 32 (35)
T PF13134_consen 12 MDFLGSASGAAVLTAFIVFLA 32 (35)
T ss_pred hhhhhcccchHHHHHHHHHHH
Confidence 489999999999999988874
No 52
>PLN03121 nucleic acid binding protein; Provisional
Probab=24.56 E-value=71 Score=30.02 Aligned_cols=58 Identities=22% Similarity=0.276 Sum_probs=38.9
Q ss_pred HHHHHHHhhhhhhhhhhhHHHHHHHHHHHHHHhhhhhhhhHhHHhhhhhhhhcchhhHHhhhHhhCC
Q 023461 66 DAKKTAERIDRQYSVSRRLNSAARTAAVRARELDREFAISVRWRSFRMDFSRNWPRYRKQLNDFLNT 132 (282)
Q Consensus 66 EARktA~rlDr~YsVSrR~A~Aar~A~erArEIDrefgIrrR~R~fs~Df~RnWP~YRRQL~dFl~T 132 (282)
+|=.-|..+|+++.||. +|....-+||+++||..++=+-. +.-|.- --|=|++|+..+
T Consensus 136 da~~KAkafDE~h~lss-------~a~a~v~~~d~~iglt~k~~~g~-~~vk~v-Deky~vs~~tks 193 (243)
T PLN03121 136 DALSKAKAFDESHQVSA-------TAAAKVAELSKRIGLTDKIFAGM-EAVRSV-DEKYHVSEFTKS 193 (243)
T ss_pred HHHHHHHHHHHhcCccH-------hhhhhhhhhhhhccchhhhhhhH-HHHHhh-hhhhhhHHHHHH
Confidence 34455788999999995 66778889999999999986533 332221 112345565544
No 53
>KOG3096 consensus Spliceosome-associated coiled-coil protein [Function unknown]
Probab=24.29 E-value=3e+02 Score=25.98 Aligned_cols=53 Identities=28% Similarity=0.481 Sum_probs=38.7
Q ss_pred HHHHHHhHHHHHhHHHHHHHHHhhhhhh-hhhhhHHHHHHHHHHHHHHhhhhhh
Q 023461 51 DAWRTANNGFEQLVFDAKKTAERIDRQY-SVSRRLNSAARTAAVRARELDREFA 103 (282)
Q Consensus 51 ~AwRsAN~gfEq~~fEARktA~rlDr~Y-sVSrR~A~Aar~A~erArEIDrefg 103 (282)
.||++-|+.+|-+...|.|-+++....- +|.+.=--+--+|+++.++++++++
T Consensus 127 eaw~~~ne~le~~l~~aqkelq~~kk~iq~vn~~RK~~Q~~ag~rL~~le~~wv 180 (225)
T KOG3096|consen 127 EAWKQYNEVLEVMLTHAQKELQKTKKLIQDVNRQRKHAQLTAGERLRELEQKWV 180 (225)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence 5999999999999998888887765432 3333334455678888888887764
No 54
>PRK05759 F0F1 ATP synthase subunit B; Validated
Probab=24.28 E-value=1.3e+02 Score=24.32 Aligned_cols=25 Identities=8% Similarity=0.432 Sum_probs=18.6
Q ss_pred HHHHHHHHHHH-HhHHHHHHHHHHhH
Q 023461 153 FRILILATWVL-PIAAPLLIGTVANN 177 (282)
Q Consensus 153 FRi~i~~tWVL-P~A~PlLIGtian~ 177 (282)
+=.|+++.|+| .|+.|++.+.+.++
T Consensus 11 ~i~Flil~~il~~~~~~pi~~~l~~R 36 (156)
T PRK05759 11 LIAFLILVWFIMKFVWPPIMKALEER 36 (156)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 33466677777 78889999998876
No 55
>COG3162 Predicted membrane protein [Function unknown]
Probab=24.07 E-value=74 Score=26.78 Aligned_cols=27 Identities=26% Similarity=0.436 Sum_probs=23.4
Q ss_pred CCchhHHhhhhcchHHHHHHHHHHHhh
Q 023461 235 KGTSFQEMVGARNLQSLMMTLLMLTLR 261 (282)
Q Consensus 235 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 261 (282)
..-+|||.|-.||--+..||++||.+-
T Consensus 11 a~p~f~eLv~kr~~Fa~~ltl~flv~Y 37 (102)
T COG3162 11 ANPRFRELVRKRRRFAVPLTLIFLVVY 37 (102)
T ss_pred cCHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346899999999999999999998764
No 56
>KOG2173 consensus Integral membrane protein [General function prediction only]
Probab=24.01 E-value=1e+02 Score=33.65 Aligned_cols=27 Identities=30% Similarity=0.562 Sum_probs=22.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023461 136 RSFATIFFLWFALSGWLFRILILATWV 162 (282)
Q Consensus 136 ks~~TiFF~WfalSGWlFRi~i~~tWV 162 (282)
-+-+|.|++|++++.|++|++=+..=+
T Consensus 215 ~T~it~~~l~lf~vy~l~~~ik~~~~I 241 (849)
T KOG2173|consen 215 ITAITYFVLWLFSVYWLFRFIKFFADI 241 (849)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356799999999999999997665544
No 57
>TIGR01144 ATP_synt_b ATP synthase, F0 subunit b. This model describes the F1/F0 ATP synthase b subunit in bacteria only. Scoring just below the trusted cutoff are the N-terminal domains of Mycobacterial b/delta fusion proteins and a subunit from an archaeon, Methanosarcina barkeri, in which the ATP synthase homolog differs in architecture and is not experimentally confirmed. This model helps resolve b from the related b' subunit. Within the family is an example from a sodium-translocating rather than proton-translocating ATP synthase.
Probab=23.89 E-value=93 Score=25.01 Aligned_cols=22 Identities=23% Similarity=0.436 Sum_probs=15.3
Q ss_pred HHHHHHHH-HhHHHHHHHHHHhH
Q 023461 156 LILATWVL-PIAAPLLIGTVANN 177 (282)
Q Consensus 156 ~i~~tWVL-P~A~PlLIGtian~ 177 (282)
|+++.|+| -|+.|++.+.+.++
T Consensus 5 Flil~~il~~~~~~pi~~~l~~R 27 (147)
T TIGR01144 5 FILLVWFCMKYVWPPLAKAIETR 27 (147)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555555 67778888888765
No 58
>PF03348 Serinc: Serine incorporator (Serinc); InterPro: IPR005016 This is a family of proteins which display differential expression in various tumour and cell lines. The function of these proteins is unknown. ; GO: 0016020 membrane
Probab=23.43 E-value=77 Score=31.20 Aligned_cols=20 Identities=20% Similarity=0.426 Sum_probs=15.6
Q ss_pred HHHHHH-HHHHHHHHHhHHHH
Q 023461 150 GWLFRI-LILATWVLPIAAPL 169 (282)
Q Consensus 150 GWlFRi-~i~~tWVLP~A~Pl 169 (282)
.|.+++ ++++.+|++|+.|-
T Consensus 111 ~W~~K~l~l~~l~v~~FfiP~ 131 (429)
T PF03348_consen 111 FWFLKFLLLIGLIVGAFFIPN 131 (429)
T ss_pred hHHHHHHHHHHHHheeEEeCc
Confidence 678888 66778888888876
No 59
>PF12732 YtxH: YtxH-like protein; InterPro: IPR024623 This family of uncharacterised proteins is found in bacteria. Proteins in this family are typically between 100 and 143 amino acids in length. The N-terminal region is the most conserved.
Probab=23.23 E-value=3.1e+02 Score=20.18 Aligned_cols=19 Identities=32% Similarity=0.433 Sum_probs=11.5
Q ss_pred hhhhHHHHHHHHHHHHHHh
Q 023461 80 VSRRLNSAARTAAVRAREL 98 (282)
Q Consensus 80 VSrR~A~Aar~A~erArEI 98 (282)
+..++.+.+..+.|.+.|+
T Consensus 53 ~k~~~~~~~~~~~e~~~e~ 71 (74)
T PF12732_consen 53 VKEKAEETADEAKEKAKEL 71 (74)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 5555666666666666554
No 60
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=23.09 E-value=46 Score=22.39 Aligned_cols=27 Identities=7% Similarity=-0.108 Sum_probs=13.1
Q ss_pred ccccccceeeeecceeccceEEEEeeeccc
Q 023461 184 FSVLTVGIYCLIGMDVLLNEWVLVRLVRGS 213 (282)
Q Consensus 184 CP~ck~~~~~~ig~~~~~~q~v~~r~~rg~ 213 (282)
||.|+.-.|---+.. +...+|+.|--.
T Consensus 3 Cp~Cg~~l~~~~~~~---~~~~vC~~Cg~~ 29 (52)
T smart00661 3 CPKCGNMLIPKEGKE---KRRFVCRKCGYE 29 (52)
T ss_pred CCCCCCccccccCCC---CCEEECCcCCCe
Confidence 677766443222211 235566666543
No 61
>PF02773 S-AdoMet_synt_C: S-adenosylmethionine synthetase, C-terminal domain; InterPro: IPR022630 The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold. This entry represents the C-terminal domain of S=adenosylmethionine synthetase and is found in association with PF00438 from PFAM and PF02772 from PFAM. S-adenosylmethionine synthetase (MAT, 2.5.1.6 from EC) is the enzyme that catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP []. AdoMet is an important methyl donor for transmethylation and is also the propylamino donor in polyamine biosynthesis. In bacteria there is a single isoform of AdoMet synthetase (gene metK), there are two in budding yeast (genes SAM1 and SAM2) and in mammals while in plants there is generally a multigene family. The sequence of AdoMet synthetase is highly conserved throughout isozymes and species. The active sites of both the Escherichia coli and rat liver MAT reside between two subunits, with contributions from side chains of residues from both subunits, resulting in a dimer as the minimal catalytic entity. The side chains that contribute to the ligand binding sites are conserved between the two proteins. In the structures of complexes with the E. coli enzyme, the phosphate groups have the same positions in the (PPi plus Pi) complex and the (ADP plus Pi) complex, and are located at the bottom of a deep cavity with the adenosyl group nearer the entrance []; GO: 0004478 methionine adenosyltransferase activity; PDB: 3IML_B 1QM4_B 1O9T_B 1O93_A 1O92_B 1O90_A 1FUG_A 1RG9_D 1XRA_A 1P7L_C ....
Probab=22.70 E-value=55 Score=28.62 Aligned_cols=35 Identities=20% Similarity=0.153 Sum_probs=26.7
Q ss_pred HHHHHhHHHHhhcccccccceeeeecceeccceEE
Q 023461 171 IGTVANNFVIKMAFSVLTVGIYCLIGMDVLLNEWV 205 (282)
Q Consensus 171 IGtian~~viEgaCP~ck~~~~~~ig~~~~~~q~v 205 (282)
-=+||||+|..|-|.-|..|.-.-||.---++=-|
T Consensus 47 aR~iAKniVaagla~~c~vqlsYaIGv~~P~si~v 81 (138)
T PF02773_consen 47 ARYIAKNIVAAGLAKRCEVQLSYAIGVAEPVSIYV 81 (138)
T ss_dssp HHHHHHHHHHTTSBSEEEEEEEE-TT-SS-SEEEE
T ss_pred HHHHHHHHHHccchHHHHhhceeeeccccCcccEE
Confidence 35799999999999999999999999875554444
No 62
>PRK14471 F0F1 ATP synthase subunit B; Provisional
Probab=22.50 E-value=1.8e+02 Score=24.03 Aligned_cols=27 Identities=19% Similarity=0.424 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHH-HhHHHHHHHHHHhH
Q 023461 151 WLFRILILATWVL-PIAAPLLIGTVANN 177 (282)
Q Consensus 151 WlFRi~i~~tWVL-P~A~PlLIGtian~ 177 (282)
|.+=.|+++.|+| -|+.|++.+.+.++
T Consensus 13 ~~~i~Flil~~ll~~~l~~pi~~~l~~R 40 (164)
T PRK14471 13 WQTILFLILLLLLAKFAWKPILGAVKER 40 (164)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 3333466666776 78889999998876
No 63
>PF11241 DUF3043: Protein of unknown function (DUF3043); InterPro: IPR021403 Some members in this family of proteins with unknown function are annotated as membrane proteins. This cannot be confirmed.
Probab=22.13 E-value=5.8e+02 Score=22.88 Aligned_cols=91 Identities=25% Similarity=0.312 Sum_probs=47.2
Q ss_pred HHHHHHHhhhhhhhhHhHHhhhhhhhhcchh----hHHhhhHhhCC--CCchHHHHHHHHHHHHH-----HHHHHHHHHH
Q 023461 91 AAVRARELDREFAISVRWRSFRMDFSRNWPR----YRKQLNDFLNT--PLGRSFATIFFLWFALS-----GWLFRILILA 159 (282)
Q Consensus 91 A~erArEIDrefgIrrR~R~fs~Df~RnWP~----YRRQL~dFl~T--PlGks~~TiFF~WfalS-----GWlFRi~i~~ 159 (282)
|+.+++|--++-.-.+|-++-+-|=+---|+ -|+-.-||.|+ .+|..|.-+.++-+.+| -++--+..++
T Consensus 28 ak~~~R~~~r~~r~~~r~aM~~GDeryLp~RDrGP~Rr~vRD~VDsR~~i~e~fmP~alv~lv~~~v~~~~~~~~~~~~~ 107 (170)
T PF11241_consen 28 AKKRAREARRERRARQREAMMTGDERYLPPRDRGPVRRYVRDYVDSRRNIGEFFMPVALVLLVLSFVVPSPQVQLYVTLA 107 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcChhhcCCcccccchhhhhhhhhhcccchHHHHHHHHHHHHHHHHHcccHHHHHHHHHH
Confidence 3333444344444456666777774333333 45667788776 45665554444444333 3334445556
Q ss_pred HHHHHhHH---HHHHHHHHhHHHHh
Q 023461 160 TWVLPIAA---PLLIGTVANNFVIK 181 (282)
Q Consensus 160 tWVLP~A~---PlLIGtian~~viE 181 (282)
+|++-++. -.++|.-.|+.+.|
T Consensus 108 ~~~~~~~~iid~~~l~r~vkk~v~~ 132 (170)
T PF11241_consen 108 MYVLLLLVIIDGVILGRRVKKRVAE 132 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 66555443 23555556666555
No 64
>PF06847 Arc_PepC_II: Archaeal Peptidase A24 C-terminus Type II; InterPro: IPR009655 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This region is of unknown function, which is found at the C terminus of archaeal preflagellin aspartic acid signal peptidases []. The preflagellin peptidase is a membrane-bound enzyme topologically similar to its counterpart in the type IV pilus system (prepilin peptidase); the two enzymes utilizing the same catalytic mechanism []. The preflagellin peptidase is required for the removal of the leader peptide from archaeal flagellin []. Preflagellin aspartic acid signal peptidases belong to the MEROPS peptidase family A24B (preflagellin peptidase, clan AD).; GO: 0008233 peptidase activity; PDB: 3S0X_B.
Probab=21.82 E-value=50 Score=26.36 Aligned_cols=17 Identities=24% Similarity=0.384 Sum_probs=10.6
Q ss_pred HHHHHhHHHHHHHHHHh
Q 023461 160 TWVLPIAAPLLIGTVAN 176 (282)
Q Consensus 160 tWVLP~A~PlLIGtian 176 (282)
||=+||..|+.+|+|-.
T Consensus 70 TpgiPFlvpIt~G~iia 86 (93)
T PF06847_consen 70 TPGIPFLVPITAGYIIA 86 (93)
T ss_dssp -----THHHHHHHHHHH
T ss_pred eCCCcCHHHHHHHHHHH
Confidence 78899999999999864
No 65
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=21.79 E-value=43 Score=36.16 Aligned_cols=39 Identities=13% Similarity=0.025 Sum_probs=33.9
Q ss_pred hhcccccccceeeeecceeccceEEEEeeeccccccccc
Q 023461 181 KMAFSVLTVGIYCLIGMDVLLNEWVLVRLVRGSLLVPRA 219 (282)
Q Consensus 181 EgaCP~ck~~~~~~ig~~~~~~q~v~~r~~rg~v~~pr~ 219 (282)
+|.||+|+=.=+..+.|..+.+-.+.|..|.|.=+.|-.
T Consensus 738 ~G~C~~C~G~G~~~~~~~f~~~~~~~C~~C~G~R~~~e~ 776 (943)
T PRK00349 738 GGRCEACQGDGVIKIEMHFLPDVYVPCDVCKGKRYNRET 776 (943)
T ss_pred CCCCCcccccceEEEEeccCCCccccCccccCccccccc
Confidence 799999987777778888888888999999999888864
No 66
>PRK14472 F0F1 ATP synthase subunit B; Provisional
Probab=21.51 E-value=1.1e+02 Score=25.73 Aligned_cols=28 Identities=14% Similarity=0.285 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHH-HhHHHHHHHHHHhH
Q 023461 150 GWLFRILILATWVL-PIAAPLLIGTVANN 177 (282)
Q Consensus 150 GWlFRi~i~~tWVL-P~A~PlLIGtian~ 177 (282)
+|..=.|+++.|+| -|+.|++.+.+.++
T Consensus 22 ~~~~i~Flil~~lL~~~l~kpi~~~l~~R 50 (175)
T PRK14472 22 FWTAVTFVIVLLILKKIAWGPILSALEER 50 (175)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 34333456666666 67889999988776
No 67
>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=21.23 E-value=38 Score=19.31 Aligned_cols=9 Identities=0% Similarity=-0.020 Sum_probs=7.9
Q ss_pred cccccccce
Q 023461 183 AFSVLTVGI 191 (282)
Q Consensus 183 aCP~ck~~~ 191 (282)
.||.|++.|
T Consensus 2 ~C~~C~~~f 10 (23)
T PF00096_consen 2 KCPICGKSF 10 (23)
T ss_dssp EETTTTEEE
T ss_pred CCCCCCCcc
Confidence 599999988
No 68
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=21.01 E-value=27 Score=30.44 Aligned_cols=39 Identities=3% Similarity=-0.114 Sum_probs=23.2
Q ss_pred HHHHhHHHHhhc-----ccccccceeeeecceeccceEEEEeeecccc
Q 023461 172 GTVANNFVIKMA-----FSVLTVGIYCLIGMDVLLNEWVLVRLVRGSL 214 (282)
Q Consensus 172 Gtian~~viEga-----CP~ck~~~~~~ig~~~~~~q~v~~r~~rg~v 214 (282)
-.+..++--|.. ||+|+.+|.-+ +++ +.--.|..|-|.+
T Consensus 103 ~klk~~l~~e~~~~~Y~Cp~C~~rytf~---eA~-~~~F~Cp~Cg~~L 146 (178)
T PRK06266 103 KKLKEQLEEEENNMFFFCPNCHIRFTFD---EAM-EYGFRCPQCGEML 146 (178)
T ss_pred HHHHHHhhhccCCCEEECCCCCcEEeHH---HHh-hcCCcCCCCCCCC
Confidence 344555544444 99999999333 222 2346788886654
No 69
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=20.46 E-value=62 Score=21.65 Aligned_cols=30 Identities=13% Similarity=-0.025 Sum_probs=17.5
Q ss_pred cccccccceeeeecceeccc--eEEEEeeecccccccc
Q 023461 183 AFSVLTVGIYCLIGMDVLLN--EWVLVRLVRGSLLVPR 218 (282)
Q Consensus 183 aCP~ck~~~~~~ig~~~~~~--q~v~~r~~rg~v~~pr 218 (282)
.||.|+... .- +.++ ++=.|..|.|+ |-..
T Consensus 1 ~CP~C~~~l---~~--~~~~~~~id~C~~C~G~-W~d~ 32 (41)
T PF13453_consen 1 KCPRCGTEL---EP--VRLGDVEIDVCPSCGGI-WFDA 32 (41)
T ss_pred CcCCCCccc---ce--EEECCEEEEECCCCCeE-EccH
Confidence 399999855 22 2223 34458888775 4443
No 70
>COG5005 Mu-like prophage protein gpG [General function prediction only]
Probab=20.27 E-value=1.5e+02 Score=26.17 Aligned_cols=36 Identities=19% Similarity=0.245 Sum_probs=30.2
Q ss_pred HHHHHHHhhhhhhhhhhhHHHHHHHHHHHHHHhhhh
Q 023461 66 DAKKTAERIDRQYSVSRRLNSAARTAAVRARELDRE 101 (282)
Q Consensus 66 EARktA~rlDr~YsVSrR~A~Aar~A~erArEIDre 101 (282)
...+.|+-.|.+|++.|++|+.-++|.+++=|...+
T Consensus 15 ~~~~laq~~~~rk~Lmr~vA~~m~sav~~nF~~~gr 50 (140)
T COG5005 15 KLEALAQVTDGRKDLMRSVAGTMRSAVEKNFELEGR 50 (140)
T ss_pred HHHHHHHhhccccHHHHHHHHHHHHHHHHHHHhcCC
Confidence 345678889999999999999999999988776643
No 71
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=20.18 E-value=46 Score=22.66 Aligned_cols=30 Identities=7% Similarity=-0.096 Sum_probs=23.1
Q ss_pred hhcccccccceeeeecceeccceEEEEeeecc
Q 023461 181 KMAFSVLTVGIYCLIGMDVLLNEWVLVRLVRG 212 (282)
Q Consensus 181 EgaCP~ck~~~~~~ig~~~~~~q~v~~r~~rg 212 (282)
|-.|++|+..|--+..+.- ...+.|-.|.+
T Consensus 5 ey~C~~Cg~~fe~~~~~~~--~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISE--DDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEEEcCC--CCCCcCCCCCC
Confidence 3469999999977776663 56888888877
Done!