RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780916|ref|YP_003065329.1| putative sigma-54-dependent
transcription regulator protein [Candidatus Liberibacter asiaticus
str. psy62]
(482 letters)
>gnl|CDD|32386 COG2204, AtoC, Response regulator containing CheY-like receiver,
AAA-type ATPase, and DNA-binding domains [Signal
transduction mechanisms].
Length = 464
Score = 274 bits (702), Expect = 4e-74
Identities = 136/482 (28%), Positives = 230/482 (47%), Gaps = 37/482 (7%)
Query: 11 KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKE 68
R+L++D D + ++++ +E GY+V ++ L +S+ +++ L + D
Sbjct: 5 ARILVVDDDPDIRELLEQALELAGYEVVTAESAEEALEALSESPFDLVLLDIRMPGMDGL 64
Query: 69 NILKNIVDKIPIVPIIVQTTQDNIKI----LNCFLYNRISKFF----LNLVSRKQLCDSI 120
+LK I + P +P+IV T +I L ++ + K F L + + L
Sbjct: 65 ELLKEIKSRDPDLPVIVMTGHGDIDTAVEALRLGAFDFLEKPFDLDRLLAIVERAL---E 121
Query: 121 ICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
+ L+ S + L+ SPAM Q+ L K ++I GE G GK+ ++
Sbjct: 122 LRELQRENRRSLKRAKSLGGELVGESPAMQQLRRLIAKVAPSDASVLITGESGTGKELVA 181
Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVD-LQTKNSAQFLGKFIEANGGTIVL 239
R IH++ RA PF VNC I ++ +E LFG T + +G+F +ANGGT+ L
Sbjct: 182 RAIHQASPRAKGPFIAVNCAAIPENLLESELFGHEKGAFTGAITRRIGRFEQANGGTLFL 241
Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
+E +PL +Q ++ ++ + E I++DVR+I T ++L +V + FR+DLY
Sbjct: 242 DEIGEMPLELQVKLLRVLQEREFERVGGNKPIKVDVRIIAATNRDLEEEVAAGRFREDLY 301
Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
YR++V + + LR R EDIP L FL+ F + S +AL+ L Y W NV+
Sbjct: 302 YRLNVVPLRLPPLRERKEDIPLLAEHFLKRFAAELGRPPKGFSPEALAALLAYDWPGNVR 361
Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS 419
EL+N++ RAVI + + + L + + L +
Sbjct: 362 ELENVVERAVILSEGPEIEVEDLPLEIL---------------------APAAEALAGPA 400
Query: 420 QESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
E+ L+++E+++I A++ SE A RLGI R TLYRK++EY I+
Sbjct: 401 GEAALPG--LPLGEALAEVERQLILQALERTGGNKSEAAERLGISRKTLYRKLKEYGIDR 458
Query: 480 DS 481
Sbjct: 459 SD 460
>gnl|CDD|33622 COG3829, RocR, Transcriptional regulator containing PAS, AAA-type
ATPase, and DNA-binding domains [Transcription / Signal
transduction mechanisms].
Length = 560
Score = 213 bits (544), Expect = 9e-56
Identities = 110/343 (32%), Positives = 169/343 (49%), Gaps = 29/343 (8%)
Query: 139 LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVN 198
D +I SPAM++V++LA++ ++I GE G GK+ +R IH RA PF +N
Sbjct: 244 FDDIIGESPAMLRVLELAKRIAKTDSTVLILGESGTGKELFARAIHNLSPRANGPFIAIN 303
Query: 199 CGMIDQDKIEKFLFGDVD---LQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYN 255
C I + +E LFG + G F ANGGT+ L+E +PL +Q ++
Sbjct: 304 CAAIPETLLESELFGYEKGAFTGASKGGK-PGLFELANGGTLFLDEIGEMPLPLQAKLLR 362
Query: 256 FIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSR 315
++ +IE I +DVR+I T +NL + FR+DLYYR++V I I LR R
Sbjct: 363 VLQEKEIERVGGTKPIPVDVRIIAATNRNLEKMIAEGTFREDLYYRLNVIPITIPPLRER 422
Query: 316 SEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDS 375
EDIP L +FL F + +S AL+LL +Y W NV+EL+N++ RAV ++
Sbjct: 423 KEDIPLLAEYFLDKFSRRYGRNVKGLSPDALALLLRYDWPGNVRELENVIERAVNLVESD 482
Query: 376 HLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRL 435
L + + + E K+ R E+ I L
Sbjct: 483 GLIDADDLPAFALEEKEPR-------------------------PETTKQIEVGSLKEAL 517
Query: 436 SDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
+ EK +I A++ + S+ A+ LGI R+TLYRK+++Y +
Sbjct: 518 EEYEKHLIREALERHGGNKSKAAKELGISRTTLYRKLKKYGLR 560
>gnl|CDD|33404 COG3604, FhlA, Transcriptional regulator containing GAF, AAA-type
ATPase, and DNA binding domains [Transcription / Signal
transduction mechanisms].
Length = 550
Score = 204 bits (519), Expect = 7e-53
Identities = 109/353 (30%), Positives = 173/353 (49%), Gaps = 17/353 (4%)
Query: 131 SQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRA 190
+ +I SPAM Q++ ++I+GE G GK+ ++R IH+ R
Sbjct: 214 QLSEVVLEVGGIIGRSPAMRQLLKEIEVVAKSDSTVLIRGETGTGKELVARAIHQLSPRR 273
Query: 191 FFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLAV 249
PF +NC + + +E LFG T G+F A+GGT+ L+E LPLA+
Sbjct: 274 DKPFVKLNCAALPESLLESELFGHEKGAFTGAINTRRGRFELADGGTLFLDEIGELPLAL 333
Query: 250 QGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINI 309
Q ++ ++ G+IE I++DVR+I T ++L V+ FR DLYYR+SVF + +
Sbjct: 334 QAKLLRVLQEGEIERVGGDRTIKVDVRVIAATNRDLEEMVRDGEFRADLYYRLSVFPLEL 393
Query: 310 STLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAV 369
LR R EDIP L +FL+ F + +S+S +AL LL+ Y W NV+EL+N++ RAV
Sbjct: 394 PPLRERPEDIPLLAGYFLEKFRRRLGRAILSLSAEALELLSSYEWPGNVRELENVVERAV 453
Query: 370 IGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQD 429
L LT + L +A T + L + ++P G+
Sbjct: 454 --LLAGRLTRRGDLCTLELSL---------SALLWKTLPAPEPS---ALPEPALP--GEH 497
Query: 430 GEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEVDSL 482
+ E+++I A++ + ARRLG+ R TL +++ I+V L
Sbjct: 498 TLREATEEFERQLIIAALEETNGNWAGAARRLGLTRRTLLYRMKRLGIKVKKL 550
>gnl|CDD|33094 COG3284, AcoR, Transcriptional activator of acetoin/glycerol
metabolism [Secondary metabolites biosynthesis,
transport, and catabolism / Transcription].
Length = 606
Score = 172 bits (436), Expect = 3e-43
Identities = 96/325 (29%), Positives = 155/325 (47%), Gaps = 50/325 (15%)
Query: 155 LARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD 214
A + +P+++QGE G GK+ L+R IH++ + A PF VNC I + IE LFG
Sbjct: 328 KAERVAATDLPVLLQGETGTGKEVLARAIHQNSEAAG-PFVAVNCAAIPEALIESELFGY 386
Query: 215 VDLQTKNSAQ--FLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIR 272
V + + + GK +A+GGT+ L+E +PLA+Q R+ ++ G + I+
Sbjct: 387 VAGAFTGARRKGYKGKLEQADGGTLFLDEIGDMPLALQSRLLRVLQEGVVTPLGGT-RIK 445
Query: 273 LDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCT 332
+D+R+I T ++L V+ FR+DLYYR++ F+I + LR RS+ IP L +
Sbjct: 446 VDIRVIAATHRDLAQLVEQGRFREDLYYRLNAFVITLPPLRERSDRIPLLDRILKRE--- 502
Query: 333 KNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKK 392
++ + D AL+ L Y W N++EL N++ R L++ + +
Sbjct: 503 --NDWRLQLDDDALARLLAYRWPGNIRELDNVIERLAA------LSDGGRIRV------- 547
Query: 393 EREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRA 452
+ L +E DIEK + A++
Sbjct: 548 -------------------SDLPPELLEEQATPRE---------DIEKAALLAALQATNG 579
Query: 453 QMSEVARRLGIGRSTLYRKIREYNI 477
+SE AR LGI RSTLYRK++ + I
Sbjct: 580 NISEAARLLGISRSTLYRKLKRHGI 604
>gnl|CDD|33093 COG3283, TyrR, Transcriptional regulator of aromatic amino acids
metabolism [Transcription / Amino acid transport and
metabolism].
Length = 511
Score = 169 bits (429), Expect = 2e-42
Identities = 98/352 (27%), Positives = 167/352 (47%), Gaps = 42/352 (11%)
Query: 129 VPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGK 188
V +Q+ + ++AVSP M VV+ A+K P++I GE G GK L++ H +
Sbjct: 195 VAAQDVS--GFEQIVAVSPKMKHVVEQAQKLAMLDAPLLITGETGTGKDLLAKACHLASP 252
Query: 189 RAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLA 248
R PF +NC + +D E LFG G F +ANGGT++L+E +
Sbjct: 253 RHSKPFLALNCASLPEDAAESELFG----HAPGDEGKKGFFEQANGGTVLLDEIGEMSPR 308
Query: 249 VQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLIN 308
+Q ++ F+ G + +DVR+I T+ NL+ V+ FR+DL+YR++V +N
Sbjct: 309 LQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQVNLVELVQKGKFREDLFYRLNVLTLN 368
Query: 309 ISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRA 368
+ LR R +DI L F+Q F + + + ++ L++LT+Y W NV++LKN + RA
Sbjct: 369 LPPLRERPQDIMPLAELFVQQFSDELGVPRPKLAADLLTVLTRYAWPGNVRQLKNAIYRA 428
Query: 369 VIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQ 428
+ L+ L + +L ++ +G+
Sbjct: 429 LTLLEGYELRIEDILLPD---------------------------------YDAATVVGE 455
Query: 429 DGEVRRLSDIEKEI-IGLAMKLYRAQMS--EVARRLGIGRSTLYRKIREYNI 477
D L +I + +LYR+ S ++A+RLG+ + + K+R+Y I
Sbjct: 456 DALEGSLDEIVSRFERSVLTRLYRSYPSTRKLAKRLGVSHTAIANKLRQYGI 507
>gnl|CDD|31414 COG1221, PspF, Transcriptional regulators containing an AAA-type
ATPase domain and a DNA-binding domain [Transcription /
Signal transduction mechanisms].
Length = 403
Score = 158 bits (401), Expect = 2e-39
Identities = 93/344 (27%), Positives = 153/344 (44%), Gaps = 25/344 (7%)
Query: 138 ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIH-ESGKRAFFPFFI 196
ALD LI SP++ ++ + + +P++I GE G GK+ +R IH S +RA PF
Sbjct: 76 ALDDLIGESPSLQELREQIKAYAPSGLPVLIIGETGTGKELFARLIHALSARRAEAPFIA 135
Query: 197 VNCGMIDQDKIEKFLFGDVD--LQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIY 254
NC ++ E LFG + G F +ANGGT+ L+E LP Q ++
Sbjct: 136 FNCAAYSENLQEAELFGHEKGAFTGAQGGKA-GLFEQANGGTLFLDEIHRLPPEGQEKLL 194
Query: 255 NFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK-DLYYRISVFLINISTLR 313
+E G+ +DVRLI T ++L + V DL R+++ I + LR
Sbjct: 195 RVLEEGEYRRVGGSQPRPVDVRLICATTEDL----EEAVLAGADLTRRLNILTITLPPLR 250
Query: 314 SRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLK 373
R EDI L FL+S + + S +AL L Y W N++ELKN++ RAV
Sbjct: 251 ERKEDILLLAEHFLKSEARRLGLPLSVDSPEALRALLAYDWPGNIRELKNLVERAVAQAS 310
Query: 374 DSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVR 433
+ ++ + + +D Q ++P +
Sbjct: 311 GEGQDLEDLIISIRLDELP----------------GLNDVPAGISLQLNLPELPLSLRET 354
Query: 434 RLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
L +E+ ++ A++ + + AR LGI R TL ++++Y +
Sbjct: 355 SLEQVEERLLQKALEQNKGNKKKAARLLGISRKTLRYRLKKYGL 398
>gnl|CDD|143926 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 130 bits (331), Expect = 6e-31
Identities = 62/171 (36%), Positives = 94/171 (54%), Gaps = 9/171 (5%)
Query: 142 LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGM 201
LI SPAM +V++LA++ ++I GE G GK+ +R IH+ RA PF VNC
Sbjct: 1 LIGESPAMQEVLELAKRVAPTDATVLITGESGTGKELFARAIHQLSPRADGPFVAVNCAA 60
Query: 202 IDQDKIEKFLFGDVDLQTKNS-----AQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNF 256
I ++ +E LFG K + + G F A+GGT+ L+E LPL +Q ++
Sbjct: 61 IPEELLESELFGHE----KGAFTGAVSDRKGLFELADGGTLFLDEIGELPLELQAKLLRV 116
Query: 257 IETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLI 307
++ G+ E I++DVR+I T ++L V FR+DLYYR++V I
Sbjct: 117 LQEGEFERVGGTKPIKVDVRIIAATNRDLEEAVAEGRFREDLYYRLNVVPI 167
>gnl|CDD|34269 COG4650, RtcR, Sigma54-dependent transcription regulator containing
an AAA-type ATPase domain and a DNA-binding domain
[Transcription / Signal transduction mechanisms].
Length = 531
Score = 67.4 bits (164), Expect = 9e-12
Identities = 72/261 (27%), Positives = 111/261 (42%), Gaps = 13/261 (4%)
Query: 132 QENEHCALDSLIAV-SPAMIQVVD-LARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGK- 188
+E L S IA +P ++++ + R A PI++ G G GK L+R I+E +
Sbjct: 175 REQTLDFLKSGIATRNPHFNRMIEQIERVAIRSRAPILLNGPTGAGKSFLARRIYELKQA 234
Query: 189 RAFF--PFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDAL 245
R F F VNC + D LFG V T G A+GG + L+E L
Sbjct: 235 RHQFSGAFVEVNCATLRGDTAMSALFGHVKGAFTGARESREGLLRSADGGMLFLDEIGEL 294
Query: 246 PLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVF 305
Q + IE + F S + D +LI T ++L V FR+DLY RI+++
Sbjct: 295 GADEQAMLLKAIEEKRFYPFGSDRQVSSDFQLIAGTVRDLRQLVAEGKFREDLYARINLW 354
Query: 306 LINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKA----LSLLT--KYPWIDNVQ 359
+ LR R EDI + + L+ + + + +A L+ T + W N +
Sbjct: 355 TFTLPGLRQRQEDIEPNLDYELERHASLTG-DSVRFNTEARRAWLAFATSPQATWRGNFR 413
Query: 360 ELKNILLRAVIGLKDSHLTED 380
EL + R +T D
Sbjct: 414 ELSASVTRMATLADSGRITLD 434
>gnl|CDD|145879 pfam02954, HTH_8, Bacterial regulatory protein, Fis family.
Length = 42
Score = 55.1 bits (134), Expect = 4e-08
Identities = 19/42 (45%), Positives = 28/42 (66%)
Query: 434 RLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
L ++EKE+I A++ S+ AR LGI R TLYRK+++Y
Sbjct: 1 SLEEVEKELIEAALERTGGNKSKAARLLGISRRTLYRKLKKY 42
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases..
Length = 151
Score = 54.5 bits (131), Expect = 6e-08
Identities = 32/139 (23%), Positives = 55/139 (39%), Gaps = 15/139 (10%)
Query: 165 PIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQ 224
+++ G G GK L+R I R PF +N + + + LFG ++
Sbjct: 21 NLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVR-----L 75
Query: 225 FLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKN 284
+A G + ++E D+L Q + +ET + R +VR+I T +
Sbjct: 76 LFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLET-----LNDLRIDRENVRVIGATNRP 130
Query: 285 LLPQVKSHVFRKDLYYRIS 303
LL + LY R+
Sbjct: 131 LLGD-----LDRALYDRLD 144
>gnl|CDD|145774 pfam02796, HTH_7, Helix-turn-helix domain of resolvase.
Length = 45
Score = 37.0 bits (86), Expect = 0.011
Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 434 RLSDIEKEIIGLAMKLYRAQMS--EVARRLGIGRSTLYRKIRE 474
R + +E I + L +S ++A+ GI RST+YR +
Sbjct: 2 RPPKLNEEDINEVITLLEEGISIKQIAKIFGISRSTVYRYLAA 44
>gnl|CDD|119388 cd00569, HTH_Hin_like, Helix-turn-helix domain of Hin and related
proteins, a family of DNA-binding domains unique to
bacteria and represented by the Hin protein of
Salmonella. The basic HTH domain is a simple fold
comprised of three core helices that form a right-handed
helical bundle. The principal DNA-protein interface is
formed by the third helix, the recognition helix,
inserting itself into the major groove of the DNA. A
diverse array of HTH domains participate in a variety of
functions that depend on their DNA-binding properties.
HTH_Hin represents one of the simplest versions of the
HTH domains; the characterization of homologous
relationships between various sequence-diverse HTH
domain families remains difficult. The Hin recombinase
induces the site-specific inversion of a chromosomal DNA
segment containing a promoter, which controls the
alternate expression of two genes by reversibly
switching orientation. The Hin recombinase consists of a
single polypeptide chain containing a DNA-binding domain
(HTH_Hin) and a catalytic domain..
Length = 42
Score = 37.0 bits (87), Expect = 0.011
Identities = 17/30 (56%), Positives = 20/30 (66%), Gaps = 2/30 (6%)
Query: 443 IGLAMKLYRAQMS--EVARRLGIGRSTLYR 470
I A +L A S E+ARRLG+ RSTLYR
Sbjct: 11 IEEARRLLAAGESVAEIARRLGVSRSTLYR 40
>gnl|CDD|31127 COG0784, CheY, FOG: CheY-like receiver [Signal transduction
mechanisms].
Length = 130
Score = 35.2 bits (80), Expect = 0.042
Identities = 17/84 (20%), Positives = 39/84 (46%), Gaps = 4/84 (4%)
Query: 11 KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQ----VNVIFLSLINCEDD 66
RVL++D + +++K +E GY+V + + ++ ++I L + D
Sbjct: 6 LRVLVVDDEPVNRRLLKRLLEDLGYEVVEAADGEEEALELLRELPQPDLILLDINMPGMD 65
Query: 67 KENILKNIVDKIPIVPIIVQTTQD 90
+L+ + + P +P+I+ T
Sbjct: 66 GIELLRRLRARGPNIPVILLTAYA 89
>gnl|CDD|143854 pfam00072, Response_reg, Response regulator receiver domain.
This domain receives the signal from the sensor partner
in bacterial two-component systems. It is usually found
N-terminal to a DNA binding effector domain.
Length = 111
Score = 34.1 bits (79), Expect = 0.080
Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 2/82 (2%)
Query: 13 VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSD-LSTISKIQVNVIFLSLINCEDDKENI 70
VLI+D D ++++ +E GY V + + L + + + ++I L + D +
Sbjct: 1 VLIVDDDPLIRELLRQLLEKEGYVVAEADDGEEALELLKEKRPDLILLDIRMPGMDGLEL 60
Query: 71 LKNIVDKIPIVPIIVQTTQDNI 92
L+ I + P P+IV T +
Sbjct: 61 LRRIRRRPPTTPVIVLTAHGDE 82
>gnl|CDD|145418 pfam02254, TrkA_N, TrkA-N domain. This domain is found in a wide
variety of proteins. These protein include potassium
channels, phosphoesterases, and various other
transporters. This domain binds to NAD.
Length = 115
Score = 34.1 bits (79), Expect = 0.10
Identities = 19/96 (19%), Positives = 43/96 (44%), Gaps = 11/96 (11%)
Query: 5 KSLDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVN--VIFLSLIN 62
+ L V++IDKD E+++ +++ G V + + +D + + + ++
Sbjct: 15 EELREGGPVVVIDKDPERVEELREE----GVPVVVGDATDEEVLEEAGIEDADAVVAATG 70
Query: 63 CEDDKENIL--KNIVDKIPIVPIIVQT-TQDNIKIL 95
DD+ NIL + P II + ++ ++L
Sbjct: 71 --DDEANILIVLLARELNPAKKIIARANDPEHAELL 104
>gnl|CDD|144936 pfam01527, Transposase_8, Transposase. Transposase proteins are
necessary for efficient DNA transposition. This family
consists of various E. coli insertion elements and other
bacterial transposases some of which are members of the
IS3 family.
Length = 75
Score = 32.7 bits (75), Expect = 0.24
Identities = 14/44 (31%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 433 RRLSDIEKE-IIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
RR S+ K + +++ A +SE+AR G+ +TLY+ ++Y
Sbjct: 5 RRYSEEFKARAVKESLE-PGASVSELAREHGVSPATLYKWRKKY 47
>gnl|CDD|32726 COG2901, Fis, Factor for inversion stimulation Fis, transcriptional
activator [Transcription / DNA replication,
recombination, and repair].
Length = 98
Score = 32.3 bits (73), Expect = 0.34
Identities = 13/43 (30%), Positives = 27/43 (62%)
Query: 435 LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
L+++E+ ++ + M+ R + A LGI R TL +K+++Y +
Sbjct: 55 LAEVEQPLLDMVMQYTRGNQTRAALMLGINRGTLRKKLKKYGL 97
>gnl|CDD|144144 pfam00440, TetR_N, Bacterial regulatory proteins, tetR family.
Length = 47
Score = 31.2 bits (72), Expect = 0.68
Identities = 9/35 (25%), Positives = 19/35 (54%), Gaps = 6/35 (17%)
Query: 442 IIGLAMKLYRAQ------MSEVARRLGIGRSTLYR 470
I+ A++L+ + + E+A+ G+ + LYR
Sbjct: 1 ILDAALELFAEKGYDATTVREIAKEAGVSKGALYR 35
>gnl|CDD|32784 COG2964, COG2964, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 220
Score = 30.2 bits (68), Expect = 1.1
Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 7/74 (9%)
Query: 410 SSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLY-------RAQMSEVARRLG 462
+ + +++L + + Q+ RL + + LY + ++ VA RLG
Sbjct: 143 NFASSVEDLVAQLLEWTIQEVNADRLLSNNAKNREIVKALYEKGIFNLKDAINIVADRLG 202
Query: 463 IGRSTLYRKIREYN 476
I R T+YR +R++
Sbjct: 203 ISRHTVYRYLRKFK 216
>gnl|CDD|147114 pfam04794, YdjC, YdjC-like protein. Family of YdjC-like proteins.
This region is possibly involved in the the cleavage of
cellobiose-phosphate.
Length = 261
Score = 29.9 bits (68), Expect = 1.5
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 8/45 (17%)
Query: 120 IICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAI 164
II A R G+V S SL+ PA LA++ D +
Sbjct: 20 IIEAHRAGIVTST--------SLMVNMPAFEHAAALAKRNPDLGV 56
>gnl|CDD|33120 COG3311, AlpA, Predicted transcriptional regulator [Transcription].
Length = 70
Score = 29.9 bits (67), Expect = 1.8
Identities = 10/21 (47%), Positives = 16/21 (76%)
Query: 454 MSEVARRLGIGRSTLYRKIRE 474
+ EVA+ G+ RST+YR I++
Sbjct: 16 LPEVAQLTGLSRSTIYRLIKD 36
>gnl|CDD|33434 COG3636, COG3636, Predicted transcriptional regulator
[Transcription].
Length = 100
Score = 29.5 bits (66), Expect = 1.9
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 454 MSEVARRLGIGRSTLYRKIRE 474
MS+VAR+ G+ R LY+ +
Sbjct: 52 MSQVARKAGLSREGLYKALSP 72
>gnl|CDD|133390 cd04762, HTH_MerR-trunc, Helix-Turn-Helix DNA binding domain of
truncated MerR-like proteins. Proteins in this family
mostly have a truncated helix-turn-helix (HTH) MerR-like
domain. They lack a portion of the C-terminal region,
called Wing 2 and the long dimerization helix that is
typically present in MerR-like proteins. These truncated
domains are found in response regulator receiver (REC)
domain proteins (i.e., CheY), cytosine-C5 specific DNA
methylases, IS607 transposase-like proteins, and RacA, a
bacterial protein that anchors chromosomes to cell
poles.
Length = 49
Score = 29.5 bits (67), Expect = 1.9
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 455 SEVARRLGIGRSTLYRKIREYNIEV 479
E A LG+ STL R ++E ++
Sbjct: 4 KEAAELLGVSPSTLRRWVKEGKLKA 28
>gnl|CDD|29071 cd00156, REC, Signal receiver domain; originally thought to be
unique to bacteria (CheY, OmpR, NtrC, and PhoB), now
recently identified in eukaroytes ETR1 Arabidopsis
thaliana; this domain receives the signal from the
sensor partner in a two-component systems; contains a
phosphoacceptor site that is phosphorylated by
histidine kinase homologs; usually found N-terminal to
a DNA binding effector domain; forms homodimers.
Length = 113
Score = 29.4 bits (66), Expect = 2.0
Identities = 19/80 (23%), Positives = 40/80 (50%), Gaps = 2/80 (2%)
Query: 14 LIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKENIL 71
LI+D D ++++ +E GY+V L+ +++ + ++I L ++ D +L
Sbjct: 1 LIVDDDPLIRELLRRLLEKEGYEVVEAEDGEEALALLAEEKPDLILLDIMMPGMDGLELL 60
Query: 72 KNIVDKIPIVPIIVQTTQDN 91
+ I + P +PII T +
Sbjct: 61 RRIRKRGPDIPIIFLTAHGD 80
>gnl|CDD|33221 COG3415, COG3415, Transposase and inactivated derivatives [DNA
replication, recombination, and repair].
Length = 138
Score = 29.1 bits (65), Expect = 2.4
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 2/40 (5%)
Query: 439 EKEIIGLAMKLYRAQMS--EVARRLGIGRSTLYRKIREYN 476
+ + +S E A+R G+ ST+YR +R Y
Sbjct: 7 NDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYR 46
>gnl|CDD|31500 COG1309, AcrR, Transcriptional regulator [Transcription].
Length = 201
Score = 29.2 bits (63), Expect = 2.8
Identities = 11/45 (24%), Positives = 24/45 (53%), Gaps = 6/45 (13%)
Query: 432 VRRLSDIEKEIIGLAMKLYRAQ------MSEVARRLGIGRSTLYR 470
+R + + I+ A++L+ + + E+A+ G+ + TLYR
Sbjct: 7 TKRKRERRERILDAALRLFAEKGYAATTVDEIAKAAGVSKGTLYR 51
>gnl|CDD|113729 pfam04967, HTH_10, HTH DNA binding domain.
Length = 53
Score = 29.1 bits (66), Expect = 2.9
Identities = 17/45 (37%), Positives = 28/45 (62%), Gaps = 6/45 (13%)
Query: 435 LSDIEKEIIGLAMKL-Y-----RAQMSEVARRLGIGRSTLYRKIR 473
L+D ++EI+ LA K+ Y R + ++A+ LGI +STL +R
Sbjct: 1 LTDRQREILRLAYKMGYFDYPRRVTLKDLAKELGISKSTLSEHLR 45
>gnl|CDD|33662 COG3872, COG3872, Predicted metal-dependent enzyme [General
function prediction only].
Length = 318
Score = 29.1 bits (65), Expect = 3.0
Identities = 11/54 (20%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 53 VNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKF 106
V + SL+ +N+ +VD+I ++P+++ + + +K+ N + K
Sbjct: 219 VGIFVYSLV----PFDNLWLRVVDRIILLPVVLGISYEVLKLTNKVRNKPVLKL 268
>gnl|CDD|31088 COG0745, OmpR, Response regulators consisting of a CheY-like
receiver domain and a winged-helix DNA-binding domain
[Signal transduction mechanisms / Transcription].
Length = 229
Score = 28.8 bits (64), Expect = 3.3
Identities = 20/83 (24%), Positives = 46/83 (55%), Gaps = 2/83 (2%)
Query: 11 KRVLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDLSTISKIQVNVIFLSLINCEDDKEN 69
R+L+++ D E +++K+++E GY+V + + + ++ Q +++ L L+ + D
Sbjct: 1 MRILLVEDDPELAELLKEYLEEEGYEVDVAADGEEALEAAREQPDLVLLDLMLPDLDGLE 60
Query: 70 ILKNI-VDKIPIVPIIVQTTQDN 91
+ + + K PIIV T +D+
Sbjct: 61 LCRRLRAKKGSGPPIIVLTARDD 83
>gnl|CDD|34868 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 28.5 bits (63), Expect = 4.2
Identities = 20/106 (18%), Positives = 36/106 (33%), Gaps = 18/106 (16%)
Query: 99 LYNRISKFFLNLVSRKQLCDSIICA-------------LREGVVPSQENEHCALDSLIAV 145
L + +SKF L L+ + + G P +E EH + +
Sbjct: 816 LVSLLSKFTLGLLESQNAIEKQKPKVPDHSYIAFCHYWKHGGSFPVEEQEHYIITPFVQK 875
Query: 146 SPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAF 191
+ ++ R A P++IQG GK + ++ F
Sbjct: 876 N-----YLNTMRAASLSNFPLLIQGPTSSGKTSMILYLARETGHKF 916
>gnl|CDD|145296 pfam02042, RWP-RK, RWP-RK domain. This domain is named RWP-RK
after a conserved motif at the C terminus of the
presumed domain. The domain is found in algal minus
dominance proteins as well as plant proteins involved in
nitrogen-controlled development.
Length = 52
Score = 28.4 bits (64), Expect = 4.2
Identities = 7/24 (29%), Positives = 13/24 (54%)
Query: 454 MSEVARRLGIGRSTLYRKIREYNI 477
+ E A+ LG+ + L + R+ I
Sbjct: 18 IKEAAKELGVCLTVLKKICRQLGI 41
>gnl|CDD|110072 pfam01044, Vinculin, Vinculin family.
Length = 850
Score = 28.2 bits (63), Expect = 5.1
Identities = 20/95 (21%), Positives = 33/95 (34%), Gaps = 19/95 (20%)
Query: 407 EGKSSDTILDNLSQESIPAIGQ------------DGEVRRLSDIEKEIIGLA--MKLYRA 452
++ + L E I EV + +II LA M +
Sbjct: 653 PPETDREEMRRLPPEEKAKIAAQVQPFLAAAHKLHREVAKWDSKGNDIIALAKRMCMIMM 712
Query: 453 QMSEVARRLGIGRSTL-----YRKIREYNIEVDSL 482
+M++ R G ++T+ +KI E EV L
Sbjct: 713 EMTDFTRGKGPLKTTMDVINAAKKIAEAGEEVTRL 747
>gnl|CDD|31384 COG1191, FliA, DNA-directed RNA polymerase specialized sigma
subunit [Transcription].
Length = 247
Score = 28.4 bits (63), Expect = 5.1
Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 432 VRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
+ L + EK ++ L K Q E+A LGI S + R ++
Sbjct: 194 IEPLPEREKLVLVLRYKEELTQK-EIAEVLGISESRVSRLHKKA 236
>gnl|CDD|32144 COG1961, PinR, Site-specific recombinases, DNA invertase Pin
homologs [DNA replication, recombination, and repair].
Length = 222
Score = 28.2 bits (62), Expect = 5.8
Identities = 17/63 (26%), Positives = 25/63 (39%), Gaps = 1/63 (1%)
Query: 421 ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQM-SEVARRLGIGRSTLYRKIREYNIEV 479
E G + R E+ + SE+AR LGI RST+YR + +
Sbjct: 146 EGGRPPGYKIKKGRKKAEEQAAAVRRLLADGLGSYSEIARALGISRSTVYRILNKLKKRG 205
Query: 480 DSL 482
+L
Sbjct: 206 GTL 208
>gnl|CDD|34205 COG4567, COG4567, Response regulator consisting of a CheY-like
receiver domain and a Fis-type HTH domain [Signal
transduction mechanisms / Transcription].
Length = 182
Score = 28.0 bits (62), Expect = 6.0
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 435 LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
+ E I ++ +SE ARRL + R TL RK+
Sbjct: 139 ADRLRWEHIQRVLEECEGNISETARRLNMHRRTLQRKL 176
>gnl|CDD|33728 COG3947, COG3947, Response regulator containing CheY-like
receiver and SARP domains [Signal transduction
mechanisms].
Length = 361
Score = 28.0 bits (62), Expect = 6.0
Identities = 17/81 (20%), Positives = 38/81 (46%), Gaps = 2/81 (2%)
Query: 12 RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
R++I+D D +K++ + G++V + V L + + ++IFL ++ +
Sbjct: 2 RIIIVDDDAAIVKLLSVILSRAGHEVRSCSHPVEALDLLEVFKPDLIFLDIVMPYMNGIE 61
Query: 70 ILKNIVDKIPIVPIIVQTTQD 90
+ + D VPII ++
Sbjct: 62 FAEQVRDIESAVPIIFISSHA 82
>gnl|CDD|33219 COG3413, COG3413, Predicted DNA binding protein [General function
prediction only].
Length = 215
Score = 28.1 bits (62), Expect = 6.0
Identities = 16/45 (35%), Positives = 27/45 (60%), Gaps = 6/45 (13%)
Query: 435 LSDIEKEIIGLAMKL-Y-----RAQMSEVARRLGIGRSTLYRKIR 473
L+D + E++ LA K+ Y R + ++A+ LGI +STL +R
Sbjct: 156 LTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLR 200
>gnl|CDD|147026 pfam04666, Glyco_transf_54, N-Acetylglucosaminyltransferase-IV
(GnT-IV) conserved region. The complex-type of
oligosaccharides are synthesized through elongation by
glycosyltransferases after trimming of the precursor
oligosaccharides transferred to proteins in the
endoplasmic reticulum. N-Acetylglucosaminyltransferases
(GnTs) take part in the formation of branches in the
biosynthesis of complex-type sugar chains. In
vertebrates, six GnTs, designated as GnT-I to -VI, which
catalyse the transfer of GlcNAc to the core mannose
residues of Asn-linked sugar chains, have been
identified. GnT-IV (EC:2.4.1.145) catalyses the transfer
of GlcNAc from UDP-GlcNAc to the GlcNAc1-2Man1-3 arm of
core oligosaccharide [Gn2(22)core oligosaccharide] and
forms GlcNAc1-4(GlcNAc1-2)Man1-3 structure on the core
oligosaccharide (Gn3(2,4,2)core oligosaccharide). In
some members the conserved region occupies all but the
very for N-terminal, where there is a signal sequence on
all members. For other members the conserved region does
not occupy the entire protein but is still to the
N-terminus of the protein.
Length = 301
Score = 27.7 bits (62), Expect = 6.4
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 315 RSEDIPWLVHFFL 327
RS+D+P LV F L
Sbjct: 222 RSKDLPRLVEFLL 234
>gnl|CDD|145169 pfam01861, DUF43, Protein of unknown function DUF43. This family
includes archaebacterial proteins of unknown function.
All the members are 350-400 amino acids long.
Length = 243
Score = 27.8 bits (62), Expect = 6.8
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 11 KRVLIIDKDDEQIKIIKDHVESYGYDV 37
KR+ ++D D+ IK I+ + G +
Sbjct: 68 KRIAVVDIDERLIKFIERVAKEEGLKI 94
>gnl|CDD|31604 COG1414, IclR, Transcriptional regulator [Transcription].
Length = 246
Score = 27.5 bits (61), Expect = 7.7
Identities = 8/16 (50%), Positives = 14/16 (87%)
Query: 455 SEVARRLGIGRSTLYR 470
+E+A RLG+ +ST++R
Sbjct: 23 AELAERLGLPKSTVHR 38
>gnl|CDD|31756 COG1568, COG1568, Predicted methyltransferases [General function
prediction only].
Length = 354
Score = 27.6 bits (61), Expect = 8.5
Identities = 13/35 (37%), Positives = 19/35 (54%)
Query: 11 KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDL 45
KR+ ++D D+ IK I+ E GY+ V DL
Sbjct: 176 KRIAVVDIDERLIKFIEKVAEELGYNNIEAFVFDL 210
>gnl|CDD|32568 COG2452, COG2452, Predicted site-specific integrase-resolvase [DNA
replication, recombination, and repair].
Length = 193
Score = 27.6 bits (61), Expect = 8.6
Identities = 13/24 (54%), Positives = 14/24 (58%)
Query: 456 EVARRLGIGRSTLYRKIREYNIEV 479
E + LGI STL R IRE I V
Sbjct: 6 EACQLLGISYSTLLRWIREGKIRV 29
>gnl|CDD|38059 KOG2848, KOG2848, KOG2848, 1-acyl-sn-glycerol-3-phosphate
acyltransferase [Lipid transport and metabolism].
Length = 276
Score = 27.5 bits (61), Expect = 8.9
Identities = 7/33 (21%), Positives = 14/33 (42%), Gaps = 8/33 (24%)
Query: 77 KIPIVPIIVQTTQDNIKILNCFLYNRISKFFLN 109
++PIVP++ + Y+ K F +
Sbjct: 195 QVPIVPVVFSSY--------GDFYSTKEKVFNS 219
>gnl|CDD|100107 cd02440, AdoMet_MTases, S-adenosylmethionine-dependent
methyltransferases (SAM or AdoMet-MTase), class I;
AdoMet-MTases are enzymes that use
S-adenosyl-L-methionine (SAM or AdoMet) as a substrate
for methyltransfer, creating the product
S-adenosyl-L-homocysteine (AdoHcy). There are at least
five structurally distinct families of AdoMet-MTases,
class I being the largest and most diverse. Within this
class enzymes can be classified by different substrate
specificities (small molecules, lipids, nucleic acids,
etc.) and different target atoms for methylation
(nitrogen, oxygen, carbon, sulfur, etc.)..
Length = 107
Score = 27.4 bits (61), Expect = 9.8
Identities = 11/71 (15%), Positives = 22/71 (30%), Gaps = 5/71 (7%)
Query: 11 KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKI---QVNVIFL--SLINCED 65
RV +D +++ + + D V D + +VI L + +
Sbjct: 22 ARVTGVDISPVALELARKAAAALLADNVEVLKGDAEELPPEADESFDVIISDPPLHHLVE 81
Query: 66 DKENILKNIVD 76
D L+
Sbjct: 82 DLARFLEEARR 92
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.323 0.141 0.401
Gapped
Lambda K H
0.267 0.0731 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,742,122
Number of extensions: 313240
Number of successful extensions: 912
Number of sequences better than 10.0: 1
Number of HSP's gapped: 891
Number of HSP's successfully gapped: 65
Length of query: 482
Length of database: 6,263,737
Length adjustment: 98
Effective length of query: 384
Effective length of database: 4,146,055
Effective search space: 1592085120
Effective search space used: 1592085120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 59 (26.5 bits)