Query psy4064
Match_columns 624
No_of_seqs 70 out of 72
Neff 1.8
Searched_HMMs 46136
Date Sat Aug 17 00:24:19 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4064.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4064hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4315|consensus 99.8 1.7E-20 3.7E-25 192.9 6.5 171 2-186 183-365 (455)
2 PF00467 KOW: KOW motif; Inte 97.8 2.4E-05 5.1E-10 55.1 3.3 31 37-67 1-31 (32)
3 PRK05609 nusG transcription an 97.4 0.00041 9E-09 62.0 6.6 48 32-79 124-171 (181)
4 PRK08559 nusG transcription an 97.0 0.0014 3E-08 59.3 6.2 56 33-88 93-150 (153)
5 TIGR00922 nusG transcription t 97.0 0.0011 2.4E-08 59.2 5.4 47 33-79 118-164 (172)
6 KOG4315|consensus 97.0 0.00027 5.9E-09 74.8 1.3 68 31-99 225-292 (455)
7 TIGR00405 L26e_arch ribosomal 96.7 0.0035 7.6E-08 55.2 6.1 54 34-87 86-141 (145)
8 TIGR01955 RfaH transcriptional 96.7 0.0026 5.5E-08 55.9 5.0 46 33-79 107-152 (159)
9 COG0250 NusG Transcription ant 96.4 0.005 1.1E-07 58.0 5.2 47 33-79 122-168 (178)
10 PRK09014 rfaH transcriptional 96.4 0.0043 9.3E-08 55.3 4.4 46 33-79 108-153 (162)
11 TIGR01956 NusG_myco NusG famil 96.2 0.0089 1.9E-07 60.0 6.1 47 33-79 204-250 (258)
12 smart00739 KOW KOW (Kyprides, 95.9 0.0076 1.7E-07 39.5 2.5 27 35-61 2-28 (28)
13 PRK12281 rplX 50S ribosomal pr 95.8 0.0097 2.1E-07 49.9 3.7 36 33-68 5-40 (76)
14 CHL00141 rpl24 ribosomal prote 95.8 0.01 2.2E-07 50.4 3.7 36 33-68 7-42 (83)
15 PRK00004 rplX 50S ribosomal pr 95.4 0.017 3.7E-07 50.6 3.6 36 33-68 3-38 (105)
16 PRK01191 rpl24p 50S ribosomal 95.3 0.022 4.8E-07 51.9 4.2 36 33-68 44-79 (120)
17 TIGR01079 rplX_bact ribosomal 94.7 0.035 7.5E-07 48.9 3.6 35 34-68 3-37 (104)
18 PTZ00194 60S ribosomal protein 94.6 0.041 9E-07 51.5 4.2 36 33-68 45-80 (143)
19 TIGR01080 rplX_A_E ribosomal p 93.8 0.075 1.6E-06 47.9 3.9 39 31-69 38-76 (114)
20 COG0198 RplX Ribosomal protein 89.6 0.43 9.3E-06 42.8 3.9 34 33-68 3-36 (104)
21 COG5164 SPT5 Transcription elo 86.8 0.92 2E-05 49.9 4.9 65 35-109 352-416 (607)
22 TIGR00739 yajC preprotein tran 86.5 1 2.2E-05 38.3 4.1 45 33-84 36-80 (84)
23 PRK05886 yajC preprotein trans 85.3 1.6 3.4E-05 39.4 4.8 47 33-86 37-83 (109)
24 PRK06531 yajC preprotein trans 84.9 1.4 3.1E-05 39.8 4.4 47 34-86 36-82 (113)
25 PRK05585 yajC preprotein trans 80.9 2.1 4.4E-05 38.0 3.8 47 33-86 51-97 (106)
26 KOG1999|consensus 77.8 2.8 6.1E-05 49.1 4.6 52 36-89 686-737 (1024)
27 PRK04333 50S ribosomal protein 76.9 3 6.4E-05 36.0 3.5 33 34-67 3-35 (84)
28 smart00719 Plus3 Short conserv 74.2 6.5 0.00014 34.2 4.9 62 34-95 28-105 (109)
29 smart00743 Agenet Tudor-like d 72.1 7.7 0.00017 29.7 4.4 53 34-87 2-57 (61)
30 PF03126 Plus-3: Plus-3 domain 72.1 3.5 7.7E-05 35.3 2.8 64 34-97 24-104 (108)
31 PRK04313 30S ribosomal protein 71.6 6 0.00013 39.9 4.6 54 32-85 169-226 (237)
32 PF02237 BPL_C: Biotin protein 69.3 5.3 0.00012 30.3 2.9 33 38-72 3-35 (48)
33 PLN00036 40S ribosomal protein 69.2 8.6 0.00019 39.3 5.2 55 31-85 171-228 (261)
34 COG1862 YajC Preprotein transl 65.8 6.1 0.00013 35.1 3.0 46 34-86 43-88 (97)
35 PTZ00223 40S ribosomal protein 65.7 9.7 0.00021 39.2 4.8 78 32-109 169-253 (273)
36 PTZ00118 40S ribosomal protein 63.3 13 0.00029 38.0 5.2 55 31-85 171-228 (262)
37 PF02699 YajC: Preprotein tran 63.0 2.4 5.2E-05 35.6 0.0 45 33-84 35-79 (82)
38 PTZ00065 60S ribosomal protein 51.2 26 0.00056 32.9 4.6 35 35-70 8-42 (130)
39 smart00333 TUDOR Tudor domain. 48.4 43 0.00093 24.8 4.6 53 34-88 2-55 (57)
40 PF04717 Phage_base_V: Phage-r 44.5 33 0.00071 27.6 3.7 33 53-85 1-33 (79)
41 PRK06955 biotin--protein ligas 40.3 52 0.0011 32.9 5.2 51 34-85 245-295 (300)
42 KOG2985|consensus 39.9 30 0.00066 36.2 3.5 13 333-345 178-190 (306)
43 PRK08330 biotin--protein ligas 38.2 67 0.0015 30.7 5.3 49 35-84 185-234 (236)
44 KOG1999|consensus 37.2 45 0.00098 39.8 4.7 46 34-81 459-504 (1024)
45 PF13861 FLgD_tudor: FlgD Tudo 35.0 31 0.00067 27.1 2.1 31 50-80 26-56 (61)
46 KOG1708|consensus 34.5 48 0.001 33.8 3.9 61 29-89 67-145 (236)
47 PF11595 DUF3245: Protein of u 32.8 21 0.00045 34.0 1.0 16 3-18 43-58 (149)
48 COG1471 RPS4A Ribosomal protei 31.1 68 0.0015 33.0 4.3 55 31-85 170-228 (241)
49 PTZ00275 biotin-acetyl-CoA-car 30.5 97 0.0021 31.1 5.2 38 34-73 233-270 (285)
50 PF08536 Whirly: Whirly transc 26.9 45 0.00098 31.8 2.1 58 35-93 68-133 (139)
51 PF15057 DUF4537: Domain of un 26.8 1.3E+02 0.0029 27.0 5.0 65 32-97 53-123 (124)
52 PF06003 SMN: Survival motor n 26.3 1.5E+02 0.0032 29.9 5.7 57 33-89 67-124 (264)
53 PF10500 SR-25: Nuclear RNA-sp 26.3 46 0.00099 33.9 2.2 7 481-487 161-167 (225)
54 PF12568 DUF3749: Acetyltransf 24.8 68 0.0015 30.1 2.9 28 62-89 46-75 (128)
55 PF04351 PilP: Pilus assembly 23.7 1.1E+02 0.0024 28.1 3.9 35 38-73 100-135 (149)
56 COG2163 RPL14A Ribosomal prote 23.0 89 0.0019 29.1 3.2 29 34-62 4-32 (125)
57 PRK07165 F0F1 ATP synthase sub 22.8 1.1E+02 0.0024 34.0 4.4 62 34-100 20-86 (507)
58 PRK13325 bifunctional biotin-- 22.3 1.6E+02 0.0034 32.8 5.5 55 34-89 274-328 (592)
59 TIGR03498 FliI_clade3 flagella 21.5 1.2E+02 0.0025 32.7 4.1 62 36-100 21-87 (418)
60 COG5164 SPT5 Transcription elo 20.8 98 0.0021 34.9 3.5 74 34-108 139-225 (607)
61 PF08863 YolD: YolD-like prote 20.8 1.7E+02 0.0037 23.6 4.1 38 36-73 40-80 (92)
62 PRK09618 flgD flagellar basal 20.3 1.5E+02 0.0033 28.1 4.2 44 37-81 91-134 (142)
63 PRK05922 type III secretion sy 20.1 1.4E+02 0.0029 32.5 4.3 56 35-90 38-98 (434)
No 1
>KOG4315|consensus
Probab=99.81 E-value=1.7e-20 Score=192.92 Aligned_cols=171 Identities=26% Similarity=0.394 Sum_probs=120.1
Q ss_pred CCCCCCCCCcCCCCCCcccccCCCCCCCccccceeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCeeEEEeec
Q psy4064 2 DVTLRPKGLGLGADKSATQITTSKSNTNPEEAKLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEHVTVVES 81 (624)
Q Consensus 2 Ep~LRPKGLGLGADrt~kq~Kp~ee~kEEEeLgLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGevVTVSEy 81 (624)
+|.+||+||||||++...++.....+...+.+..+.++++. +|+|++.++++|++|+|+..--+.++
T Consensus 183 ~~~~rpkglGLGa~~~~~~~~~~~~pek~~v~eeKke~~k~-------------~g~dd~~~g~~vr~~~g~~~~~~~ki 249 (455)
T KOG4315|consen 183 EPFLRPKGLGLGADPALKPKALLVQPEKNEVKEEKKEAYKR-------------QGFDDHAGGVAVRMAIGGKKGLFGKI 249 (455)
T ss_pred ccccCCCCcccCCCccccccccccCcccccchhhhhhhhhh-------------cccccccCceeEEEeeccccccccee
Confidence 58899999999999988765544444445555556666554 99999999999999999999999999
Q ss_pred eeEecChHHHhhhhcccchhhHHHHHhhhHhhhhhHH----HhhhcccCCC-------CchhhhhhhhcCCCCCcHHHHh
Q psy4064 82 LLLRVTQSEYDKNSRVINMNKYEEYKEKDAKQSNIEK----VKDKSENNHR-------GEQHEKQYSKYRNSSDSEYEEK 150 (624)
Q Consensus 82 aVRpVSkKEYDKnSKdLNksKYEEYKkkEkEk~rIEk----er~K~e~n~~-------~s~heKq~sk~rnSsDS~~~ek 150 (624)
.+.|||..+|..++.|||..+|++||.+..-+...++ .++.+..+.+ .+-.++.++.+.|-..+.+ +|
T Consensus 250 ~~~~~S~~~~~~~~vgin~~~y~e~kerdr~~~e~~k~~ld~rq~~ksts~r~~~~d~k~yk~k~~~~k~Dr~s~ke-ek 328 (455)
T KOG4315|consen 250 VCLPVSRKEYERVKVGINKVEYDEFKERDRLERERKKSDLDSRQPSKSTSGRDQRSDSKSYKEKHASSKQDRGSTKE-EK 328 (455)
T ss_pred EeccCcchhhhhhhhccchhhhhhhhhhhHHHHHHhhhhhhhccccCCcCCccccccccchhhhhccccccccchhh-hh
Confidence 9999999999999999999999999954432222111 1122222222 1222233333333333333 88
Q ss_pred hcCCccccceehhhhccCCch-HHHHHHhhhhccCCC
Q psy4064 151 KMKPYKTNELLSRVILRNSDS-EYEEKKMKQYKTNEP 186 (624)
Q Consensus 151 ~~K~W~r~eLlVRfIDrn~~~-~~~~~~~~~~~~~~~ 186 (624)
+.++|+|.+|+|||||.+|-- +|-++||.---.--|
T Consensus 329 ~~k~wlR~dl~VR~is~d~Kgg~ly~~K~~i~dv~gp 365 (455)
T KOG4315|consen 329 NNKSWLRSDLKVRFISKDVKGGRLYEKKVRIVDVVGP 365 (455)
T ss_pred ccchhhhcceeEEeeccccccchhhhcccceecccCC
Confidence 999999999999999999963 444566654443333
No 2
>PF00467 KOW: KOW motif; InterPro: IPR005824 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 [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=97.78 E-value=2.4e-05 Score=55.12 Aligned_cols=31 Identities=32% Similarity=0.460 Sum_probs=29.6
Q ss_pred eCceEEEeccCCCCcccceeeecCCCceEEE
Q psy4064 37 KNCCVKITGGMFKNNYGKLESFNEDSGRVVV 67 (624)
Q Consensus 37 KGAfVkIVSGPHKGLYGKVEGLDpDNgRVMV 67 (624)
+|..|+|++|||+|..|+|..+|+++.+|+|
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~v 31 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSKVRVTV 31 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTTTEEEE
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCCCEEEE
Confidence 5899999999999999999999999999987
No 3
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=97.39 E-value=0.00041 Score=62.01 Aligned_cols=48 Identities=15% Similarity=0.252 Sum_probs=43.7
Q ss_pred ccceeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCeeEEEe
Q psy4064 32 EAKLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEHVTVV 79 (624)
Q Consensus 32 eLgLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGevVTVS 79 (624)
...+.+|.-|.|++||++|+-|.|..+|.++.||+|.|-+-|+.+.|.
T Consensus 124 ~~~~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~l~~~G~~~~v~ 171 (181)
T PRK05609 124 KVDFEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVLVSIFGRETPVE 171 (181)
T ss_pred ccCCCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEEEEECCCceEEE
Confidence 367889999999999999999999999999999999999999875553
No 4
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=97.04 E-value=0.0014 Score=59.26 Aligned_cols=56 Identities=21% Similarity=0.242 Sum_probs=50.7
Q ss_pred cceeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCee--EEEeeceeEecCh
Q psy4064 33 AKLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEH--VTVVESLLLRVTQ 88 (624)
Q Consensus 33 LgLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGev--VTVSEyaVRpVSk 88 (624)
..+.+|..|.|++||++|.=|.|..+|++..+|.|.|.--... |||....|+||-.
T Consensus 93 ~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~~~~pv~v~~~~~~~~~~ 150 (153)
T PRK08559 93 EGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEAAVPIPVTVRGDQVRVVKK 150 (153)
T ss_pred cCCCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECCcceeeEEEeccEEEEecc
Confidence 5689999999999999999999999999999988888877766 9999999999853
No 5
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=97.03 E-value=0.0011 Score=59.17 Aligned_cols=47 Identities=17% Similarity=0.263 Sum_probs=43.0
Q ss_pred cceeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCeeEEEe
Q psy4064 33 AKLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEHVTVV 79 (624)
Q Consensus 33 LgLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGevVTVS 79 (624)
..+.+|..|.|++||++|+=|.|..+|.++.||+|.|-+-|+.+.|.
T Consensus 118 ~~~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~v~~~g~~~~v~ 164 (172)
T TIGR00922 118 IDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFGRETPVE 164 (172)
T ss_pred cCCCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEEEEECCCceEEE
Confidence 55889999999999999999999999999999999999999876554
No 6
>KOG4315|consensus
Probab=96.97 E-value=0.00027 Score=74.77 Aligned_cols=68 Identities=15% Similarity=0.063 Sum_probs=61.4
Q ss_pred cccceeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCeeEEEeeceeEecChHHHhhhhcccc
Q psy4064 31 EEAKLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEHVTVVESLLLRVTQSEYDKNSRVIN 99 (624)
Q Consensus 31 EeLgLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGevVTVSEyaVRpVSkKEYDKnSKdLN 99 (624)
...++.+|-+|+++.|+++|+||+|++++++ .+.++++++|-++|+++||-.+++.+.|+.++-.+..
T Consensus 225 g~dd~~~g~~vr~~~g~~~~~~~ki~~~~~S-~~~~~~~~vgin~~~y~e~kerdr~~~e~~k~~ld~r 292 (455)
T KOG4315|consen 225 GFDDHAGGVAVRMAIGGKKGLFGKIVCLPVS-RKEYERVKVGINKVEYDEFKERDRLERERKKSDLDSR 292 (455)
T ss_pred ccccccCceeEEEeecccccccceeEeccCc-chhhhhhhhccchhhhhhhhhhhHHHHHHhhhhhhhc
Confidence 3467889999999999999999999999988 7799999999999999999999999999998665543
No 7
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=96.74 E-value=0.0035 Score=55.20 Aligned_cols=54 Identities=24% Similarity=0.258 Sum_probs=50.0
Q ss_pred ceeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCee--EEEeeceeEecC
Q psy4064 34 KLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEH--VTVVESLLLRVT 87 (624)
Q Consensus 34 gLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGev--VTVSEyaVRpVS 87 (624)
.+.+|..|.|++||++|+=|.|..+|....+|.|.|..-+.. |+|....|+++.
T Consensus 86 ~~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~l~~~~~~~~v~v~~~~l~~~~ 141 (145)
T TIGR00405 86 SIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIEAAVPIPVTVKGDQVRIIQ 141 (145)
T ss_pred ccCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEEEEEcCccceEEEeeeEEEEec
Confidence 488999999999999999999999999889999999999999 999988888775
No 8
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=96.70 E-value=0.0026 Score=55.95 Aligned_cols=46 Identities=20% Similarity=0.169 Sum_probs=41.4
Q ss_pred cceeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCeeEEEe
Q psy4064 33 AKLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEHVTVV 79 (624)
Q Consensus 33 LgLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGevVTVS 79 (624)
..+.+|.-|.|+.||++|+-|.|..+| ++.||.|.|.+=|+.+.|.
T Consensus 107 ~~~~~G~~V~V~~GPf~g~~g~v~~~~-~~~r~~v~l~~~gr~~~v~ 152 (159)
T TIGR01955 107 TLPYKGDKVRITDGAFAGFEAIFLEPD-GEKRSMLLLNMIGKQIKVS 152 (159)
T ss_pred cCCCCCCEEEEeccCCCCcEEEEEEEC-CCceEEEEEhhhCCceEEE
Confidence 568899999999999999999999999 6779999999999886654
No 9
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=96.41 E-value=0.005 Score=57.95 Aligned_cols=47 Identities=21% Similarity=0.330 Sum_probs=44.8
Q ss_pred cceeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCeeEEEe
Q psy4064 33 AKLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEHVTVV 79 (624)
Q Consensus 33 LgLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGevVTVS 79 (624)
..+.+|..|.|++|||+|.=|+|+-+|++.+++.|-|.+=|+.++|.
T Consensus 122 ~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~v~ifgr~tPVe 168 (178)
T COG0250 122 VDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVSIFGRPTPVE 168 (178)
T ss_pred ccCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEEEEEeCCceEEE
Confidence 68999999999999999999999999999999999999999998883
No 10
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=96.38 E-value=0.0043 Score=55.28 Aligned_cols=46 Identities=20% Similarity=0.142 Sum_probs=41.6
Q ss_pred cceeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCeeEEEe
Q psy4064 33 AKLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEHVTVV 79 (624)
Q Consensus 33 LgLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGevVTVS 79 (624)
..+.+|.-|.|+.||++|+-|.|+.+| +..|++|.|.+-|+.+.|.
T Consensus 108 ~~~~~G~~V~I~~Gp~~g~eg~v~~~~-~~~r~~v~v~~~gr~~~v~ 153 (162)
T PRK09014 108 ETPKPGDKVIITEGAFEGLQAIYTEPD-GEARSILLLNLLNKQVKHS 153 (162)
T ss_pred cCCCCCCEEEEecCCCCCcEEEEEEeC-CCeEEEEeehhhCCcEEEE
Confidence 357899999999999999999999999 7888999999999887664
No 11
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=96.23 E-value=0.0089 Score=59.98 Aligned_cols=47 Identities=26% Similarity=0.414 Sum_probs=43.8
Q ss_pred cceeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCeeEEEe
Q psy4064 33 AKLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEHVTVV 79 (624)
Q Consensus 33 LgLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGevVTVS 79 (624)
..+.+|..|.|++||+.|+-|.|+.+|++..||.|.|.|-|+.+.|.
T Consensus 204 ~~f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~VlV~IfGR~TpVe 250 (258)
T TIGR01956 204 SKFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEVEILGKSVDVD 250 (258)
T ss_pred cCCCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEEEEecCCcEEEE
Confidence 45889999999999999999999999999999999999999987764
No 12
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=95.85 E-value=0.0076 Score=39.54 Aligned_cols=27 Identities=22% Similarity=0.395 Sum_probs=24.6
Q ss_pred eeeCceEEEeccCCCCcccceeeecCC
Q psy4064 35 LVKNCCVKITGGMFKNNYGKLESFNED 61 (624)
Q Consensus 35 LkKGAfVkIVSGPHKGLYGKVEGLDpD 61 (624)
+.+|..|+|+.|||.|..|.|..+|.+
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~~ 28 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDGE 28 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcCC
Confidence 568999999999999999999999753
No 13
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=95.84 E-value=0.0097 Score=49.87 Aligned_cols=36 Identities=31% Similarity=0.336 Sum_probs=34.0
Q ss_pred cceeeCceEEEeccCCCCcccceeeecCCCceEEEE
Q psy4064 33 AKLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVK 68 (624)
Q Consensus 33 LgLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVR 68 (624)
+.|.+|.-|+|++|+++|.=|+|..+|+++.+|+|.
T Consensus 5 ~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve 40 (76)
T PRK12281 5 LKVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVE 40 (76)
T ss_pred ccccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 578999999999999999999999999999999885
No 14
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=95.80 E-value=0.01 Score=50.39 Aligned_cols=36 Identities=28% Similarity=0.322 Sum_probs=34.1
Q ss_pred cceeeCceEEEeccCCCCcccceeeecCCCceEEEE
Q psy4064 33 AKLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVK 68 (624)
Q Consensus 33 LgLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVR 68 (624)
+.|.+|..|+|++|+++|.=|+|..+|.++.+|+|.
T Consensus 7 ~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve 42 (83)
T CHL00141 7 MHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVK 42 (83)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 578999999999999999999999999999999884
No 15
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=95.36 E-value=0.017 Score=50.57 Aligned_cols=36 Identities=25% Similarity=0.292 Sum_probs=33.6
Q ss_pred cceeeCceEEEeccCCCCcccceeeecCCCceEEEE
Q psy4064 33 AKLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVK 68 (624)
Q Consensus 33 LgLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVR 68 (624)
..|.+|..|+|++|+++|.=|+|..+|+++.+|+|.
T Consensus 3 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 38 (105)
T PRK00004 3 MKIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVE 38 (105)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 358899999999999999999999999999999984
No 16
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=95.26 E-value=0.022 Score=51.88 Aligned_cols=36 Identities=31% Similarity=0.427 Sum_probs=34.0
Q ss_pred cceeeCceEEEeccCCCCcccceeeecCCCceEEEE
Q psy4064 33 AKLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVK 68 (624)
Q Consensus 33 LgLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVR 68 (624)
..|.+|..|+|++|+++|.=|+|..+|+...+|+|.
T Consensus 44 ~~IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~Ve 79 (120)
T PRK01191 44 LPVRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVE 79 (120)
T ss_pred ceEeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEe
Confidence 578899999999999999999999999999999985
No 17
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=94.66 E-value=0.035 Score=48.88 Aligned_cols=35 Identities=29% Similarity=0.370 Sum_probs=33.1
Q ss_pred ceeeCceEEEeccCCCCcccceeeecCCCceEEEE
Q psy4064 34 KLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVK 68 (624)
Q Consensus 34 gLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVR 68 (624)
.|++|..|+|++|+++|.=|+|..+|++..+|+|.
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve 37 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVE 37 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEC
Confidence 57899999999999999999999999999999984
No 18
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=94.62 E-value=0.041 Score=51.49 Aligned_cols=36 Identities=17% Similarity=0.186 Sum_probs=34.0
Q ss_pred cceeeCceEEEeccCCCCcccceeeecCCCceEEEE
Q psy4064 33 AKLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVK 68 (624)
Q Consensus 33 LgLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVR 68 (624)
..|++|.-|+|++|+++|.=|+|..+|+..++|+|.
T Consensus 45 ~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVE 80 (143)
T PTZ00194 45 MPVRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIE 80 (143)
T ss_pred ceeecCCEEEEecCCCCCCceEEEEEEcCCCEEEEe
Confidence 568999999999999999999999999999999985
No 19
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=93.77 E-value=0.075 Score=47.87 Aligned_cols=39 Identities=26% Similarity=0.273 Sum_probs=35.2
Q ss_pred cccceeeCceEEEeccCCCCcccceeeecCCCceEEEEE
Q psy4064 31 EEAKLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKL 69 (624)
Q Consensus 31 EeLgLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRL 69 (624)
+...|++|.-|+|++|+++|.=|+|..+|+...+|+|.=
T Consensus 38 r~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Veg 76 (114)
T TIGR01080 38 RALPVRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEG 76 (114)
T ss_pred ccceeecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcC
Confidence 346899999999999999999999999999999988853
No 20
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=89.59 E-value=0.43 Score=42.83 Aligned_cols=34 Identities=32% Similarity=0.315 Sum_probs=30.6
Q ss_pred cceeeCceEEEeccCCCCcccceeeecCCCceEEEE
Q psy4064 33 AKLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVK 68 (624)
Q Consensus 33 LgLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVR 68 (624)
+-+.+|..|+|++|+++|.-|+|..++|+. |+|.
T Consensus 3 ~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~--V~VE 36 (104)
T COG0198 3 MKVKKGDTVKVIAGKDKGKEGKVLKVLPKK--VVVE 36 (104)
T ss_pred cceecCCEEEEEecCCCCcceEEEEEecCe--EEEE
Confidence 458899999999999999999999999998 6654
No 21
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=86.79 E-value=0.92 Score=49.92 Aligned_cols=65 Identities=22% Similarity=0.324 Sum_probs=51.3
Q ss_pred eeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCeeEEEeeceeEecChHHHhhhhcccchhhHHHHHhh
Q psy4064 35 LVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEHVTVVESLLLRVTQSEYDKNSRVINMNKYEEYKEK 109 (624)
Q Consensus 35 LkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGevVTVSEyaVRpVSkKEYDKnSKdLNksKYEEYKkk 109 (624)
...|..|+|-.|+|+|+-|-|--+|.+++| |.|..++++|||.-.-|-..+.+- --.-|+|+-++
T Consensus 352 ~aigktVrIr~g~yKG~lGVVKdv~~~~ar--VeLhs~nK~VTI~K~~l~y~~reG--------e~ity~e~vnr 416 (607)
T COG5164 352 PAIGKTVRIRCGEYKGHLGVVKDVDRNIAR--VELHSNNKFVTIEKSRLAYLGREG--------EGITYDELVNR 416 (607)
T ss_pred cccCceEEEeecccccccceeeeccCceEE--EEEecCCceEEeehhheEEecccc--------cccchhhhhhh
Confidence 345999999999999999999999988876 689999999999887776554432 11448876544
No 22
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=86.51 E-value=1 Score=38.27 Aligned_cols=45 Identities=22% Similarity=0.398 Sum_probs=36.3
Q ss_pred cceeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCeeEEEeeceeE
Q psy4064 33 AKLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEHVTVVESLLL 84 (624)
Q Consensus 33 LgLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGevVTVSEyaVR 84 (624)
-.|++|.-|...+| +||+|..+|+|. |.|.+| .|-.++|+-.++.
T Consensus 36 ~~L~~Gd~VvT~gG----i~G~V~~i~d~~--v~vei~-~g~~i~~~r~aI~ 80 (84)
T TIGR00739 36 ESLKKGDKVLTIGG----IIGTVTKIAENT--IVIELN-DNTEITFSKNAIV 80 (84)
T ss_pred HhCCCCCEEEECCC----eEEEEEEEeCCE--EEEEEC-CCeEEEEEhHHhh
Confidence 47999999999875 899999999874 577877 4567888877764
No 23
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=85.33 E-value=1.6 Score=39.43 Aligned_cols=47 Identities=17% Similarity=0.114 Sum_probs=38.9
Q ss_pred cceeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCeeEEEeeceeEec
Q psy4064 33 AKLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEHVTVVESLLLRV 86 (624)
Q Consensus 33 LgLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGevVTVSEyaVRpV 86 (624)
-.|++|.-|...+| +||+|..+++| .|+|.+| .|-.++|.-.++..|
T Consensus 37 ~~Lk~GD~VvT~gG----i~G~V~~I~d~--~v~leia-~gv~i~~~r~AI~~v 83 (109)
T PRK05886 37 ESLQPGDRVHTTSG----LQATIVGITDD--TVDLEIA-PGVVTTWMKLAVRDR 83 (109)
T ss_pred HhcCCCCEEEECCC----eEEEEEEEeCC--EEEEEEC-CCeEEEEEhhheeee
Confidence 47999999998875 89999999864 6888887 467899999988844
No 24
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=84.85 E-value=1.4 Score=39.81 Aligned_cols=47 Identities=21% Similarity=0.342 Sum_probs=39.4
Q ss_pred ceeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCeeEEEeeceeEec
Q psy4064 34 KLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEHVTVVESLLLRV 86 (624)
Q Consensus 34 gLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGevVTVSEyaVRpV 86 (624)
.|++|.-|+..+| +||+|..+|+|+..|.|.. .|-.|+|.=.++.-|
T Consensus 36 sLk~GD~VvT~GG----i~G~V~~I~~~~~~v~le~--~gv~i~v~r~AI~~V 82 (113)
T PRK06531 36 AIQKGDEVVTIGG----LYGTVDEVDTEAKTIVLDV--DGVYLTFELAAIKRV 82 (113)
T ss_pred hcCCCCEEEECCC----cEEEEEEEecCCCEEEEEE--CCEEEEEEhhHhhhh
Confidence 7999999998875 8999999999988888885 678888887777644
No 25
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=80.93 E-value=2.1 Score=38.00 Aligned_cols=47 Identities=28% Similarity=0.384 Sum_probs=38.5
Q ss_pred cceeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCeeEEEeeceeEec
Q psy4064 33 AKLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEHVTVVESLLLRV 86 (624)
Q Consensus 33 LgLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGevVTVSEyaVRpV 86 (624)
-.|++|.-|...+| +||+|.++|+| .|+|.+|=| -.|+|.-.++.-|
T Consensus 51 ~~Lk~Gd~VvT~gG----i~G~Vv~i~~~--~v~lei~~g-~~i~~~r~aI~~v 97 (106)
T PRK05585 51 SSLAKGDEVVTNGG----IIGKVTKVSED--FVIIELNDD-TEIKIQKSAIAAV 97 (106)
T ss_pred HhcCCCCEEEECCC----eEEEEEEEeCC--EEEEEECCC-eEEEEEhHHhhhh
Confidence 48999999999875 89999999874 688888754 6888888877654
No 26
>KOG1999|consensus
Probab=77.83 E-value=2.8 Score=49.08 Aligned_cols=52 Identities=23% Similarity=0.158 Sum_probs=46.6
Q ss_pred eeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCeeEEEeeceeEecChH
Q psy4064 36 VKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEHVTVVESLLLRVTQS 89 (624)
Q Consensus 36 kKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGevVTVSEyaVRpVSkK 89 (624)
..|..|.|..|||+|..|-|.-+.+|++| |.|..++++|+|....+..|+.-
T Consensus 686 l~GktVrI~~Gp~KG~~GivkD~~~~~ar--VELhs~~~ti~vd~~~~~~v~~~ 737 (1024)
T KOG1999|consen 686 LLGKTVRIRLGPKKGYLGIVKDVNGDTAR--VELHSKCVTIKVDRLKRKIVGST 737 (1024)
T ss_pred hcCcEEEEecCCcccccceeEeccCCeeE--EEEEeccEEEEechhhceEEeec
Confidence 35889999999999999999999888875 68999999999999998888766
No 27
>PRK04333 50S ribosomal protein L14e; Validated
Probab=76.94 E-value=3 Score=35.96 Aligned_cols=33 Identities=15% Similarity=0.022 Sum_probs=28.7
Q ss_pred ceeeCceEEEeccCCCCcccceeeecCCCceEEE
Q psy4064 34 KLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVV 67 (624)
Q Consensus 34 gLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMV 67 (624)
.+.+|..|.+..|+++|.+.-|..+- |..||+|
T Consensus 3 ~v~~GrvV~~~~Grd~gk~~vIv~i~-d~~~vlV 35 (84)
T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDII-DKNFVLV 35 (84)
T ss_pred cccccEEEEEeccCCCCCEEEEEEEe-cCCEEEE
Confidence 46789999999999999999999985 4577888
No 28
>smart00719 Plus3 Short conserved domain in transcriptional regulators. Plus3 domains occur in the Saccharomyces cerevisiae Rtf1p protein, which interacts with Spt6p, and in parsley CIP, which interacts with the bZIP protein CPRF1.
Probab=74.20 E-value=6.5 Score=34.23 Aligned_cols=62 Identities=19% Similarity=0.267 Sum_probs=43.7
Q ss_pred ceeeCceEEEeccCCCC---cc--cceeeecCC---------CceEEEEEeeCC--eeEEEeeceeEecChHHHhhhh
Q psy4064 34 KLVKNCCVKITGGMFKN---NY--GKLESFNED---------SGRVVVKLALGD--EHVTVVESLLLRVTQSEYDKNS 95 (624)
Q Consensus 34 gLkKGAfVkIVSGPHKG---LY--GKVEGLDpD---------NgRVMVRLAIGG--evVTVSEyaVRpVSkKEYDKnS 95 (624)
....|+||.|--||+.. .| ++|.|+..- .--+.+.|+.|+ +.+.++...=.|+|++||++.-
T Consensus 28 ~~v~GcFVRv~ig~~~~~~~~Yrl~qI~gv~~~~k~Y~~~~~~t~~~L~v~~g~~~~~~~i~~iSn~~fte~E~~~w~ 105 (109)
T smart00719 28 SKVVGCFVRVKIGPNDQKQPIYRLVQVTGVKEADKPYELGGKTTNVLLEVLNGDSEKVVQINFISNQDFTEEEFQRWK 105 (109)
T ss_pred HhceEeEEEEEECCCCCCCCeEEEEEEeeEEecCcceecCCceeeEEEEEecCCceEEEEEEEecCCCCCHHHHHHHH
Confidence 46789999999998843 56 688888552 112455555565 4577777777899999988764
No 29
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=72.10 E-value=7.7 Score=29.65 Aligned_cols=53 Identities=15% Similarity=0.009 Sum_probs=43.6
Q ss_pred ceeeCceEEEeccCCCCcc-cceeeecCCCceEEEEEee--CCeeEEEeeceeEecC
Q psy4064 34 KLVKNCCVKITGGMFKNNY-GKLESFNEDSGRVVVKLAL--GDEHVTVVESLLLRVT 87 (624)
Q Consensus 34 gLkKGAfVkIVSGPHKGLY-GKVEGLDpDNgRVMVRLAI--GGevVTVSEyaVRpVS 87 (624)
.+.+|..|-+..=...+-| |+|..+++ +.+..|.+.- .+...+|....|||..
T Consensus 2 ~~~~G~~Ve~~~~~~~~W~~a~V~~~~~-~~~~~V~~~~~~~~~~e~v~~~~LRp~~ 57 (61)
T smart00743 2 DFKKGDRVEVFSKEEDSWWEAVVTKVLG-DGKYLVRYLTESEPLKETVDWSDLRPHP 57 (61)
T ss_pred CcCCCCEEEEEECCCCEEEEEEEEEECC-CCEEEEEECCCCcccEEEEeHHHcccCC
Confidence 4678999988864455566 89999988 5679999998 8889999999999875
No 30
>PF03126 Plus-3: Plus-3 domain; InterPro: IPR004343 The yeast Paf1 complex consists of Pfa1, Rtf1, Cdc73, Ctr9, and Leo1. The complex regulates histone H2B ubiquitination, histone H3 methylation, RNA polymerase II carboxy-terminal domain (CTD) Ser2 phosphorylation, and RNA 3' end processing. The conservation of Paf1 complex function in higher eukaryotes has been confirmed in human cells, Drosophila and Arabidopsis. The Plus3 domain spans the most conserved regions of the Rtf1 protein and is surrounded by regions of low complexity and coiled-coil propensity []. It contains only a limited number of highly conserved amino acids, among which are three positively charged residues that gave the Plus3 domain its name. The capacity to bind single-stranded DNA is at least one function of the Plus3 domain []. The plus-3 domain is about 90 residues in length and is often found associated with the GYF domain (IPR003169 from INTERPRO). The Plus3 domain structure consists of six alpha helices intervened by a sequence of six beta strands in a mixed alpha/beta topology. Beta strands 1, 2, 5, and 6 compose a four-stranded antiparallel beta sheet with a beta-hairpin insertion formed by strands 3 and 4. The N-terminal helices alpha1-alpha3 and C-terminal helix alpha6 pack together to form an alpha subdomain, while the beta strands and the small 3(10) helix alpha 4 form a beta subdomain. The two subdomains pack together to form a compact, globular protein [].; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent, 0016570 histone modification, 0005634 nucleus; PDB: 2BZE_A 3U1U_B 2DB9_A.
Probab=72.07 E-value=3.5 Score=35.34 Aligned_cols=64 Identities=14% Similarity=0.188 Sum_probs=41.0
Q ss_pred ceeeCceEEEeccCCCC------cccceeeecCCC---------ceEEEEEeeCC--eeEEEeeceeEecChHHHhhhhc
Q psy4064 34 KLVKNCCVKITGGMFKN------NYGKLESFNEDS---------GRVVVKLALGD--EHVTVVESLLLRVTQSEYDKNSR 96 (624)
Q Consensus 34 gLkKGAfVkIVSGPHKG------LYGKVEGLDpDN---------gRVMVRLAIGG--evVTVSEyaVRpVSkKEYDKnSK 96 (624)
..+.|+||.|.-|+... .-++|.|+.+.. --..+.|+.|+ +.+.++...=.|+|++||++.-.
T Consensus 24 ~~v~G~fVRv~ig~~~~~~~~~Yrl~qI~~v~~~~k~Y~~~~~~t~~~L~l~~g~~~r~~~i~~vSn~~~te~E~~~w~~ 103 (108)
T PF03126_consen 24 DAVVGCFVRVNIGPNDYTQNPVYRLCQIVGVKEGKKPYKLGSKKTNKYLVLRHGNSERDFPIDMVSNSPFTEEEFERWKQ 103 (108)
T ss_dssp HHHTT-EEEEEEETTSSS-E--EEEEEEEEEEEEEEEEEETTEEEEEEEEEEETTEEEEEEGGGBBSS---HHHHHHHHH
T ss_pred HheeEEEEEEEecCCCCCCceeEEEEEEEEEecccccEecCCeEEEEEEEEEECCceeEEEeEeeECCCCCHHHHHHHHH
Confidence 45689999999999854 336788887643 33567777776 34555666667888888777654
Q ss_pred c
Q psy4064 97 V 97 (624)
Q Consensus 97 d 97 (624)
.
T Consensus 104 ~ 104 (108)
T PF03126_consen 104 S 104 (108)
T ss_dssp H
T ss_pred H
Confidence 3
No 31
>PRK04313 30S ribosomal protein S4e; Validated
Probab=71.57 E-value=6 Score=39.86 Aligned_cols=54 Identities=17% Similarity=0.264 Sum_probs=44.0
Q ss_pred ccceeeCceEEEeccCCCCcccceeeecCCC----ceEEEEEeeCCeeEEEeeceeEe
Q psy4064 32 EAKLVKNCCVKITGGMFKNNYGKLESFNEDS----GRVVVKLALGDEHVTVVESLLLR 85 (624)
Q Consensus 32 eLgLkKGAfVkIVSGPHKGLYGKVEGLDpDN----gRVMVRLAIGGevVTVSEyaVRp 85 (624)
...+..|+.|.|+.|.|.|.-|+|..+...- ..|.|.-+-|++..|+.+|++..
T Consensus 169 ~i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~~G~~F~T~~~~vfvI 226 (237)
T PRK04313 169 HIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKDGEKFETILDYVFVI 226 (237)
T ss_pred EEecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcCCCCEEEEEeeeEEEE
Confidence 3678889999999999999999999997544 44677767777788888887653
No 32
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=69.26 E-value=5.3 Score=30.27 Aligned_cols=33 Identities=21% Similarity=0.224 Sum_probs=27.5
Q ss_pred CceEEEeccCCCCcccceeeecCCCceEEEEEeeC
Q psy4064 38 NCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALG 72 (624)
Q Consensus 38 GAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIG 72 (624)
|.-|.|.. +..-.-|.+.|+| ++|+++|+++-|
T Consensus 3 G~~V~v~~-~~~~~~G~~~gId-~~G~L~v~~~~g 35 (48)
T PF02237_consen 3 GQEVRVET-GDGEIEGIAEGID-DDGALLVRTEDG 35 (48)
T ss_dssp TSEEEEEE-TSCEEEEEEEEEE-TTSEEEEEETTE
T ss_pred CCEEEEEE-CCeEEEEEEEEEC-CCCEEEEEECCC
Confidence 66777777 7777899999998 678899999877
No 33
>PLN00036 40S ribosomal protein S4; Provisional
Probab=69.23 E-value=8.6 Score=39.30 Aligned_cols=55 Identities=22% Similarity=0.233 Sum_probs=44.6
Q ss_pred cccceeeCceEEEeccCCCCcccceeeecCC---CceEEEEEeeCCeeEEEeeceeEe
Q psy4064 31 EEAKLVKNCCVKITGGMFKNNYGKLESFNED---SGRVVVKLALGDEHVTVVESLLLR 85 (624)
Q Consensus 31 EeLgLkKGAfVkIVSGPHKGLYGKVEGLDpD---NgRVMVRLAIGGevVTVSEyaVRp 85 (624)
+...+..|+.|.|+.|.|.|.-|+|..+.-. -..|.|.-+-|+...|+.+|++..
T Consensus 171 ~~ikfe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d~~g~~F~T~~~~vfvI 228 (261)
T PLN00036 171 DFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVI 228 (261)
T ss_pred eEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEE
Confidence 3467888999999999999999999888722 125788888888899998887755
No 34
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=65.81 E-value=6.1 Score=35.08 Aligned_cols=46 Identities=22% Similarity=0.327 Sum_probs=37.4
Q ss_pred ceeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCeeEEEeeceeEec
Q psy4064 34 KLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEHVTVVESLLLRV 86 (624)
Q Consensus 34 gLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGevVTVSEyaVRpV 86 (624)
.|++|.-|+..+| ++|+|..+++|. +.|.|+ .|..++|.-.++..|
T Consensus 43 sL~kGD~VvT~gG----i~G~V~~v~d~~--v~I~l~-~~~~i~~~k~aI~~v 88 (97)
T COG1862 43 SLKKGDEVVTIGG----IVGTVTKVGDDT--VEIELG-DGTKIKFEKEAIATV 88 (97)
T ss_pred hccCCCEEEEcCC----eEEEEEEEecCc--EEEEEC-CCeEEEEEHHHHHhh
Confidence 7899999998875 789999999888 777777 677788876666543
No 35
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=65.71 E-value=9.7 Score=39.20 Aligned_cols=78 Identities=22% Similarity=0.212 Sum_probs=53.0
Q ss_pred ccceeeCceEEEeccCCCCcccceeeecCCC---ceEEEEEeeCCeeEEEeeceeEecCh--HHHh--hhhcccchhhHH
Q psy4064 32 EAKLVKNCCVKITGGMFKNNYGKLESFNEDS---GRVVVKLALGDEHVTVVESLLLRVTQ--SEYD--KNSRVINMNKYE 104 (624)
Q Consensus 32 eLgLkKGAfVkIVSGPHKGLYGKVEGLDpDN---gRVMVRLAIGGevVTVSEyaVRpVSk--KEYD--KnSKdLNksKYE 104 (624)
...+..|+.|.|+.|.|.|.-|+|..+.-.- ..|.|.-+-|+...|+..|++..=.. +-|- -..+-|-..-.|
T Consensus 169 ~ikfe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d~~g~~F~T~~~~VfvIG~~~~kp~IsLp~~kgi~~~~~e 248 (273)
T PTZ00223 169 LIKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRAANIFVIGKDMNSVPVTLPKQQGLRINVIQ 248 (273)
T ss_pred EEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEeCCCCCcceECcCCCCccccHHH
Confidence 3678889999999999999999999984332 35777778888888888877654221 1111 234445555555
Q ss_pred HHHhh
Q psy4064 105 EYKEK 109 (624)
Q Consensus 105 EYKkk 109 (624)
+..++
T Consensus 249 ~~~~~ 253 (273)
T PTZ00223 249 EREEK 253 (273)
T ss_pred HHHHH
Confidence 54333
No 36
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=63.32 E-value=13 Score=38.02 Aligned_cols=55 Identities=24% Similarity=0.219 Sum_probs=44.4
Q ss_pred cccceeeCceEEEeccCCCCcccceeeecCCC---ceEEEEEeeCCeeEEEeeceeEe
Q psy4064 31 EEAKLVKNCCVKITGGMFKNNYGKLESFNEDS---GRVVVKLALGDEHVTVVESLLLR 85 (624)
Q Consensus 31 EeLgLkKGAfVkIVSGPHKGLYGKVEGLDpDN---gRVMVRLAIGGevVTVSEyaVRp 85 (624)
+...+..|+.|.|+.|.|.|.-|+|....-.- ..|.|.-+-|+...|+.+|++..
T Consensus 171 ~~ikfe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~d~~g~~F~T~~~~vfvI 228 (262)
T PTZ00118 171 EFLKFEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKDSRGKTFATRLSNVFVI 228 (262)
T ss_pred eEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEEeCCCCeEEEEeeeEEEE
Confidence 34678889999999999999999998866322 35778888888899998887755
No 37
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=62.98 E-value=2.4 Score=35.61 Aligned_cols=45 Identities=31% Similarity=0.420 Sum_probs=0.5
Q ss_pred cceeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCeeEEEeeceeE
Q psy4064 33 AKLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEHVTVVESLLL 84 (624)
Q Consensus 33 LgLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGevVTVSEyaVR 84 (624)
..|++|.-|...+| +||+|..+|+| .|+|.+|- |-.++|.-.++.
T Consensus 35 ~~Lk~Gd~VvT~gG----i~G~V~~i~~~--~v~lei~~-g~~i~v~k~aI~ 79 (82)
T PF02699_consen 35 ASLKPGDEVVTIGG----IYGTVVEIDDD--TVVLEIAP-GVEITVEKSAIA 79 (82)
T ss_dssp G---------------------------------------------------
T ss_pred HcCCCCCEEEECCc----EEEEEEEEeCC--EEEEEECC-CeEEEEEHHHhH
Confidence 47999999999875 89999999655 46788887 467777766654
No 38
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=51.24 E-value=26 Score=32.91 Aligned_cols=35 Identities=17% Similarity=0.009 Sum_probs=30.5
Q ss_pred eeeCceEEEeccCCCCcccceeeecCCCceEEEEEe
Q psy4064 35 LVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLA 70 (624)
Q Consensus 35 LkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLA 70 (624)
+.+|..|+|..||+.|.-+.|.-+ -|..||+|-=.
T Consensus 8 VEiGRVvli~~Gp~~GKL~vIVDI-ID~nRvLVDGP 42 (130)
T PTZ00065 8 VEPGRLCLIQYGPDAGKLCFIVDI-VTPTRVLVDGA 42 (130)
T ss_pred eeeceEEEEecCCCCCCEEEEEEE-EcCCeEEEeCC
Confidence 568999999999999999998888 47788998766
No 39
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=48.39 E-value=43 Score=24.81 Aligned_cols=53 Identities=9% Similarity=-0.142 Sum_probs=39.4
Q ss_pred ceeeCceEEEeccCC-CCcccceeeecCCCceEEEEEeeCCeeEEEeeceeEecCh
Q psy4064 34 KLVKNCCVKITGGMF-KNNYGKLESFNEDSGRVVVKLALGDEHVTVVESLLLRVTQ 88 (624)
Q Consensus 34 gLkKGAfVkIVSGPH-KGLYGKVEGLDpDNgRVMVRLAIGGevVTVSEyaVRpVSk 88 (624)
.+++|..|.+.- .. .=.-|+|++++++ ..+.|.+-=-|...+|....|+++..
T Consensus 2 ~~~~G~~~~a~~-~d~~wyra~I~~~~~~-~~~~V~f~D~G~~~~v~~~~l~~l~~ 55 (57)
T smart00333 2 TFKVGDKVAARW-EDGEWYRARIIKVDGE-QLYEVFFIDYGNEEVVPPSDLRPLPE 55 (57)
T ss_pred CCCCCCEEEEEe-CCCCEEEEEEEEECCC-CEEEEEEECCCccEEEeHHHeecCCC
Confidence 356787777775 32 2233899999988 77899887767788999888888754
No 40
>PF04717 Phage_base_V: Phage-related baseplate assembly protein; InterPro: IPR006531 This domain occurs in a family of phage (and bacteriocin) proteins related to the phage P2 V gene product, which forms the small spike at the tip of the tail []. Homologs in general are annotated as baseplate assembly protein V. At least one member is encoded within a region of Pectobacterium carotovorum (Erwinia carotovora) described as a bacteriocin, a phage tail-derived module able to kill bacteria closely related to the host strain. It is also found in Vgr-related proteins. Genes encoding type VI secretion systems (T6SS) are widely distributed in pathogenic Gram-negative bacterial species. In Vibrio cholerae, T6SS have been found to secrete three related proteins extracellularly, VgrG-1, VgrG-2, and VgrG-3. VgrG-1 can covalently cross-link actin in vitro, and this activity was used to demonstrate that V. cholerae can translocate VgrG-1 into macrophages by a T6SS-dependent mechanism. VgrG-related proteins likely assemble into a trimeric complex that is analogous to that formed by the two trimeric proteins gp27 and gp5 that make up the baseplate "tail spike" of Escherichia coli bacteriophage T4. The VgrG components of the T6SS apparatus might assemble a "cell-puncturing device" analogous to phage tail spikes to deliver effector protein domains through membranes of target host cells []. Gp5 is an integral component of the virion baseplate of bacteriophage T4. T4 Gp5 consists of 3 domains connected via long linkers: the N-terminal oligosaccharide/oligonucleotide-binding (OB)-fold domain, the middle lysozyme domain, and the C-terminal triplestranded-helix. The equivalent of the Gp5 OB-fold domain in the structure of VgrG is the domain of unknown function comprising residues 380-470 and conserved in all known VgrGs. This entry represents the OB-fold domain which consists of a 5-stranded antiparallel-barrel with a Greek-key topology [].; PDB: 3AQJ_C 3QR8_A 2P5Z_X.
Probab=44.47 E-value=33 Score=27.64 Aligned_cols=33 Identities=24% Similarity=0.347 Sum_probs=22.1
Q ss_pred cceeeecCCCceEEEEEeeCCeeEEEeeceeEe
Q psy4064 53 GKLESFNEDSGRVVVKLALGDEHVTVVESLLLR 85 (624)
Q Consensus 53 GKVEGLDpDNgRVMVRLAIGGevVTVSEyaVRp 85 (624)
|.|..+|++++||-|+|...+..+|.=-..+.+
T Consensus 1 G~V~~v~~~~grvrV~~~~~~~~~s~Wl~~~~~ 33 (79)
T PF04717_consen 1 GTVTAVDPDKGRVRVRFPDDGDIVSDWLPVLQP 33 (79)
T ss_dssp EEEEEEETTTTEEEEE-B-CTTEEEEEEEE--S
T ss_pred CeEEEEECCCCEEEEEEecCCCccceEEEeeeh
Confidence 789999999999999996555565544444443
No 41
>PRK06955 biotin--protein ligase; Provisional
Probab=40.28 E-value=52 Score=32.92 Aligned_cols=51 Identities=10% Similarity=0.127 Sum_probs=36.6
Q ss_pred ceeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCeeEEEeeceeEe
Q psy4064 34 KLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEHVTVVESLLLR 85 (624)
Q Consensus 34 gLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGevVTVSEyaVRp 85 (624)
.+..|.-|.|..+.-.-+-|.+.||| ++|+++|++.=|-+.+..-|..+++
T Consensus 245 ~~~~g~~V~v~~~~~~~~~G~~~gId-~~G~L~v~~~~g~~~~~sGeV~~~~ 295 (300)
T PRK06955 245 HAYAGREVVLLEDGAELARGVAHGID-ETGQLLLDTPAGRQAIAAGDVSLRE 295 (300)
T ss_pred hhcCCCeEEEEECCCcEEEEEEeeEC-CCceEEEEeCCCeEEEEEEEEEEec
Confidence 45679999987653334689999999 6678999977665556666655554
No 42
>KOG2985|consensus
Probab=39.87 E-value=30 Score=36.19 Aligned_cols=13 Identities=46% Similarity=0.590 Sum_probs=6.9
Q ss_pred HhhhhhcccCCCC
Q psy4064 333 KSRKNKKRHHSSS 345 (624)
Q Consensus 333 ~~~~~~~~~~~~~ 345 (624)
.-||.++|.-..+
T Consensus 178 s~rKkkkRrrd~S 190 (306)
T KOG2985|consen 178 SVRKKKKRRRDES 190 (306)
T ss_pred chhhhhhhccccc
Confidence 3456666654433
No 43
>PRK08330 biotin--protein ligase; Provisional
Probab=38.22 E-value=67 Score=30.73 Aligned_cols=49 Identities=22% Similarity=0.196 Sum_probs=32.9
Q ss_pred eeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCe-eEEEeeceeE
Q psy4064 35 LVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDE-HVTVVESLLL 84 (624)
Q Consensus 35 LkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGe-vVTVSEyaVR 84 (624)
+..|.-|.|..+...-..|.+.|+| ++|.++|+++-|.. .+..-|-.++
T Consensus 185 ~~~g~~v~~~~~~~~~~~G~~~gI~-~~G~L~v~~~~g~~~~~~~gev~~~ 234 (236)
T PRK08330 185 MILGKRVKIIGDGEILVEGIAEDID-EFGALILRLDDGTVKKVLYGDVSLR 234 (236)
T ss_pred HhcCCeEEEEECCcEEEEEEEEEEC-CCCEEEEEECCCCEEEEEEEEEEEe
Confidence 4568888887654221249999998 66889999995542 4444454444
No 44
>KOG1999|consensus
Probab=37.21 E-value=45 Score=39.75 Aligned_cols=46 Identities=17% Similarity=0.251 Sum_probs=33.5
Q ss_pred ceeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCeeEEEeec
Q psy4064 34 KLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEHVTVVES 81 (624)
Q Consensus 34 gLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGevVTVSEy 81 (624)
-+.+|.+|+|++|+|.|-=|-|.-|+.. .|||---+..+.++|.-.
T Consensus 459 yF~~GDhVKVi~G~~eG~tGlVvrVe~~--~vi~~Sd~t~eel~Vf~~ 504 (1024)
T KOG1999|consen 459 YFEPGDHVKVIAGRYEGDTGLVVRVEQG--DVILLSDLTMEELKVFAR 504 (1024)
T ss_pred hccCCCeEEEEeccccCCcceEEEEeCC--eEEEEecCccceeeEEeh
Confidence 4677999999999999999999999654 444444444444554433
No 45
>PF13861 FLgD_tudor: FlgD Tudor-like domain; PDB: 3OSV_A 3C12_A.
Probab=34.96 E-value=31 Score=27.13 Aligned_cols=31 Identities=23% Similarity=0.314 Sum_probs=25.0
Q ss_pred CcccceeeecCCCceEEEEEeeCCeeEEEee
Q psy4064 50 NNYGKLESFNEDSGRVVVKLALGDEHVTVVE 80 (624)
Q Consensus 50 GLYGKVEGLDpDNgRVMVRLAIGGevVTVSE 80 (624)
-.+|+|+|++-+++.+++.|.=++..|+++.
T Consensus 26 ~~~g~V~sV~~~~g~~~L~l~~~~~~v~l~~ 56 (61)
T PF13861_consen 26 LVSGRVESVTFSGGGPMLNLGGGGSTVPLSD 56 (61)
T ss_dssp EEEEEEEEEEEETTEEEEEETTTCEEEECCC
T ss_pred EEEEEEEEEEEcCCeEEEEEecCCcEEEHHH
Confidence 4689999999999999888866666677654
No 46
>KOG1708|consensus
Probab=34.48 E-value=48 Score=33.83 Aligned_cols=61 Identities=20% Similarity=0.122 Sum_probs=46.9
Q ss_pred CccccceeeCceEEEeccCCCCcccceeeecCCCceEEEEE-------------eeCCeeEEEeece-----eEecChH
Q psy4064 29 NPEEAKLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKL-------------ALGDEHVTVVESL-----LLRVTQS 89 (624)
Q Consensus 29 EEEeLgLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRL-------------AIGGevVTVSEya-----VRpVSkK 89 (624)
-+++-.+..|..|.|+.|.-+|.-|.|.-+=.+++-|||.= -.-|.+|..-..+ |++|+..
T Consensus 67 ~d~dw~ff~GDtVeVlvGkDkGkqG~Vtqv~r~~s~VvV~gln~k~r~~gsekeg~pgtivk~EaPlhvsk~VmLvdp~ 145 (236)
T KOG1708|consen 67 IDEDWHFFFGDTVEVLVGKDKGKQGEVTQVIRHRSWVVVKGLNTKYRHMGSEKEGEPGTIVKSEAPLHVSKQVMLVDPE 145 (236)
T ss_pred cccceeEecCCEEEEEecccCCccceEEEEeecCceEEEcccchhhhhhcccccCCCceEEeecCCceecceeEEECcc
Confidence 34566888999999999999999999999999999999952 2334455544444 7777654
No 47
>PF11595 DUF3245: Protein of unknown function (DUF3245); InterPro: IPR021641 This is a family of proteins conserved in fungi. The function is not known, and there is no S. cerevisiae member.
Probab=32.78 E-value=21 Score=34.03 Aligned_cols=16 Identities=50% Similarity=0.727 Sum_probs=11.8
Q ss_pred CCCCCCCCcCCCCCCc
Q psy4064 3 VTLRPKGLGLGADKSA 18 (624)
Q Consensus 3 p~LRPKGLGLGADrt~ 18 (624)
+..||-.|||||-...
T Consensus 43 ~~~~P~rLGLGA~ip~ 58 (149)
T PF11595_consen 43 FTARPERLGLGAPIPQ 58 (149)
T ss_pred cccCCccccCCCcCch
Confidence 3567999999987543
No 48
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=31.10 E-value=68 Score=32.98 Aligned_cols=55 Identities=20% Similarity=0.279 Sum_probs=42.5
Q ss_pred cccceeeCceEEEeccCCCCcccceeeecCCC----ceEEEEEeeCCeeEEEeeceeEe
Q psy4064 31 EEAKLVKNCCVKITGGMFKNNYGKLESFNEDS----GRVVVKLALGDEHVTVVESLLLR 85 (624)
Q Consensus 31 EeLgLkKGAfVkIVSGPHKGLYGKVEGLDpDN----gRVMVRLAIGGevVTVSEyaVRp 85 (624)
+.+.+.+|+.|.|+.|.|.|.-|+|-.+.--- .-|.|.=+.|+...|+..|++..
T Consensus 170 ~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~~~g~~F~T~~~yVfvI 228 (241)
T COG1471 170 EHIKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVEDEEGNTFQTIKDYVFVI 228 (241)
T ss_pred eEeccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEecCCCCceEEeeeEEEEE
Confidence 44788899999999999999999998775431 22566666777888888887643
No 49
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=30.46 E-value=97 Score=31.09 Aligned_cols=38 Identities=18% Similarity=0.124 Sum_probs=30.6
Q ss_pred ceeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCC
Q psy4064 34 KLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGD 73 (624)
Q Consensus 34 gLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGG 73 (624)
.+..|..|.|..|. .-..|.+.||| ++|+++|++.-|+
T Consensus 233 ~~~~g~~V~v~~~~-~~~~G~~~gId-~~G~L~i~~~~G~ 270 (285)
T PTZ00275 233 LLYKDKKVLIDQDN-ELIVGYLQGLL-HDGSLLLLREKNK 270 (285)
T ss_pred hccCCCEEEEEeCC-CEEEEEEEEEC-CCCeEEEEeCCCC
Confidence 34569999998764 56899999999 6678999988776
No 50
>PF08536 Whirly: Whirly transcription factor; InterPro: IPR013742 This is a family of plant transcription factors. ; PDB: 3R9Y_A 3N1I_A 3N1K_A 3RA0_A 3N1H_A 3N1J_A 3N1L_A 3R9Z_A 1L3A_D.
Probab=26.90 E-value=45 Score=31.82 Aligned_cols=58 Identities=16% Similarity=0.166 Sum_probs=37.6
Q ss_pred eeeCceEEEeccCCCC-----cccc---eeeecCCCceEEEEEeeCCeeEEEeeceeEecChHHHhh
Q psy4064 35 LVKNCCVKITGGMFKN-----NYGK---LESFNEDSGRVVVKLALGDEHVTVVESLLLRVTQSEYDK 93 (624)
Q Consensus 35 LkKGAfVkIVSGPHKG-----LYGK---VEGLDpDNgRVMVRLAIGGevVTVSEyaVRpVSkKEYDK 93 (624)
|....-+-+..-|++| .-.| |+-+ ||-+-.++.|++-+....+.|.+-.|||..||.-
T Consensus 68 l~~~~s~effHdP~~~~s~~G~v~K~Lkv~p~-~dgsg~f~~Lsv~~~~~~~~~~~~ipVt~aEfav 133 (139)
T PF08536_consen 68 LGARESCEFFHDPNMGSSNEGKVRKSLKVEPL-PDGSGYFFNLSVQNKLLNGDENFSIPVTKAEFAV 133 (139)
T ss_dssp --TT--EEEEE-TTTTSTTTTSEEEEEEEEE--TTSSEEEEEEEEEECCCTEEEEEEEEEEHHHHHH
T ss_pred hccCCceEEEeccccCCCCCCceEEEEEeEEC-CCCCceEEEEEEecccccccceEEEechHHHHHH
Confidence 4444445555555543 2223 4555 3544689999999998999999999999999863
No 51
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=26.81 E-value=1.3e+02 Score=27.01 Aligned_cols=65 Identities=12% Similarity=0.099 Sum_probs=47.6
Q ss_pred ccceeeCceEEEeccCCCCcc--cceeee----cCCCceEEEEEeeCCeeEEEeeceeEecChHHHhhhhcc
Q psy4064 32 EAKLVKNCCVKITGGMFKNNY--GKLESF----NEDSGRVVVKLALGDEHVTVVESLLLRVTQSEYDKNSRV 97 (624)
Q Consensus 32 eLgLkKGAfVkIVSGPHKGLY--GKVEGL----DpDNgRVMVRLAIGGevVTVSEyaVRpVSkKEYDKnSKd 97 (624)
...|.+|.+|+...=|....| |+|.+. -.....++|.+- +|+.+.|--..+..++..-|++-+.-
T Consensus 53 ~~~L~~GD~VLA~~~~~~~~Y~Pg~V~~~~~~~~~~~~~~~V~f~-ng~~~~vp~~~~~~I~~~~y~~~v~~ 123 (124)
T PF15057_consen 53 RHSLQVGDKVLAPWEPDDCRYGPGTVIAGPERRASEDKEYTVRFY-NGKTAKVPRGEVIWISPSYYERAVEY 123 (124)
T ss_pred cCcCCCCCEEEEecCcCCCEEeCEEEEECccccccCCceEEEEEE-CCCCCccchhhEEECCHHHHHHHHhh
Confidence 346788999998876666667 577752 224444777765 55589999999999999999887643
No 52
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=26.30 E-value=1.5e+02 Score=29.91 Aligned_cols=57 Identities=18% Similarity=-0.034 Sum_probs=40.5
Q ss_pred cceeeCceEEEec-cCCCCcccceeeecCCCceEEEEEeeCCeeEEEeeceeEecChH
Q psy4064 33 AKLVKNCCVKITG-GMFKNNYGKLESFNEDSGRVVVKLALGDEHVTVVESLLLRVTQS 89 (624)
Q Consensus 33 LgLkKGAfVkIVS-GPHKGLYGKVEGLDpDNgRVMVRLAIGGevVTVSEyaVRpVSkK 89 (624)
..|++|..|..+= +--.-.-++|++||++++.++|++.-=|....|.-.-|+|.+..
T Consensus 67 ~~WkvGd~C~A~~s~Dg~~Y~A~I~~i~~~~~~~~V~f~gYgn~e~v~l~dL~~~~~~ 124 (264)
T PF06003_consen 67 KKWKVGDKCMAVYSEDGQYYPATIESIDEEDGTCVVVFTGYGNEEEVNLSDLKPSEGD 124 (264)
T ss_dssp T---TT-EEEEE-TTTSSEEEEEEEEEETTTTEEEEEETTTTEEEEEEGGGEEETT--
T ss_pred cCCCCCCEEEEEECCCCCEEEEEEEEEcCCCCEEEEEEcccCCeEeeehhhhcccccc
Confidence 5899999998872 12122448999999999999999988888888888888998876
No 53
>PF10500 SR-25: Nuclear RNA-splicing-associated protein; InterPro: IPR019532 SR-25, otherwise known as ADP-ribosylation factor-like factor 6-interacting protein 4, is expressed in virtually all tissue types. At the N terminus there is a repeat of serine-arginine (SR repeat), and towards the middle of the protein there are clusters of both serines and of basic amino acids. The presence of many nuclear localisation signals strongly implies that this is a nuclear protein that may contribute to RNA splicing []. SR-25 is also implicated, along with heat-shock-protein-27, as a mediator in the Rac1 (GTPase ras-related C3 botulinum toxin substrate 1; also see IPR019093 from INTERPRO) signalling pathway [].
Probab=26.26 E-value=46 Score=33.88 Aligned_cols=7 Identities=43% Similarity=0.781 Sum_probs=2.9
Q ss_pred CchHHHh
Q psy4064 481 SSSEYEK 487 (624)
Q Consensus 481 ~~~~~~~ 487 (624)
.-.||++
T Consensus 161 TkEEyea 167 (225)
T PF10500_consen 161 TKEEYEA 167 (225)
T ss_pred CHHHHHH
Confidence 3344443
No 54
>PF12568 DUF3749: Acetyltransferase (GNAT) domain; InterPro: IPR024612 This domain is found in uncharacterised proteins from Gammaproteobacteria, and is approximately 40 amino acids in length. It contains two completely conserved residues (D and I) that may be functionally important. Proteins having this domain are frequently annotated as acetyltransferases of the GNAT family; however there is little accompanying annotation to confirm this.; PDB: 2K5T_A.
Probab=24.82 E-value=68 Score=30.10 Aligned_cols=28 Identities=18% Similarity=0.377 Sum_probs=21.9
Q ss_pred CceEE--EEEeeCCeeEEEeeceeEecChH
Q psy4064 62 SGRVV--VKLALGDEHVTVVESLLLRVTQS 89 (624)
Q Consensus 62 NgRVM--VRLAIGGevVTVSEyaVRpVSkK 89 (624)
|.|++ |++.+.++.-.++..|||+||.-
T Consensus 46 NdRlLgAv~v~~~~~~~~L~~l~VRevTRr 75 (128)
T PF12568_consen 46 NDRLLGAVKVTISGQQAELSDLCVREVTRR 75 (128)
T ss_dssp TTEEEEEEEEEEETTEEEEEEEEE-TT-SS
T ss_pred chheeeeEEEEEcCcceEEeeEEEeecccc
Confidence 66665 78888899999999999999964
No 55
>PF04351 PilP: Pilus assembly protein, PilP; InterPro: IPR007446 The PilP family are periplasmic proteins involved in the biogenesis of type IV pili [].; PDB: 2Y4Y_B 2Y4X_A 2IVW_A 2LC4_A.
Probab=23.69 E-value=1.1e+02 Score=28.05 Aligned_cols=35 Identities=23% Similarity=0.401 Sum_probs=26.6
Q ss_pred CceEEEeccCCCCc-ccceeeecCCCceEEEEEeeCC
Q psy4064 38 NCCVKITGGMFKNN-YGKLESFNEDSGRVVVKLALGD 73 (624)
Q Consensus 38 GAfVkIVSGPHKGL-YGKVEGLDpDNgRVMVRLAIGG 73 (624)
|....|--|-|-|+ ||+|+.|+++.. .|+.+...+
T Consensus 100 g~v~~V~~G~yiG~n~G~I~~Is~~~I-~l~E~v~d~ 135 (149)
T PF04351_consen 100 GKVYRVKVGDYIGQNYGRITSISEDSI-ELVEIVPDG 135 (149)
T ss_dssp TEEEEEETTEEETTTTEEEEEEETTEE-EEEEEEE-S
T ss_pred CCEEEecCCCEeccCCCEEEEEeCCeE-EEEEEcccC
Confidence 77788888999888 999999998777 444554433
No 56
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=23.00 E-value=89 Score=29.13 Aligned_cols=29 Identities=21% Similarity=0.227 Sum_probs=26.2
Q ss_pred ceeeCceEEEeccCCCCcccceeeecCCC
Q psy4064 34 KLVKNCCVKITGGMFKNNYGKLESFNEDS 62 (624)
Q Consensus 34 gLkKGAfVkIVSGPHKGLYGKVEGLDpDN 62 (624)
-+.+|.-|+|+.|.+.|...-|..+=+||
T Consensus 4 ~l~~GrVvvv~~GR~aGkk~VIv~~iDd~ 32 (125)
T COG2163 4 SLEVGRVVVVTAGRFAGKKVVIVKIIDDN 32 (125)
T ss_pred cccCCeEEEEecceeCCceEEEEEEccCC
Confidence 36789999999999999999998887788
No 57
>PRK07165 F0F1 ATP synthase subunit alpha; Validated
Probab=22.77 E-value=1.1e+02 Score=33.98 Aligned_cols=62 Identities=15% Similarity=0.241 Sum_probs=46.5
Q ss_pred ceeeCceEEEeccCCCCcccceeeecCCCceEEE-----EEeeCCeeEEEeeceeEecChHHHhhhhcccch
Q psy4064 34 KLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVV-----KLALGDEHVTVVESLLLRVTQSEYDKNSRVINM 100 (624)
Q Consensus 34 gLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMV-----RLAIGGevVTVSEyaVRpVSkKEYDKnSKdLNk 100 (624)
....|..|.|-.|+ +.+|.|.++++|++-||+ -|+.|..+....+.+-.||+..= .+++||-
T Consensus 20 ~~~~ge~~~~~~~~--~~~g~V~~~~~~~v~~~~l~~~~gi~~G~~V~~tg~~~~vpvg~~l---LGRVvd~ 86 (507)
T PRK07165 20 DYQQNQFFTLKNNP--NVKAFVISATEDKAYLLINNEKGKIKINDELIELNNTNKVKTSKEY---FGKIIDI 86 (507)
T ss_pred CCCcCCEEEECCCC--eEEEEEEEEeCCeEEEEEccCccCCCCCCEEEECCCccEEECCccc---cCCEECC
Confidence 45567778875454 389999999999998887 46778888888888888888764 4555554
No 58
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=22.31 E-value=1.6e+02 Score=32.82 Aligned_cols=55 Identities=15% Similarity=0.041 Sum_probs=39.6
Q ss_pred ceeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCeeEEEeeceeEecChH
Q psy4064 34 KLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEHVTVVESLLLRVTQS 89 (624)
Q Consensus 34 gLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGevVTVSEyaVRpVSkK 89 (624)
.+..|..|.|+.....-..|.+.|||+ +|.++|+..=|.+.+.--|..+++...+
T Consensus 274 ~~~~gk~V~v~~~~~~~~~Gi~~GId~-~G~L~l~~~~g~~~~~sGEVslr~~~~~ 328 (592)
T PRK13325 274 NRDHGKAVLLLRDGETVFEGTVKGVDG-QGVLHLETAEGKQTVVSGEISLRSDDRP 328 (592)
T ss_pred hccCCCeEEEEeCCCcEEEEEEEEECC-CCEEEEEECCCeEEEEEEeEEEeecCCc
Confidence 345699999875444558999999995 6789999876656666667777655433
No 59
>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Probab=21.45 E-value=1.2e+02 Score=32.66 Aligned_cols=62 Identities=21% Similarity=0.101 Sum_probs=45.9
Q ss_pred eeCceEEEeccCCCCcccceeeecCCCceEEE-----EEeeCCeeEEEeeceeEecChHHHhhhhcccch
Q psy4064 36 VKNCCVKITGGMFKNNYGKLESFNEDSGRVVV-----KLALGDEHVTVVESLLLRVTQSEYDKNSRVINM 100 (624)
Q Consensus 36 kKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMV-----RLAIGGevVTVSEyaVRpVSkKEYDKnSKdLNk 100 (624)
..|.+|.|..+--..++|.|.+|++|++++|+ -|.+|..++...+.+..||+..= .+++||-
T Consensus 21 ~~ge~~~i~~~~~~~~~~eVv~~~~~~v~l~~~~~~~gi~~G~~V~~tg~~~~i~vg~~l---LGRViD~ 87 (418)
T TIGR03498 21 RLGDRCAIRARDGRPVLAEVVGFNGDRVLLMPFEPLEGVGLGCAVFAREGPLAVRPHPSW---LGRVINA 87 (418)
T ss_pred CCCCEEEEEcCCCCEEEEEEEEEcCCeEEEEEccCCcCCCCCCEEEECCCccEEEeChhh---cCCEECC
Confidence 57888988431111379999999999998887 57778888888899999999643 3555544
No 60
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=20.79 E-value=98 Score=34.95 Aligned_cols=74 Identities=12% Similarity=0.049 Sum_probs=49.3
Q ss_pred ceeeCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCeeEE-------------EeeceeEecChHHHhhhhcccch
Q psy4064 34 KLVKNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEHVT-------------VVESLLLRVTQSEYDKNSRVINM 100 (624)
Q Consensus 34 gLkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGevVT-------------VSEyaVRpVSkKEYDKnSKdLNk 100 (624)
++.+|.+|+|+.|.|++--|.|-.+|.+-+..|-.--...-+|+ -++|.|.-+= +=|.++.-||++
T Consensus 139 ~f~~gD~vkVI~g~~~~d~g~V~rI~~~~vtF~s~~~~~e~tI~sr~l~ks~~tta~ss~Y~lhd~V-~l~~~~vaci~s 217 (607)
T COG5164 139 GFYKGDLVKVIEGGEMVDIGTVPRIDGEKVTFNSENFKSESTIKSRGLSKSIDTTATSSIYKLHDYV-DLFLEKVACINS 217 (607)
T ss_pred ccccCCeEEEeccccccccceEEEecCceeEEccccccccceEEeccccccccccchhhhhhhhhhh-hhhhcceeEEee
Confidence 56679999999999999999999999887755543333333332 1333322111 123456789999
Q ss_pred hhHHHHHh
Q psy4064 101 NKYEEYKE 108 (624)
Q Consensus 101 sKYEEYKk 108 (624)
..+|-||-
T Consensus 218 id~Dv~kv 225 (607)
T COG5164 218 IDFDVEKV 225 (607)
T ss_pred cccchhhh
Confidence 99888663
No 61
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=20.75 E-value=1.7e+02 Score=23.58 Aligned_cols=38 Identities=21% Similarity=0.303 Sum_probs=28.9
Q ss_pred eeCceEEE---eccCCCCcccceeeecCCCceEEEEEeeCC
Q psy4064 36 VKNCCVKI---TGGMFKNNYGKLESFNEDSGRVVVKLALGD 73 (624)
Q Consensus 36 kKGAfVkI---VSGPHKGLYGKVEGLDpDNgRVMVRLAIGG 73 (624)
..+..|.| ..|-+..+.|.|..+|+.+..++|.-+-++
T Consensus 40 ~~~~~v~ity~~~g~~~~~~G~I~~id~~~~~l~~~~~~~~ 80 (92)
T PF08863_consen 40 QENQPVTITYYEDGYYQSVTGTIHKIDEINRTLKLKDEDGE 80 (92)
T ss_pred cCCCEEEEEEEECCeeEEEEEEEEEEcCCCCEEEEEeCCCC
Confidence 33444443 468889999999999999999988886533
No 62
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=20.32 E-value=1.5e+02 Score=28.09 Aligned_cols=44 Identities=11% Similarity=-0.025 Sum_probs=32.8
Q ss_pred eCceEEEeccCCCCcccceeeecCCCceEEEEEeeCCeeEEEeec
Q psy4064 37 KNCCVKITGGMFKNNYGKLESFNEDSGRVVVKLALGDEHVTVVES 81 (624)
Q Consensus 37 KGAfVkIVSGPHKGLYGKVEGLDpDNgRVMVRLAIGGevVTVSEy 81 (624)
.|..|.+..+.=....|.|+++--.++ .++.+.++|..|.++..
T Consensus 91 VGk~V~~~~~~g~~~tG~V~~V~~~~g-~~~~~~v~G~~~~ls~i 134 (142)
T PRK09618 91 IGKEVEWEGEDGEIVSGTVTSVKQKDG-DYPLVLDNGTWIVADNV 134 (142)
T ss_pred hCCEEEEEeCCCCEEEEEEEEEEEcCC-cEEEEEECCEEEeccce
Confidence 388888876665678999999986666 44456689988888653
No 63
>PRK05922 type III secretion system ATPase; Validated
Probab=20.11 E-value=1.4e+02 Score=32.51 Aligned_cols=56 Identities=13% Similarity=0.095 Sum_probs=44.0
Q ss_pred eeeCceEEEeccCCCCcccceeeecCCCceEEE-----EEeeCCeeEEEeeceeEecChHH
Q psy4064 35 LVKNCCVKITGGMFKNNYGKLESFNEDSGRVVV-----KLALGDEHVTVVESLLLRVTQSE 90 (624)
Q Consensus 35 LkKGAfVkIVSGPHKGLYGKVEGLDpDNgRVMV-----RLAIGGevVTVSEyaVRpVSkKE 90 (624)
...|..|.|..+...++.|.|.+|+.|.+.+|+ -|++|..++...+.+-.||...=
T Consensus 38 ~~~ge~~~i~~~~~~~~~~eVv~~~~~~~~l~~~~~~~gi~~G~~V~~~~~~~~v~vg~~l 98 (434)
T PRK05922 38 ACLGELCQISLSKSPPILAEVIGFHNRTTLLMSLSPIHYVALGAEVLPLRRPPSLHLSDHL 98 (434)
T ss_pred CCCCCEEEEecCCCCeeEEEEEEEeCCeEEEEEccCCCCCCCCCEEEeCCCCcEEEcChhh
Confidence 446888888643334589999999999998887 57778888888888888888763
Done!