Query gi|254780980|ref|YP_003065393.1| hypothetical protein CLIBASIA_04405 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 121
No_of_seqs 2 out of 4
Neff 1.4
Searched_HMMs 39220
Date Mon May 30 03:14:15 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780980.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01010 BexC_CtrB_KpsE polys 90.5 0.55 1.4E-05 27.4 4.7 57 53-109 165-224 (364)
2 PTZ00208 65 kDa invariant surf 55.8 20 0.0005 18.0 4.6 43 42-84 109-151 (436)
3 PRK10824 hypothetical protein; 50.1 7.3 0.00019 20.6 1.0 26 18-49 81-106 (115)
4 PRK01558 V-type ATP synthase s 47.3 27 0.00068 17.2 8.2 84 29-112 6-98 (198)
5 KOG2008 consensus 44.0 30 0.00077 16.9 3.9 26 57-82 125-150 (426)
6 pfam12575 DUF3753 Protein of u 39.4 25 0.00064 17.3 2.4 28 86-113 8-35 (72)
7 COG3370 Uncharacterized protei 34.2 32 0.00081 16.7 2.3 44 4-47 17-64 (113)
8 COG3445 Acid-induced glycyl ra 30.1 17 0.00043 18.4 0.3 19 81-99 10-28 (127)
9 PRK01326 prsA foldase protein 29.7 49 0.0013 15.6 2.6 37 1-37 1-49 (310)
10 COG3937 Uncharacterized conser 28.5 54 0.0014 15.3 5.0 50 26-75 17-66 (108)
11 COG4010 Uncharacterized protei 27.4 56 0.0014 15.2 2.8 36 25-70 51-86 (170)
12 COG1291 MotA Flagellar motor c 26.8 58 0.0015 15.1 4.4 37 5-44 181-217 (266)
13 TIGR01579 MiaB-like-C MiaB-lik 25.8 39 0.00099 16.2 1.6 56 16-73 363-440 (492)
14 KOG4108 consensus 25.5 61 0.0015 15.0 5.3 55 44-98 89-152 (174)
15 COG3629 DnrI DNA-binding trans 24.5 58 0.0015 15.1 2.2 37 79-117 39-75 (280)
16 TIGR00308 TRM1 N2,N2-dimethylg 23.7 66 0.0017 14.8 2.6 36 83-120 383-418 (462)
17 PRK08124 flagellar motor prote 23.7 66 0.0017 14.8 5.7 19 7-25 183-201 (263)
18 TIGR02878 spore_ypjB sporulati 22.8 62 0.0016 15.0 2.1 23 32-56 5-27 (234)
19 COG1753 Predicted antotoxin, c 22.2 71 0.0018 14.6 2.5 36 70-105 28-63 (74)
20 pfam06932 DUF1283 Protein of u 21.5 73 0.0019 14.5 4.8 83 5-93 10-93 (109)
21 TIGR02982 heterocyst_DevA ABC 20.8 45 0.0012 15.8 1.1 80 12-94 44-143 (220)
No 1
>TIGR01010 BexC_CtrB_KpsE polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family; InterPro: IPR005705 This family contains gamma proteobacterial proteins involved in ATP-dependent capsule polysaccharide export , .; GO: 0015542 sugar efflux transmembrane transporter activity, 0006859 extracellular carbohydrate transport, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=90.47 E-value=0.55 Score=27.43 Aligned_cols=57 Identities=23% Similarity=0.349 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-HCCCHHHHHHHHHCCCCCHHHH--HHHHHHHHH
Q ss_conf 88889999999999999999865443-0678999999983668010345--443478754
Q gi|254780980|r 53 THRLAQERVEAAEKRVKEVEERATAS-RKLSVDELANAFWDLSDEDKNA--FTGNVKQEV 109 (121)
Q Consensus 53 ~HrLAqE~VE~A~kRVKE~EE~a~A~-r~L~~DeL~~~F~~L~~e~k~~--F~~~vk~~v 109 (121)
.||.++|.|.-||+.||+|+++-++. ..|+-=--.|-..|+.+|-.+. .+-+++.+.
T Consensus 165 ~~R~~~d~~~FaE~~V~~A~~~l~~~~~~L~~yq~~n~~~Dp~~qs~a~~~Lis~l~~eL 224 (364)
T TIGR01010 165 NERARKDTIAFAEEEVKEAEQRLNATKAELLKYQIKNKVLDPKAQSEAQLSLISTLEGEL 224 (364)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 899999999999999999999899999999998985478780789999999999798669
No 2
>PTZ00208 65 kDa invariant surface glycoprotein; Provisional
Probab=55.79 E-value=20 Score=17.99 Aligned_cols=43 Identities=28% Similarity=0.287 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH
Q ss_conf 9998647789988889999999999999999865443067899
Q gi|254780980|r 42 MIKEANFKISETHRLAQERVEAAEKRVKEVEERATASRKLSVD 84 (121)
Q Consensus 42 MiKEA~~~i~E~HrLAqE~VE~A~kRVKE~EE~a~A~r~L~~D 84 (121)
..+.|+-++.+----|+.+.|.|+++-.+|-+-+.-.||-+.|
T Consensus 109 I~~kAKd~i~kqlpeAkk~geea~k~~~~Vk~AAk~ArG~~ld 151 (436)
T PTZ00208 109 IFEKAKDGIAKQLPEAKKAGEEAEKLHQEVKKAAKNARGWRLD 151 (436)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf 9999876675417377888999999999999999861277766
No 3
>PRK10824 hypothetical protein; Provisional
Probab=50.10 E-value=7.3 Score=20.60 Aligned_cols=26 Identities=46% Similarity=0.839 Sum_probs=14.1
Q ss_pred HHHHHHEEECCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 74101112030467876545678999986477
Q gi|254780980|r 18 IGGCDIVIGRTEDLLNKLQKNSTQMIKEANFK 49 (121)
Q Consensus 18 I~GC~iVigrtEDllNklqknS~~MiKEA~~~ 49 (121)
||||||+. .+...=+ -..+++||.-+
T Consensus 81 IGG~DI~~----em~~~Ge--L~~ll~ea~~k 106 (115)
T PRK10824 81 VGGCDIVI----EMYQRGE--LQQLIKETAAK 106 (115)
T ss_pred ECCHHHHH----HHHHCCC--HHHHHHHHHCC
T ss_conf 64089999----9997787--99999996223
No 4
>PRK01558 V-type ATP synthase subunit E; Provisional
Probab=47.31 E-value=27 Score=17.17 Aligned_cols=84 Identities=29% Similarity=0.349 Sum_probs=55.6
Q ss_pred HHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHCCCHHHHHHHHHCC----CCCHHH
Q ss_conf 4678765456789-99986477899888899999999999----99999865443067899999998366----801034
Q gi|254780980|r 29 EDLLNKLQKNSTQ-MIKEANFKISETHRLAQERVEAAEKR----VKEVEERATASRKLSVDELANAFWDL----SDEDKN 99 (121)
Q Consensus 29 EDllNklqknS~~-MiKEA~~~i~E~HrLAqE~VE~A~kR----VKE~EE~a~A~r~L~~DeL~~~F~~L----~~e~k~ 99 (121)
.+|++||.+...- --.||.-=|++++.=|++-|++|++. ++++++.+..-++-+.++|.-|.-|+ -++=.+
T Consensus 6 q~Lidki~~eGVekg~~eA~~IIa~A~~~A~~Iv~~Ae~eAe~i~~~AekeA~~~k~~~~~aL~~A~rd~ll~lk~~i~~ 85 (198)
T PRK01558 6 KDLINKIKKDGLEEAERLANEIILNAKEEAEAIVLKAEEEAKELKAKAEKEANDYKRHSLEASRQAIRDLIIGFEKNLKS 85 (198)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999987889999999999999999999999999999999999999899999967999999999999999999999
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 5443478754321
Q gi|254780980|r 100 AFTGNVKQEVCKV 112 (121)
Q Consensus 100 ~F~~~vk~~vckv 112 (121)
-|++.++..|-++
T Consensus 86 ~~~~~v~~~v~~~ 98 (198)
T PRK01558 86 LFKAALKDEVAEV 98 (198)
T ss_pred HHHHHHHHHHHHH
T ss_conf 9999999999986
No 5
>KOG2008 consensus
Probab=44.04 E-value=30 Score=16.86 Aligned_cols=26 Identities=31% Similarity=0.322 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 99999999999999998654430678
Q gi|254780980|r 57 AQERVEAAEKRVKEVEERATASRKLS 82 (121)
Q Consensus 57 AqE~VE~A~kRVKE~EE~a~A~r~L~ 82 (121)
-+|-.+++-|||+|+|+.-++.-.+.
T Consensus 125 ~~evlnh~~qrV~EaE~e~t~aE~~H 150 (426)
T KOG2008 125 WQEVLNHATQRVMEAEQEKTRAELVH 150 (426)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999999987778899877
No 6
>pfam12575 DUF3753 Protein of unknown function (DUF3753). This family of proteins is found in viruses. Proteins in this family are approximately 70 amino acids in length. There is a conserved YLK sequence motif. There are two completely conserved residues (D and F) that may be functionally important.
Probab=39.35 E-value=25 Score=17.33 Aligned_cols=28 Identities=29% Similarity=0.360 Sum_probs=22.1
Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHHHE
Q ss_conf 9999836680103454434787543210
Q gi|254780980|r 86 LANAFWDLSDEDKNAFTGNVKQEVCKVK 113 (121)
Q Consensus 86 L~~~F~~L~~e~k~~F~~~vk~~vckvk 113 (121)
+...||..+|+|.+-|++.|++-.-.-+
T Consensus 8 ifGvFlss~ddDfe~Fi~vV~sVltdk~ 35 (72)
T pfam12575 8 IFGVFLSSSDDDFENFINVVKSVLTDKK 35 (72)
T ss_pred HHHHHCCCCHHHHHHHHHHHHHHHCCCC
T ss_conf 8866506876679999999999975996
No 7
>COG3370 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.15 E-value=32 Score=16.72 Aligned_cols=44 Identities=27% Similarity=0.338 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHHHHHHH----HEEECCHHHHHHHHHHHHHHHHHHH
Q ss_conf 6777888999999974101----1120304678765456789999864
Q gi|254780980|r 4 KILMTSAFSTTLLTIGGCD----IVIGRTEDLLNKLQKNSTQMIKEAN 47 (121)
Q Consensus 4 K~Lm~S~~~TT~lTI~GC~----iVigrtEDllNklqknS~~MiKEA~ 47 (121)
|-+.+-.|.+-..--+--+ |..|+.|++|-+.+++++.|+-++.
T Consensus 17 K~~~al~fA~ns~knk~~~dVelifFGpse~~la~~~~~~l~~l~~~~ 64 (113)
T COG3370 17 KALTALNFAYNSVKNKWFEDVELIFFGPSEKLLAKNDGDSLKMLQELR 64 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHCEEEEEECCHHHHHHHCCHHHHHHHHHHH
T ss_conf 999999999999875234126899977259999825467999999999
No 8
>COG3445 Acid-induced glycyl radical enzyme [General function prediction only]
Probab=30.11 E-value=17 Score=18.36 Aligned_cols=19 Identities=37% Similarity=0.683 Sum_probs=14.7
Q ss_pred CCHHHHHHHHHCCCCCHHH
Q ss_conf 7899999998366801034
Q gi|254780980|r 81 LSVDELANAFWDLSDEDKN 99 (121)
Q Consensus 81 L~~DeL~~~F~~L~~e~k~ 99 (121)
-.-|+|.|.||-|||+...
T Consensus 10 aand~llnsfwlldsek~e 28 (127)
T COG3445 10 AANDDLLNSFWLLDSEKGE 28 (127)
T ss_pred CCCHHHHHHEEEECCCCCC
T ss_conf 2337565321432056671
No 9
>PRK01326 prsA foldase protein PrsA; Reviewed
Probab=29.71 E-value=49 Score=15.55 Aligned_cols=37 Identities=22% Similarity=0.513 Sum_probs=25.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHH-------HEE--E---CCHHHHHHHHH
Q ss_conf 9146777888999999974101-------112--0---30467876545
Q gi|254780980|r 1 MKAKILMTSAFSTTLLTIGGCD-------IVI--G---RTEDLLNKLQK 37 (121)
Q Consensus 1 MkAK~Lm~S~~~TT~lTI~GC~-------iVi--g---rtEDllNklqk 37 (121)
||-|+++..+.....++..||+ ++- | .-+|+.+.+-.
T Consensus 1 MKKKl~~~~~~~~svl~LaaCs~~~~~~~vat~kgg~IT~~e~Y~~~K~ 49 (310)
T PRK01326 1 MKKKLIAGAVTLLSVATLAACSKTNDNTKVISMKGDTITVSDFYNEVKN 49 (310)
T ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCEEHHHHHHHHHC
T ss_conf 9088999999999999998716999880689824993429999999846
No 10
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=28.49 E-value=54 Score=15.33 Aligned_cols=50 Identities=22% Similarity=0.399 Sum_probs=41.9
Q ss_pred ECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 03046787654567899998647789988889999999999999999865
Q gi|254780980|r 26 GRTEDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEERA 75 (121)
Q Consensus 26 grtEDllNklqknS~~MiKEA~~~i~E~HrLAqE~VE~A~kRVKE~EE~a 75 (121)
|-+--+-++.+|-+-.|||..++---|+.++-++-+.++..--.+.++..
T Consensus 17 G~~a~~~ek~~klvDelVkkGeln~eEak~~vddl~~q~k~~~~e~e~K~ 66 (108)
T COG3937 17 GLAAETAEKVQKLVDELVKKGELNAEEAKRFVDDLLRQAKEAQGELEEKI 66 (108)
T ss_pred CHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 38999999999999999982787899999999999999898760277763
No 11
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.37 E-value=56 Score=15.21 Aligned_cols=36 Identities=28% Similarity=0.383 Sum_probs=24.5
Q ss_pred EECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 2030467876545678999986477899888899999999999999
Q gi|254780980|r 25 IGRTEDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKE 70 (121)
Q Consensus 25 igrtEDllNklqknS~~MiKEA~~~i~E~HrLAqE~VE~A~kRVKE 70 (121)
.++.+|.||++| ++-+++.|+|-- +++|+--.+.+-
T Consensus 51 L~~~~~~Ln~~Q--------~~L~~lcet~~~--~l~e~~~~~~~~ 86 (170)
T COG4010 51 LKRINDMLNSIQ--------EELLELCETVSS--DLPEQWIEKLKR 86 (170)
T ss_pred HHHHHHHHHHHH--------HHHHHHHHCCCH--HHHHHHHHHHHH
T ss_conf 999999999999--------999999843723--326889999999
No 12
>COG1291 MotA Flagellar motor component [Cell motility and secretion]
Probab=26.81 E-value=58 Score=15.15 Aligned_cols=37 Identities=32% Similarity=0.335 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHHHHHHEEECCHHHHHHHHHHHHHHHH
Q ss_conf 7778889999999741011120304678765456789999
Q gi|254780980|r 5 ILMTSAFSTTLLTIGGCDIVIGRTEDLLNKLQKNSTQMIK 44 (121)
Q Consensus 5 ~Lm~S~~~TT~lTI~GC~iVigrtEDllNklqknS~~MiK 44 (121)
..++.||++|++-|..|-.+++. +-|||++.+..-++
T Consensus 181 ~~iA~Alv~T~~Gi~~ay~~~~P---~a~kLk~~~~~e~~ 217 (266)
T COG1291 181 ALIAAALVGTLYGIFLAYGLFGP---LANKLKQKSDEEVK 217 (266)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHH
T ss_conf 89999999999999999897868---89999888899999
No 13
>TIGR01579 MiaB-like-C MiaB-like tRNA modifying enzyme; InterPro: IPR006467 This clade of sequences is closely related to MiaB, a modifier of isopentenylated adenosine-37 of certain eukaryotic and bacterial tRNAs (see IPR006463 from INTERPRO). Sequence alignments suggest that these sequences perform the same chemical transformation as MiaB, perhaps on a different (or differently modified) tRNA base substrate. This clade represents a subfamily that spans low GC Gram-positive bacteria, alpha and epsilon proteobacteria, Campylobacter, Porphyromonas, Aquifex, Thermotoga, Chlamydia, Treponema and Fusobacterium , , ..
Probab=25.80 E-value=39 Score=16.18 Aligned_cols=56 Identities=18% Similarity=0.254 Sum_probs=37.7
Q ss_pred HHHHHHHHEEEC-CHHHHHHHHHHHHHHHHHH-------------------HHHH--HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 997410111203-0467876545678999986-------------------4778--99888899999999999999998
Q gi|254780980|r 16 LTIGGCDIVIGR-TEDLLNKLQKNSTQMIKEA-------------------NFKI--SETHRLAQERVEAAEKRVKEVEE 73 (121)
Q Consensus 16 lTI~GC~iVigr-tEDllNklqknS~~MiKEA-------------------~~~i--~E~HrLAqE~VE~A~kRVKE~EE 73 (121)
..-.|||+..|- ||+ .....+|++|+|+- +|+- -=-.+.++||+..-.+-.+.+..
T Consensus 363 ~~~~gtD~IVGFP~E~--eedFq~t~~~~~~~~~~~~HiFpyS~R~~T~A~~m~~rf~v~~~~~KeR~~~L~~~~~~~~~ 440 (492)
T TIGR01579 363 DYAFGTDVIVGFPGES--EEDFQETLRIVKEIEFSGLHIFPYSARPGTPASAMDDRFKVPETIKKERVKRLKELAEKVYQ 440 (492)
T ss_pred CCCCCCCEEEECCCCC--HHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 6303760374088898--89999999998526602133542688432812047874427611588999999999888889
No 14
>KOG4108 consensus
Probab=25.53 E-value=61 Score=15.00 Aligned_cols=55 Identities=22% Similarity=0.291 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHCCCHHHHHHHHHCCCCCHH
Q ss_conf 98647789988889999999999999999865---------44306789999999836680103
Q gi|254780980|r 44 KEANFKISETHRLAQERVEAAEKRVKEVEERA---------TASRKLSVDELANAFWDLSDEDK 98 (121)
Q Consensus 44 KEA~~~i~E~HrLAqE~VE~A~kRVKE~EE~a---------~A~r~L~~DeL~~~F~~L~~e~k 98 (121)
+++++.-.|+-+|++|--|.-+.|||+---.- --..|-|+---.|.+||-+..+-
T Consensus 89 ~~~~Y~~~~a~~lt~elae~I~~rvK~l~~~RYK~Vv~V~ige~~gqGv~~~sr~lWD~~~D~~ 152 (174)
T KOG4108 89 ADAEYDPDEALQLTKELAEEIKDRVKELGYPRYKYVVQVMIGEQLGQGVYIASRCLWDEDRDGF 152 (174)
T ss_pred HHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEHHHHCCHHHHHHHHHHCCCCCCC
T ss_conf 3520698999999999999999999751897547899988766646507887776402466874
No 15
>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]
Probab=24.49 E-value=58 Score=15.12 Aligned_cols=37 Identities=22% Similarity=0.479 Sum_probs=23.6
Q ss_pred HCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHEEEEC
Q ss_conf 067899999998366801034544347875432102211
Q gi|254780980|r 79 RKLSVDELANAFWDLSDEDKNAFTGNVKQEVCKVKKITV 117 (121)
Q Consensus 79 r~L~~DeL~~~F~~L~~e~k~~F~~~vk~~vckvkkitv 117 (121)
+-+|.|.++.+||.-+++.-+. .|+.+-+++.+|+.-
T Consensus 39 ~~vsRe~l~~llWe~~~~~~Ar--~nLR~~l~~lRk~l~ 75 (280)
T COG3629 39 KPVSREKLAGLLWEDSDPSRAR--ANLRTTLHNLRKLLG 75 (280)
T ss_pred CCCCHHHHHHHCCCCCCHHHHH--HHHHHHHHHHHHHCC
T ss_conf 8625999997635889826789--899999999997348
No 16
>TIGR00308 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase; InterPro: IPR002905 This enzyme 2.1.1.32 from EC uses S-adenosyl-L-methionine to methylate tRNA: S-AdoMet + tRNA = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs . The enzyme is found in both eukaryotes and archaea .; GO: 0003723 RNA binding, 0004809 tRNA (guanine-N2-)-methyltransferase activity, 0008033 tRNA processing.
Probab=23.69 E-value=66 Score=14.79 Aligned_cols=36 Identities=28% Similarity=0.309 Sum_probs=24.5
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHEEEECCCC
Q ss_conf 99999998366801034544347875432102211799
Q gi|254780980|r 83 VDELANAFWDLSDEDKNAFTGNVKQEVCKVKKITVPPS 120 (121)
Q Consensus 83 ~DeL~~~F~~L~~e~k~~F~~~vk~~vckvkkitvpps 120 (121)
+-.+.+..-+=.+.++-+|-+. +++|++-+++|||-
T Consensus 383 v~~~L~~~~~E~~~~~vg~Y~~--~~ia~~~~~~~PPl 418 (462)
T TIGR00308 383 VLKLLEKIKDELSIPPVGYYDL--HEIAKVLKLSVPPL 418 (462)
T ss_pred HHHHHHHHHHHHCCCCCCCCCH--HHHHHHHCCCCCCH
T ss_conf 9999999887505887354377--88988843789988
No 17
>PRK08124 flagellar motor protein MotA; Validated
Probab=23.67 E-value=66 Score=14.79 Aligned_cols=19 Identities=32% Similarity=0.343 Sum_probs=8.7
Q ss_pred HHHHHHHHHHHHHHHHHEE
Q ss_conf 7888999999974101112
Q gi|254780980|r 7 MTSAFSTTLLTIGGCDIVI 25 (121)
Q Consensus 7 m~S~~~TT~lTI~GC~iVi 25 (121)
|+-||+||+.-+.-|.++.
T Consensus 183 mA~ALvtT~yGvllAn~~~ 201 (263)
T PRK08124 183 ISAAFVATLLGIFTGYVLW 201 (263)
T ss_pred HHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999999999999
No 18
>TIGR02878 spore_ypjB sporulation protein YpjB; InterPro: IPR014231 Proteins in thie entry, typified by YpjB, are restricted to a subset of the endospore-forming bacteria which includes Bacillus species, but not species. In Bacillus subtilis, ypjB was found to be part of the sigma-E regulon . Sigma-E is a sporulation sigma factor that regulates expression in the mother cell compartment. Null mutants of ypjB show a sporulation defect, but this gene is not, however, a part of the endospore formation minimal gene set..
Probab=22.76 E-value=62 Score=14.97 Aligned_cols=23 Identities=26% Similarity=0.582 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8765456789999864778998888
Q gi|254780980|r 32 LNKLQKNSTQMIKEANFKISETHRL 56 (121)
Q Consensus 32 lNklqknS~~MiKEA~~~i~E~HrL 56 (121)
||.+-..++||+|+++++ |+-++
T Consensus 5 Ln~~sD~vLqL~K~~~~E--eA~qv 27 (234)
T TIGR02878 5 LNDLSDQVLQLVKQEKYE--EAKQV 27 (234)
T ss_pred HHHHHHHHHHHHHHHHHH--HHHHH
T ss_conf 555789999999855579--99999
No 19
>COG1753 Predicted antotoxin, copG family [Signal transduction mechanisms]
Probab=22.21 E-value=71 Score=14.61 Aligned_cols=36 Identities=19% Similarity=0.270 Sum_probs=23.3
Q ss_pred HHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf 999865443067899999998366801034544347
Q gi|254780980|r 70 EVEERATASRKLSVDELANAFWDLSDEDKNAFTGNV 105 (121)
Q Consensus 70 E~EE~a~A~r~L~~DeL~~~F~~L~~e~k~~F~~~v 105 (121)
+|-.+-..+|+-..|-|.+|||.+|+++---++--.
T Consensus 28 dvI~~l~~kKr~~levl~~~~g~~s~eEvek~~~e~ 63 (74)
T COG1753 28 DVIRELIEKKRGNLEVLMRAFGTLSEEEVEKIKKEE 63 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 999999987520089999990798688999999998
No 20
>pfam06932 DUF1283 Protein of unknown function (DUF1283). This family consists of several hypothetical proteins of around 115 residues in length which seem to be specific to Enterobacteria. The function of the family is unknown.
Probab=21.52 E-value=73 Score=14.53 Aligned_cols=83 Identities=24% Similarity=0.363 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHHHHH-HHHHEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH
Q ss_conf 777888999999974-1011120304678765456789999864778998888999999999999999986544306789
Q gi|254780980|r 5 ILMTSAFSTTLLTIG-GCDIVIGRTEDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEERATASRKLSV 83 (121)
Q Consensus 5 ~Lm~S~~~TT~lTI~-GC~iVigrtEDllNklqknS~~MiKEA~~~i~E~HrLAqE~VE~A~kRVKE~EE~a~A~r~L~~ 83 (121)
.|+..+..++++.-+ -|-+|||-..+-+.|- --||-|| .--++|.|-+.--..+||....++---.++-+---
T Consensus 10 Ll~~~awq~~a~a~~sT~~~v~~~gd~~lske---~Arq~kE---qW~~tr~LR~KVN~R~EKefDK~D~A~D~~d~C~~ 83 (109)
T pfam06932 10 LLLLLAWQTTALAQASTCVLVIESGDSAQSRE---AARQSKE---QWNDTRSLRNKVNKRAEKEFDKADKAFDARDKCNK 83 (109)
T ss_pred HHHHHHHHHHHHHCCCEEEEEECCCCCHHHHH---HHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999842135432664478507996330399---9998798---68788999999868887620378876505877762
Q ss_pred HHHHHHHHCC
Q ss_conf 9999998366
Q gi|254780980|r 84 DELANAFWDL 93 (121)
Q Consensus 84 DeL~~~F~~L 93 (121)
..-+|++|.-
T Consensus 84 S~N~NAYWEp 93 (109)
T pfam06932 84 SANVNAYWEP 93 (109)
T ss_pred CCCCCEEECC
T ss_conf 1564002368
No 21
>TIGR02982 heterocyst_DevA ABC exporter ATP-binding subunit, DevA family; InterPro: IPR014324 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry represents the ATP-binding subunit DevA, found mostly in the Cyanobacteria, but also in the Planctomycetes. Cyanobacterial examples are involved in heterocyst formation, by which some fraction of members of the colony undergo a developmental change and become capable of nitrogen fixation. The ABC transporter encoded by the devBCA operon is induced by nitrogen deficiency and is necessary for the formation of the laminated layer which envelops heterocysts , . It is thought to be involved in the export of either the heterocyst-specific glycolipids found in the laminated layer, or an enzyme essential for their formation..
Probab=20.82 E-value=45 Score=15.79 Aligned_cols=80 Identities=26% Similarity=0.319 Sum_probs=38.4
Q ss_pred HHHHHHHHHHH-------H-EEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHH-----HHHHHHHHH
Q ss_conf 99999974101-------1-1203046787654567899998647789988889-----9999999-----999999998
Q gi|254780980|r 12 STTLLTIGGCD-------I-VIGRTEDLLNKLQKNSTQMIKEANFKISETHRLA-----QERVEAA-----EKRVKEVEE 73 (121)
Q Consensus 12 ~TT~lTI~GC~-------i-VigrtEDllNklqknS~~MiKEA~~~i~E~HrLA-----qE~VE~A-----~kRVKE~EE 73 (121)
-||+||.+||= + |.|. -|+...++.+.-|.-.-=-|--+|-|- ..-|.-| +-.-+|..+
T Consensus 44 KTTLLtLiG~LR~~Q~G~L~vlg~---~L~ga~~~~l~~~RR~iGyIFQ~HNLl~~LTA~QNVqM~~eL~~~~~~~~~~~ 120 (220)
T TIGR02982 44 KTTLLTLIGGLRSVQEGSLKVLGQ---ELKGASKKELVQVRRNIGYIFQAHNLLGFLTARQNVQMALELQPNLSAQEARE 120 (220)
T ss_pred HHHHHHHHHHHCCCCCCEEEEECC---HHCCCCHHHHHHHHHHCCCEECCCHHCHHHHHHHHHHHHHHHHHHCCHHHHHH
T ss_conf 688999887625655560478220---10267888999998763914412000100017788864898876116889999
Q ss_pred HHHHH-HCCCHHHHHHHHH-CCC
Q ss_conf 65443-0678999999983-668
Q gi|254780980|r 74 RATAS-RKLSVDELANAFW-DLS 94 (121)
Q Consensus 74 ~a~A~-r~L~~DeL~~~F~-~L~ 94 (121)
+|.+- ...|+.+-.+|+- |||
T Consensus 121 ~a~~~L~~VGL~~~~~y~P~~LS 143 (220)
T TIGR02982 121 KARAMLEAVGLGDRLDYYPENLS 143 (220)
T ss_pred HHHHHHHHHCHHHHHHHCCCCCC
T ss_conf 99999986060125540524367
Done!