RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 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|183114 PRK11388, PRK11388, DNA-binding transcriptional regulator DhaR;
Provisional.
Length = 638
Score = 179 bits (455), Expect = 2e-45
Identities = 110/350 (31%), Positives = 169/350 (48%), Gaps = 50/350 (14%)
Query: 139 LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVN 198
D + SP M +++ R+A + P+++ GE GVGK L++ IH +RA P+ VN
Sbjct: 324 FDHMPQDSPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHNESERAAGPYIAVN 383
Query: 199 CGMIDQDKI-EKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFI 257
C + + + E+FL D T + L KF A+GGT+ LE+ + L +Q + +
Sbjct: 384 CQLYPDEALAEEFLGSDR---TDSENGRLSKFELAHGGTLFLEKVEYLSPELQSALLQVL 440
Query: 258 ETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSE 317
+TG I DSR I +DVR+I T +L V+ + F + LYY + F I I LR R E
Sbjct: 441 KTGVITRLDSRRLIPVDVRVIATTTADLAMLVEQNRFSRQLYYALHAFEITIPPLRMRRE 500
Query: 318 DIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRA-------VI 370
DIP LV+ L+S K ++ I D AL+ L Y W N EL++++ I
Sbjct: 501 DIPALVNNKLRSL-EKRFSTRLKIDDDALARLVSYRWPGNDFELRSVIENLALSSDNGRI 559
Query: 371 GLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL-DNLSQESIPAIGQD 429
L D L E L + S T L +LS
Sbjct: 560 RLSD--LPEH---LFTEQAT-----------------DDVSATRLSTSLS---------- 587
Query: 430 GEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
L+++EKE I A ++ ++ E+A LGIGR+TL+RK++++ I+
Sbjct: 588 -----LAELEKEAIINAAQVCGGRIQEMAALLGIGRTTLWRKMKQHGIDA 632
>gnl|CDD|182412 PRK10365, PRK10365, transcriptional regulatory protein ZraR;
Provisional.
Length = 441
Score = 171 bits (435), Expect = 3e-43
Identities = 131/466 (28%), Positives = 219/466 (46%), Gaps = 40/466 (8%)
Query: 13 VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
+L++D D I++ + +GY+V + N S + +++ V L L + E D
Sbjct: 8 ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66
Query: 70 ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
LK I P +P+++ T +++ L + + + L ++ AL
Sbjct: 67 TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAHTHS 126
Query: 130 PSQE--NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
E + ++ SPAM ++ ++I G+ G GK+ ++R IH S
Sbjct: 127 IDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHASS 186
Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
R+ P +NC +++ +E LFG + T + G+F+EA+GGT+ L+E +
Sbjct: 187 ARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246
Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
+Q R+ I+ +++ S I +DVRLI T ++L +V + FR+DLYYR++V
Sbjct: 247 PMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNVVA 306
Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
I + +LR R EDIP L FLQ F +N + +A+ LL Y W N++EL+N +
Sbjct: 307 IEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAVE 366
Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
RAV+ LL+ E ERE A T IP
Sbjct: 367 RAVV--------------LLTGEYISERELPLAIAST------------------PIPL- 393
Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
GQ +++ L ++EKE+I A++ +E AR+LGI R TL K+
Sbjct: 394 GQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439
>gnl|CDD|162544 TIGR01817, nifA, Nif-specific regulatory protein. This model
represents NifA, a DNA-binding regulatory protein for
nitrogen fixation. The model produces scores between the
trusted and noise cutoffs for a well-described NifA
homolog in Aquifex aeolicus (which lacks nitrogenase),
for transcriptional activators of alternative
nitrogenases (VFe or FeFe instead of MoFe), and
truncated forms.
Length = 534
Score = 163 bits (415), Expect = 9e-41
Identities = 112/363 (30%), Positives = 170/363 (46%), Gaps = 16/363 (4%)
Query: 123 ALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRF 182
LR+ D +I SPAM QVVD AR ++++GE G GK+ +++
Sbjct: 179 QLRDKAPEIARRRSGKEDGIIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKA 238
Query: 183 IHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEE 241
IH RA PF VNC + + +E LFG + T AQ G+F A+GGT+ L+E
Sbjct: 239 IHYLSPRAKRPFVKVNCAALSETLLESELFGHEKGAFTGAIAQRKGRFELADGGTLFLDE 298
Query: 242 PDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYR 301
+ A Q ++ ++ G+ E +++DVRL+ T ++L V FR DLYYR
Sbjct: 299 IGEISPAFQAKLLRVLQEGEFERVGGNRTLKVDVRLVAATNRDLEEAVAKGEFRADLYYR 358
Query: 302 ISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQEL 361
I+V I + LR R EDIP L FL+ F +N + ++I+ A+ +L W NV+EL
Sbjct: 359 INVVPIFLPPLRERREDIPLLAEAFLEKFNRENG-RPLTITPSAIRVLMSCKWPGNVREL 417
Query: 362 KNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQE 421
+N L R + +T F + + A TC S D +
Sbjct: 418 ENCLERTATLSRSGTITRSDFSC------QSGQCLSPMLAKTCPHGHISIDPLAGTTPPH 471
Query: 422 SIPAIGQDGEVR----RLSDIEKEIIGLAMKLYRAQMSEVARRLGIG-RSTLYRKIREYN 476
S + GE LS+ E+ I A++ ++ AR LG+ R Y +R+ N
Sbjct: 472 SPASAALPGEPGLSGPTLSERERLI--AALEQAGWVQAKAARLLGMTPRQVGYA-LRKLN 528
Query: 477 IEV 479
IE+
Sbjct: 529 IEM 531
>gnl|CDD|163070 TIGR02915, PEP_resp_reg, putative PEP-CTERM system response
regulator. Members of this protein family share
full-length homology with (but do not include) the
acetoacetate metabolism regulatory protein AtoC. These
proteins have a Fis family DNA binding sequence
(pfam02954), a response regulator receiver domain
(pfam00072), and sigma-54 interaction domain
(pfam00158).
Length = 445
Score = 162 bits (411), Expect = 2e-40
Identities = 104/341 (30%), Positives = 157/341 (46%), Gaps = 34/341 (9%)
Query: 138 ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIV 197
AL LI SP M ++ K I +++ GE G GK+ L+R +H+ R F +
Sbjct: 137 ALRGLITSSPGMQKICRTIEKIAPSDITVLLLGESGTGKEVLARALHQLSDRKDKRFVAI 196
Query: 198 NCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNF 256
NC I ++ +E LFG + T Q LGK A+GGT+ L+E LPL +Q ++ F
Sbjct: 197 NCAAIPENLLESELFGYEKGAFTGAVKQTLGKIEYAHGGTLFLDEIGDLPLNLQAKLLRF 256
Query: 257 IETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRS 316
++ IE R I +DVR++ T ++L + FR+DL+YRI+ I I LRSR
Sbjct: 257 LQERVIERLGGREEIPVDVRIVCATNQDLKRMIAEGTFREDLFYRIAEISITIPPLRSRD 316
Query: 317 EDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSH 376
D L + FL+ F + K +D AL L + W NV+EL+N + RAVI + +
Sbjct: 317 GDAVLLANAFLERFARELKRKTKGFTDDALRALEAHAWPGNVRELENKVKRAVIMAEGNQ 376
Query: 377 LTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLS 436
+T + D LD + P EVR
Sbjct: 377 ITAE-------------------------------DLGLDARERAETPLEVNLREVR--E 403
Query: 437 DIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
E+E + A+ ++ A LGI R TLY ++++ I
Sbjct: 404 RAEREAVRKAIARVDGNIARAAELLGITRPTLYDLMKKHGI 444
>gnl|CDD|162545 TIGR01818, ntrC, nitrogen regulation protein NR(I). This model
represents NtrC, a DNA-binding response regulator that
is phosphorylated by NtrB and interacts with sigma-54.
NtrC usually controls the expression of glutamine
synthase, GlnA, and may be called GlnL, GlnG, etc.
Length = 463
Score = 158 bits (402), Expect = 3e-39
Identities = 129/478 (26%), Positives = 228/478 (47%), Gaps = 32/478 (6%)
Query: 13 VLIIDKDDEQIK-IIKDHVESYGYDV--FIVNVSDLSTISKIQVNVIFLSLINCEDDKEN 69
V ++D DD I+ +++ + GY+V F S L +++ Q +++ + +D +
Sbjct: 1 VWVVD-DDRSIRWVLEKALSRAGYEVRTFGNAASVLRALARGQPDLLITDVRMPGEDGLD 59
Query: 70 ILKNIVDKIPIVPIIVQTTQ-DNIKILNCF---LYNRISKFF-----LNLVSRKQLCDSI 120
+L I + P +P+IV T D + + + + K F + LV R ++
Sbjct: 60 LLPQIKKRHPQLPVIVMTAHSDLDTAVAAYQRGAFEYLPKPFDLDEAVTLVER-----AL 114
Query: 121 ICALREGVVPSQENEHCALDSLIAVSPAMIQVVD-LARKAGDCAIPIMIQGEFGVGKKRL 179
A + +P+ E LI +PAM +V + R + I ++I GE G GK+ +
Sbjct: 115 AHAQEQVALPADAGEAEDSAELIGEAPAMQEVFRAIGRLSRS-DITVLINGESGTGKELV 173
Query: 180 SRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIV 238
+R +H RA PF +N I +D IE LFG + T + + G+F +A+GGT+
Sbjct: 174 ARALHRHSPRANGPFIALNMAAIPKDLIESELFGHEKGAFTGANTRRQGRFEQADGGTLF 233
Query: 239 LEEPDALPLAVQGRIYNFIETGKIEFF--DSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
L+E +PL Q R+ + G EF+ R I++DVR++ T +NL V+ FR+
Sbjct: 234 LDEIGDMPLDAQTRLLRVLADG--EFYRVGGRTPIKVDVRIVAATHQNLEALVRQGKFRE 291
Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWID 356
DL++R++V I++ LR R EDIP L FL + ++ + +AL L + W
Sbjct: 292 DLFHRLNVIRIHLPPLRERREDIPRLARHFLALAARELDVEPKLLDPEALERLKQLRWPG 351
Query: 357 NVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILD 416
NV++L+N+ + + L+ G+ ++ S D L+
Sbjct: 352 NVRQLENLCRWLTVMASGDEVLVSDLPAELALTGRPASAPDSDG-------QDSWDEALE 404
Query: 417 NLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE 474
+++++ Q R L + E+ ++ A++ R E A LG GR+TL RK++E
Sbjct: 405 AWAKQALSRGEQGLLDRALPEFERPLLEAALQHTRGHKQEAAALLGWGRNTLTRKLKE 462
>gnl|CDD|182758 PRK10820, PRK10820, DNA-binding transcriptional regulator TyrR;
Provisional.
Length = 520
Score = 158 bits (402), Expect = 3e-39
Identities = 100/350 (28%), Positives = 165/350 (47%), Gaps = 41/350 (11%)
Query: 134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFP 193
N+ A ++AVSP M QVV+ ARK P++I G+ G GK L+ H R P
Sbjct: 198 NDDSAFSQIVAVSPKMRQVVEQARKLAMLDAPLLITGDTGTGKDLLAYACHLRSPRGKKP 257
Query: 194 FFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGK---FIEANGGTIVLEEPDALPLAVQ 250
F +NC I D +E LFG N+ + GK F +ANGG+++L+E + +Q
Sbjct: 258 FLALNCASIPDDVVESELFGHAPGAYPNALE--GKKGFFEQANGGSVLLDEIGEMSPRMQ 315
Query: 251 GRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINIS 310
++ F+ G + +DVR+I T+KNL+ V+ FR+DLYYR++V +N+
Sbjct: 316 AKLLRFLNDGTFRRVGEDHEVHVDVRVICATQKNLVELVQKGEFREDLYYRLNVLTLNLP 375
Query: 311 TLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVI 370
LR R +DI L F+ F + + + ++ ++LT+Y W NV++LKN + RA+
Sbjct: 376 PLRDRPQDIMPLTELFVARFADEQGVPRPKLAADLNTVLTRYGWPGNVRQLKNAIYRALT 435
Query: 371 GLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDG 430
L+ L +L ++ A + ++
Sbjct: 436 QLEGYELRPQDILL---------PDYDAAVA--------VGEDAMEG------------- 465
Query: 431 EVRRLSDIEKEI-IGLAMKLYRAQMS--EVARRLGIGRSTLYRKIREYNI 477
L +I + +LYR S ++A+RLG+ + + K+REY +
Sbjct: 466 ---SLDEITSRFERSVLTRLYRNYPSTRKLAKRLGVSHTAIANKLREYGL 512
>gnl|CDD|183099 PRK11361, PRK11361, acetoacetate metabolism regulatory protein
AtoC; Provisional.
Length = 457
Score = 157 bits (398), Expect = 7e-39
Identities = 130/490 (26%), Positives = 218/490 (44%), Gaps = 61/490 (12%)
Query: 12 RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
R+LI+D +D +++ G++ N + L + I +V+ + + E D
Sbjct: 6 RILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIK 65
Query: 70 ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF----LNLVSRKQL----C 117
LK + P+I+ T + ++ L C ++ + K F LNL+ ++ L
Sbjct: 66 ALKEMRSHETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQLQSM 125
Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
I L + + S + H ++ SPAM+ + K ++I GE G GK+
Sbjct: 126 KKEIRHLHQALSTSWQWGH-----ILTNSPAMMDICKDTAKIALSQASVLISGESGTGKE 180
Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGT 236
++R IH + +RA PF VNC + + +E LFG + T G F AN GT
Sbjct: 181 LIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGHEKGAFTGAQTLRQGLFERANEGT 240
Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
++L+E +PL +Q ++ ++ + E I++D+R+I T ++L VK FR+
Sbjct: 241 LLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFRE 300
Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWID 356
DL+YR++V + + LR R EDI L + FLQ F ++N I I A+SLLT + W
Sbjct: 301 DLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWPG 360
Query: 357 NVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILD 416
N++EL N++ RAV+ + + S+ +
Sbjct: 361 NIRELSNVIERAVV---------------------------MNSGPIIF-----SEDLPP 388
Query: 417 NLSQESIPAIG----QDGEVRRL----SDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTL 468
+ Q A GE R L +EK II ++ + A LGI R L
Sbjct: 389 QIRQPVCNAGEVKTAPVGE-RNLKEEIKRVEKRIIMEVLEQQEGNRTRTALMLGISRRAL 447
Query: 469 YRKIREYNIE 478
K++EY I+
Sbjct: 448 MYKLQEYGID 457
>gnl|CDD|182842 PRK10923, glnG, nitrogen regulation protein NR(I); Provisional.
Length = 469
Score = 155 bits (394), Expect = 2e-38
Identities = 115/428 (26%), Positives = 200/428 (46%), Gaps = 34/428 (7%)
Query: 66 DKENILKNIVDKIPIVPIIVQTTQDNIKI-LNCF---LYNRISKFF-----LNLVSRKQL 116
D +LK I + P++P+I+ T ++ ++ + ++ + K F + LV R
Sbjct: 61 DGLALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERA-- 118
Query: 117 CDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGK 176
I +E P + +I +PAM V + + +I ++I GE G GK
Sbjct: 119 ----ISHYQEQQQPRNIQVNGPTTDIIGEAPAMQDVFRIIGRLSRSSISVLINGESGTGK 174
Query: 177 KRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL-GKFIEANGG 235
+ ++ +H RA PF +N I +D IE LFG + G+F +A+GG
Sbjct: 175 ELVAHALHRHSPRAKAPFIALNMAAIPKDLIESELFGHEKGAFTGANTIRQGRFEQADGG 234
Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
T+ L+E +PL VQ R+ + G+ +++DVR+I T +NL +V+ FR
Sbjct: 235 TLFLDEIGDMPLDVQTRLLRVLADGQFYRVGGYAPVKVDVRIIAATHQNLEQRVQEGKFR 294
Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
+DL++R++V +++ LR R EDIP L FLQ + ++ + + + LT+ W
Sbjct: 295 EDLFHRLNVIRVHLPPLRERREDIPRLARHFLQVAARELGVEAKLLHPETEAALTRLAWP 354
Query: 356 DNVQELKNIL-LRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTI 414
NV++L+N V+ L +D L E+ T D+
Sbjct: 355 GNVRQLENTCRWLTVMAAGQEVLIQDLPGELF------------ESTVPESTSQMQPDSW 402
Query: 415 LDNLSQESIPAIGQDGEVRRLSD----IEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYR 470
L+Q + A+ + G LS+ +E+ ++ A++ + E AR LG GR+TL R
Sbjct: 403 ATLLAQWADRAL-RSGHQNLLSEAQPELERTLLTTALRHTQGHKQEAARLLGWGRNTLTR 461
Query: 471 KIREYNIE 478
K++E +E
Sbjct: 462 KLKELGME 469
>gnl|CDD|162808 TIGR02329, propionate_PrpR, propionate catabolism operon regulatory
protein PrpR. At least five distinct pathways exists
for the catabolism of propionate by way of
propionyl-CoA. Members of this family represent the
transcriptional regulatory protein PrpR, whose gene is
found in most cases divergently transcribed from an
operon for the methylcitric acid cycle of propionate
catabolism. 2-methylcitric acid, a catabolite by this
pathway, is a coactivator of PrpR.
Length = 526
Score = 141 bits (357), Expect = 4e-34
Identities = 89/346 (25%), Positives = 153/346 (44%), Gaps = 42/346 (12%)
Query: 139 LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVN 198
LD L+ S M QV L R ++I GE G GK+ +++ IH+ R FPF +N
Sbjct: 211 LDDLLGASAPMEQVRALVRLYARSDATVLILGESGTGKELVAQAIHQLSGRRDFPFVAIN 270
Query: 199 CGMIDQDKIEKFLFGDVDLQTKNSAQ--FLGKFIEANGGTIVLEEPDALPLAVQGRIYNF 256
CG I + +E LFG + + + G A+ GT+ L+E +PL +Q R+
Sbjct: 271 CGAIAESLLEAELFGYEEGAFTGARRGGRTGLIEAAHRGTLFLDEIGEMPLPLQTRLLRV 330
Query: 257 IETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRS 316
+E ++ + +DVR++ T L V+ FR+DL+YR+S+ I + LR R
Sbjct: 331 LEEREVVRVGGTEPVPVDVRVVAATHCALTTAVQQGRFRRDLFYRLSILRIALPPLRERP 390
Query: 317 EDI-PWLVHFFLQSFC------TKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAV 369
DI P + +Q+ ++ A + ++ L +YPW NV+EL+N++ R
Sbjct: 391 GDILPLAAEYLVQAAAALRLPDSEAAAQVLAGVADPLQ---RYPWPGNVRELRNLVERLA 447
Query: 370 IGLK--DSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIG 427
+ L + + L+ E L++ S
Sbjct: 448 LELSAMPAGALTPDVLRALAPE----------------------------LAEASGKGKT 479
Query: 428 QDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
+R S +E + A++ + A+ LGI R+TL+R+++
Sbjct: 480 SALSLRERSRVEALAVRAALERFGGDRDAAAKALGISRTTLWRRLK 525
>gnl|CDD|179916 PRK05022, PRK05022, anaerobic nitric oxide reductase transcription
regulator; Provisional.
Length = 509
Score = 131 bits (332), Expect = 4e-31
Identities = 98/356 (27%), Positives = 175/356 (49%), Gaps = 45/356 (12%)
Query: 130 PSQENEHCALDS--LIAVSPAM------IQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
++ AL +I SPAM I+VV + ++I GE GVGK+ ++R
Sbjct: 175 VAEFLRQEALKEGEMIGQSPAMQQLKKEIEVV------AASDLNVLILGETGVGKELVAR 228
Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTK------NSAQFLGKFIEANGG 235
IH + RA P +NC + + E LFG V K S + GKF A+GG
Sbjct: 229 AIHAASPRADKPLVYLNCAALPESLAESELFGHV----KGAFTGAISNR-SGKFELADGG 283
Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
T+ L+E LPLA+Q ++ ++ G+I+ S ++R+DVR+I T ++L +V++ FR
Sbjct: 284 TLFLDEIGELPLALQAKLLRVLQYGEIQRVGSDRSLRVDVRVIAATNRDLREEVRAGRFR 343
Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
DLY+R+SVF +++ LR R +D+ L +FL+ + ++ + +S A + L Y W
Sbjct: 344 ADLYHRLSVFPLSVPPLRERGDDVLLLAGYFLEQNRARLGLRSLRLSPAAQAALLAYDWP 403
Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
NV+EL++++ RA + + ++ L + H + ++ L
Sbjct: 404 GNVRELEHVISRAALLARARG---AGRIVTLEAQ-------HLDLP---------AEVAL 444
Query: 416 DNLSQESIPAIGQDGEVRRLSDI-EKEIIGLAMKLYRAQMSEVARRLGIGRSTLYR 470
+ PA +R ++ ++++I A+ ++ + AR L + R+ L+R
Sbjct: 445 PPPEAAAAPAAVVSQNLREATEAFQRQLIRQALAQHQGNWAAAARALELDRANLHR 500
>gnl|CDD|185070 PRK15115, PRK15115, response regulator GlrR; Provisional.
Length = 444
Score = 127 bits (321), Expect = 6e-30
Identities = 98/361 (27%), Positives = 172/361 (47%), Gaps = 6/361 (1%)
Query: 12 RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKEN 69
+L++D D +K++ + S GY V L +++ +V+++ L E D
Sbjct: 7 HLLLVDDDPGLLKLLGMRLTSEGYSVVTAESGQEALRVLNREKVDLVISDLRMDEMDGMQ 66
Query: 70 ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
+ I P +P+I+ T +I + F V R L +I AL E
Sbjct: 67 LFAEIQKVQPGMPVIILTAHGSIPDAVAATQQGVFSFLTKPVDRDALYKAIDDAL-EQSA 125
Query: 130 PSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR 189
P+ + +++ SP M+++++ AR + ++I G+ G GK+ L++ IH + R
Sbjct: 126 PATDERWRE--AIVTRSPLMLRLLEQARMVAQSDVSVLINGQSGTGKEILAQAIHNASPR 183
Query: 190 AFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLA 248
A PF +NCG + + +E LFG T + G F A GGT+ L+E +P
Sbjct: 184 ASKPFIAINCGALPEQLLESELFGHARGAFTGAVSNREGLFQAAEGGTLFLDEIGDMPAP 243
Query: 249 VQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLIN 308
+Q ++ ++ K+ S I +DVR+I T ++L + FR+DLYYR++V +
Sbjct: 244 LQVKLLRVLQERKVRPLGSNRDIDIDVRIISATHRDLPKAMARGEFREDLYYRLNVVSLK 303
Query: 309 ISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRA 368
I L R+EDIP L + L+ ++ + S A+ L W NV++L N++ +
Sbjct: 304 IPALAERTEDIPLLANHLLRQAAERHKPFVRAFSTDAMKRLMTASWPGNVRQLVNVIEQC 363
Query: 369 V 369
V
Sbjct: 364 V 364
>gnl|CDD|185327 PRK15429, PRK15429, formate hydrogenlyase transcriptional activator
FhlA; Provisional.
Length = 686
Score = 124 bits (313), Expect = 5e-29
Identities = 117/434 (26%), Positives = 185/434 (42%), Gaps = 70/434 (16%)
Query: 58 LSLINCEDD-----KENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVS 112
L L CE+ +L+ I +++ I + N Y I + LV
Sbjct: 312 LKLAQCEEKVFTTTNLKLLRQIAERVAIA------------VDNALAYQEIHRLKERLVD 359
Query: 113 RKQLCDSIICALREGV--VPSQENEHCALDSLIAVSPAMIQV---VDLARKAGDCAIPIM 167
AL E + V S+ E +I S AM V V++ ++ D + +
Sbjct: 360 EN-------LALTEQLNNVDSEFGE------IIGRSEAMYSVLKQVEMVAQS-DSTV--L 403
Query: 168 IQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFL 226
I GE G GK+ ++R IH R +NC + +E LFG + T SAQ +
Sbjct: 404 ILGETGTGKELIARAIHNLSGRNNRRMVKMNCAAMPAGLLESDLFGHERGAFTGASAQRI 463
Query: 227 GKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLL 286
G+F A+ ++ L+E +PL +Q ++ ++ + E S I+ DVRLI T ++L
Sbjct: 464 GRFELADKSSLFLDEVGDMPLELQPKLLRVLQEQEFERLGSNKIIQTDVRLIAATNRDLK 523
Query: 287 PQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKAL 346
V FR DLYYR++VF I++ LR R EDIP LV F + SI + L
Sbjct: 524 KMVADREFRSDLYYRLNVFPIHLPPLRERPEDIPLLVKAFTFKIARRMGRNIDSIPAETL 583
Query: 347 SLLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYT 406
L+ W NV+EL+N++ RAV LL+R + T T
Sbjct: 584 RTLSNMEWPGNVRELENVIERAV---------------LLTRGNVLQLSLPDITLPEPET 628
Query: 407 EGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRS 466
++ + G+D E + + + KE G+ A A+RLG+ R+
Sbjct: 629 PPAATV----------VAQEGED-EYQLIVRVLKETNGVV-----AGPKGAAQRLGLKRT 672
Query: 467 TLYRKIREYNIEVD 480
TL +++ I+
Sbjct: 673 TLLSRMKRLGIDKS 686
>gnl|CDD|185322 PRK15424, PRK15424, propionate catabolism operon regulatory protein
PrpR; Provisional.
Length = 538
Score = 116 bits (293), Expect = 1e-26
Identities = 93/358 (25%), Positives = 152/358 (42%), Gaps = 64/358 (17%)
Query: 139 LDSLIAVSPAMIQVVDL----ARKAGDCAIPIMIQGEFGVGKKRLSRFIH---------E 185
L L+ SP M QV AR + ++IQGE G GK+ ++ IH
Sbjct: 218 LGDLLGQSPQMEQVRQTILLYARSSAA----VLIQGETGTGKELAAQAIHREYFARHDAR 273
Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQ--FLGKFIEANGGTIVLEEPD 243
GK++ PF VNCG I + +E LFG + S + G F A+GGT+ L+E
Sbjct: 274 QGKKSH-PFVAVNCGAIAESLLEAELFGYEEGAFTGSRRGGRAGLFEIAHGGTLFLDEIG 332
Query: 244 ALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRIS 303
+PL +Q R+ +E ++ + +DVR+I T +L V+ FR+DL+YR+S
Sbjct: 333 EMPLPLQTRLLRVLEEKEVTRVGGHQPVPVDVRVISATHCDLEEDVRQGRFRRDLFYRLS 392
Query: 304 VFLINISTLRSRSEDIPWL-VHFFLQSFC------TKNAIKQISISDKALSLLTKYPWID 356
+ + + LR R DI L F QS + + + + +LL Y W
Sbjct: 393 ILRLQLPPLRERVADILPLAESFLKQSLAALSAPFSAALRQGLQ---QCETLLLHYDWPG 449
Query: 357 NVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILD 416
NV+EL+N++ +R L LS E +
Sbjct: 450 NVRELRNLM--------------ERLALFLSVEPT--------------------PDLTP 475
Query: 417 NLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE 474
Q +P + ++ + + A++ + + A LGI R+TL+R+++
Sbjct: 476 QFLQLLLPELARESAKTPAPRLLAATLQQALERFNGDKTAAANYLGISRTTLWRRLKA 533
>gnl|CDD|163093 TIGR02974, phageshock_pspF, psp operon transcriptional activator
PspF. Members of this protein family are PspF, the
sigma-54-dependent transcriptional activator of the
phage shock protein (psp) operon, in Escherichia coli
and numerous other species. The psp operon is induced by
a number of stress conditions, including heat shock,
ethanol, and filamentous phage infection. Changed
com_name to adhere to TIGR role notes conventions.
09/15/06 - DMH.
Length = 329
Score = 112 bits (282), Expect = 2e-25
Identities = 69/230 (30%), Positives = 113/230 (49%), Gaps = 2/230 (0%)
Query: 142 LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGM 201
LI S A ++V++ + P++I GE G GK+ ++ +H KR P +NC
Sbjct: 1 LIGESNAFLEVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYLSKRWQGPLVKLNCAA 60
Query: 202 IDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETG 260
+ ++ ++ LFG + T + G+F A+GGT+ L+E L VQ ++ IE G
Sbjct: 61 LSENLLDSELFGHEAGAFTGAQKRHQGRFERADGGTLFLDELATASLLVQEKLLRVIEYG 120
Query: 261 KIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIP 320
+ E +++DVRL+ T +L FR DL R++ +I + LR R EDI
Sbjct: 121 EFERVGGSQTLQVDVRLVCATNADLPALAAEGRFRADLLDRLAFDVITLPPLRERQEDIM 180
Query: 321 WLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPWIDNVQELKNILLRAV 369
L F + + + +A L +Y W NV+ELKN++ R+V
Sbjct: 181 LLAEHFAIRMARELGLPLFPGFTPQAREQLLEYHWPGNVRELKNVVERSV 230
>gnl|CDD|183227 PRK11608, pspF, phage shock protein operon transcriptional
activator; Provisional.
Length = 326
Score = 95.5 bits (238), Expect = 2e-20
Identities = 66/248 (26%), Positives = 123/248 (49%), Gaps = 2/248 (0%)
Query: 139 LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVN 198
D+L+ + + ++V++ + P++I GE G GK+ ++ +H R PF +N
Sbjct: 5 KDNLLGEANSFLEVLEQVSRLAPLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLN 64
Query: 199 CGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFI 257
C ++++ ++ LFG + T + G+F A+GGT+ L+E P+ VQ ++ I
Sbjct: 65 CAALNENLLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDELATAPMLVQEKLLRVI 124
Query: 258 ETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSE 317
E G++E ++++VRL+ T +L V FR DL R++ ++ + LR R
Sbjct: 125 EYGELERVGGSQPLQVNVRLVCATNADLPAMVAEGKFRADLLDRLAFDVVQLPPLRERQS 184
Query: 318 DIPWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSH 376
DI + F C + + +++A L Y W N++ELKN++ R+V S
Sbjct: 185 DIMLMAEHFAIQMCRELGLPLFPGFTERARETLLNYRWPGNIRELKNVVERSVYRHGTSE 244
Query: 377 LTEDRFVL 384
D ++
Sbjct: 245 YPLDNIII 252
>gnl|CDD|162672 TIGR02040, PpsR-CrtJ, transcriptional regulator PpsR. This model
represents the transcriptional regulator PpsR which is
strictly associated with photosynthetic proteobacteria
and found in photosynthetic operons. PpsR has been
reported to be a repressor. These proteins contain a
Helix-Turn_Helix motif of the "fis" type (pfam02954).
Length = 442
Score = 34.8 bits (80), Expect = 0.051
Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 432 VRRLSD-IEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
VR +D +E+ I A++L R + A LG+ R +LY K+R Y +
Sbjct: 396 VRETTDVVEQLCIEAALELTRDNRASAAEILGLSRQSLYVKLRRYGL 442
>gnl|CDD|162580 TIGR01884, cas_HTH, CRISPR locus-related DNA-binding protein. Most
but not all examples of this family are associated with
CRISPR loci, a combination of DNA repeats and
characteristic proteins encoded near the repeat cluster.
The C-terminal region of this protein is homologous to
DNA-binding helix-turn-helix domains with predicted
transcriptional regulatory activity.
Length = 203
Score = 33.1 bits (76), Expect = 0.14
Identities = 14/64 (21%), Positives = 31/64 (48%), Gaps = 6/64 (9%)
Query: 411 SDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYR 470
S+ ++D + + +P + LS E +++ + + +A++LG ST+ R
Sbjct: 123 SEELIDFILLDLVPLL------AGLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISR 176
Query: 471 KIRE 474
+RE
Sbjct: 177 HLRE 180
>gnl|CDD|149019 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 139
Score = 32.7 bits (75), Expect = 0.21
Identities = 23/129 (17%), Positives = 48/129 (37%), Gaps = 18/129 (13%)
Query: 165 PIMIQGEFGVGKKRLSRFIHESGKRAF--FPFFIVNCGMIDQDKIEKFLFGDVDLQTKNS 222
+++ G G GK L+ + A P F V + +D E+ L G ++ +
Sbjct: 1 GVLLVGPPGTGKSELAERL----AAALSNRPVFYV---QLTRDTTEEDLKGRRNIANGTT 53
Query: 223 AQFLGKFIEA--NGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLD------ 274
+ G + A G VL+E + V + + ++ ++ + +++
Sbjct: 54 SWVDGPLVRAAREGEIAVLDEINRANPDVLNSLLSLLDERRLLLPEGGELVKVAPDDFAK 113
Query: 275 -VRLIFLTE 282
RLI
Sbjct: 114 RFRLIATMN 122
>gnl|CDD|180266 PRK05803, PRK05803, sporulation sigma factor SigK; Reviewed.
Length = 233
Score = 32.6 bits (75), Expect = 0.25
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 5/36 (13%)
Query: 435 LSDIEKEII----GLAMKLYRAQMSEVARRLGIGRS 466
L + EKE+I GL + Q E+A+ LGI RS
Sbjct: 176 LDEREKEVIEMRYGLGNGKEKTQR-EIAKALGISRS 210
>gnl|CDD|128665 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 32.0 bits (72), Expect = 0.33
Identities = 20/123 (16%), Positives = 46/123 (37%), Gaps = 9/123 (7%)
Query: 165 PIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQ 224
I+I G G GK L+R + ++ I ++ +++ L V + + +
Sbjct: 4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSG 63
Query: 225 FLGKFI------EANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLI 278
L + + ++L+E +L A Q + +E ++ ++ +I
Sbjct: 64 ELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKS---EKNLTVI 120
Query: 279 FLT 281
T
Sbjct: 121 LTT 123
>gnl|CDD|179020 PRK00430, fis, global DNA-binding transcriptional dual regulator
Fis; Provisional.
Length = 95
Score = 30.4 bits (69), Expect = 1.0
Identities = 13/43 (30%), Positives = 26/43 (60%)
Query: 435 LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
L+++E ++ + M+ R + A LGI R TL +K+++Y +
Sbjct: 52 LAEVEAPLLDMVMQYTRGNQTRAALMLGINRGTLRKKLKKYGM 94
>gnl|CDD|130825 TIGR01764, excise, DNA binding domain, excisionase family. An
excisionase, or Xis protein, is a small protein that
binds and promotes excisive recombination; it is not
enzymatically active. This model represents a number of
putative excisionases and related proteins from
temperate phage, plasmids, and transposons, as well as
DNA binding domains of other proteins, such as a DNA
modification methylase. This model identifies mostly
small proteins and N-terminal regions of large proteins,
but some proteins appear to have two copies. This domain
appears similar, in both sequence and predicted
secondary structure (PSIPRED) to the MerR family of
transcriptional regulators (pfam00376).
Length = 49
Score = 30.3 bits (69), Expect = 1.2
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 455 SEVARRLGIGRSTLYRKIRE 474
E A LG+ + T+YR I E
Sbjct: 5 EEAAEYLGVSKDTVYRLIHE 24
>gnl|CDD|162975 TIGR02684, dnstrm_HI1420, probable addiction module antidote
protein. gene pairs, when found on the bacterial
chromosome, are located often with prophage regions, but
also both in integrated plasmid regions and in
housekeeping gene regions. Analysis suggests that the
gene pair may serve as an addiction module.
Length = 89
Score = 29.6 bits (67), Expect = 1.8
Identities = 7/21 (33%), Positives = 15/21 (71%)
Query: 454 MSEVARRLGIGRSTLYRKIRE 474
M+++AR+ G+ R +LY+ +
Sbjct: 46 MTQLARKTGLSRESLYKALSG 66
>gnl|CDD|180133 PRK05565, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 247
Score = 29.4 bits (67), Expect = 1.8
Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 17/73 (23%)
Query: 13 VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLINCEDDKENILK 72
V+ D ++E + + + ++ G D V +D+S E+D EN+++
Sbjct: 33 VIAYDINEEAAQELLEEIKEEGGDAIAV-KADVS----------------SEEDVENLVE 75
Query: 73 NIVDKIPIVPIIV 85
IV+K + I+V
Sbjct: 76 QIVEKFGKIDILV 88
>gnl|CDD|183559 PRK12496, PRK12496, hypothetical protein; Provisional.
Length = 164
Score = 29.6 bits (67), Expect = 1.9
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 14/62 (22%)
Query: 419 SQESIPAIGQ----DGEVRRLSDIEKEIIGLAMKL--------YRAQMSEVARRLGIGRS 466
S ESI + + G++ RLS+ + E++ LA++L Y Q VA++L I
Sbjct: 56 SPESIEKVEEAAIKTGDLMRLSNTDIEVLALALELNGTLYTDDYGIQ--NVAKKLNIKFE 113
Query: 467 TL 468
+
Sbjct: 114 NI 115
>gnl|CDD|114641 pfam05930, Phage_AlpA, Prophage CP4-57 regulatory protein (AlpA).
This family consists of several short bacterial and
phage proteins which are related to the E. coli protein
AlpA. AlpA suppress two phenotypes of a delta lon
protease mutant, overproduction of capsular
polysaccharide and sensitivity to UV light. Several of
the sequences in this family are thought to be
DNA-binding proteins.
Length = 51
Score = 29.2 bits (66), Expect = 2.4
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 454 MSEVARRLGIGRSTLYRKIRE 474
+ EV + G+ RST+YR I++
Sbjct: 6 LKEVEQLTGLSRSTIYRLIKD 26
>gnl|CDD|182015 PRK09646, PRK09646, RNA polymerase sigma factor SigK; Reviewed.
Length = 194
Score = 29.3 bits (66), Expect = 2.4
Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 433 RRLSDIEKEIIGLAMKLYRA-QMSEVARRLGIGRSTLYRKIRE 474
L+D ++E + LA Y EVA RL + T+ ++R+
Sbjct: 141 DALTDTQRESVTLAY--YGGLTYREVAERLAVPLGTVKTRMRD 181
>gnl|CDD|163446 TIGR03734, PRTRC_parB, PRTRC system ParB family protein. A novel
genetic system characterized by six major proteins,
included a ParB homolog and a ThiF homolog, is
designated PRTRC, or ParB-Related,ThiF-Related Cassette.
It is often found on plasmids. This protein family the
member related to ParB, and is designated PRTRC system
ParB family protein.
Length = 554
Score = 28.9 bits (65), Expect = 3.3
Identities = 21/70 (30%), Positives = 29/70 (41%), Gaps = 25/70 (35%)
Query: 423 IPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMS--------------------EVARRLG 462
IPA+ ++ L+D E E L + RA MS E ARRLG
Sbjct: 66 IPAL-----IKVLTDEEAEAAALIENVQRADMSPAEEAEAAARLLGRCKGDREEAARRLG 120
Query: 463 IGRSTLYRKI 472
+TL R++
Sbjct: 121 WSPATLDRRL 130
>gnl|CDD|128638 smart00344, HTH_ASNC, helix_turn_helix ASNC type. AsnC: an
autogenously regulated activator of asparagine
synthetase A transcription in Escherichia coli.
Length = 108
Score = 28.6 bits (65), Expect = 4.1
Identities = 10/39 (25%), Positives = 27/39 (69%)
Query: 435 LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
L +I+++I+ K R ++E+A+++G+ ST++ +++
Sbjct: 1 LDEIDRKILEELQKDARISLAELAKKVGLSPSTVHNRVK 39
>gnl|CDD|181747 PRK09274, PRK09274, peptide synthase; Provisional.
Length = 552
Score = 27.9 bits (63), Expect = 5.2
Identities = 12/34 (35%), Positives = 21/34 (61%), Gaps = 4/34 (11%)
Query: 158 KAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAF 191
KAG A+P+++ + G+G K L + + E+ AF
Sbjct: 88 KAG--AVPVLV--DPGMGIKNLKQCLAEAQPDAF 117
>gnl|CDD|148413 pfam06792, UPF0261, Uncharacterized protein family (UPF0261).
Length = 403
Score = 27.9 bits (63), Expect = 6.4
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 9/52 (17%)
Query: 11 KRVLII---DKDDEQIKIIKDHVESYGYDVFIVNVSDLST------ISKIQV 53
K +LII D E+++ ++D +E+ G +V +++VS L IS +V
Sbjct: 2 KTILIIGTLDTKGEELRFLRDLIEAQGLEVLVIDVSVLGPPSFPVDISAEEV 53
>gnl|CDD|180766 PRK06940, PRK06940, short chain dehydrogenase; Provisional.
Length = 275
Score = 27.7 bits (62), Expect = 6.5
Identities = 11/43 (25%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 11 KRVLIIDKDDEQIKIIKDHVESYGYDV--FIVNVSDLSTISKI 51
K+VL+ D ++E ++ + G+DV V+VS ++ +
Sbjct: 25 KKVLLADYNEENLEAAAKTLREAGFDVSTQEVDVSSRESVKAL 67
>gnl|CDD|183457 PRK12344, PRK12344, putative alpha-isopropylmalate/homocitrate
synthase family transferase; Provisional.
Length = 524
Score = 27.4 bits (62), Expect = 8.8
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 5/28 (17%)
Query: 454 MSEVARRLGIGRSTLYRKIREYNIEVDS 481
+SE+A GRS + K +E I++D
Sbjct: 331 VSELA-----GRSNILAKAKELGIDLDK 353
>gnl|CDD|150115 pfam09339, HTH_IclR, IclR helix-turn-helix domain.
Length = 52
Score = 27.4 bits (62), Expect = 9.0
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 455 SEVARRLGIGRSTLYR 470
+E+ARR G+ +ST +R
Sbjct: 22 TEIARRTGLPKSTAHR 37
>gnl|CDD|128724 smart00448, REC, cheY-homologous receiver domain. CheY regulates
the clockwise rotation of E. coli flagellar motors.
This domain contains a phosphoacceptor site that is
phosphorylated by histidine kinase homologues.
Length = 55
Score = 27.2 bits (61), Expect = 10.0
Identities = 12/50 (24%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 11 KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFL 58
R+L++D D +++K +E GY+V + L + + + ++I L
Sbjct: 1 MRILVVDDDPLLRELLKALLEREGYEVDEATDGEEALELLKEEKPDLILL 50
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.323 0.141 0.401
Gapped
Lambda K H
0.267 0.0684 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 7,823,737
Number of extensions: 520082
Number of successful extensions: 1168
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1133
Number of HSP's successfully gapped: 64
Length of query: 482
Length of database: 5,994,473
Length adjustment: 97
Effective length of query: 385
Effective length of database: 3,898,497
Effective search space: 1500921345
Effective search space used: 1500921345
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 (26.6 bits)