Align RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate BPHYT_RS20740 BPHYT_RS20740 D-ribose transporter ATP binding protein
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__BFirm:BPHYT_RS20740 Length = 503 Score = 372 bits (954), Expect = e-107 Identities = 212/494 (42%), Positives = 312/494 (63%), Gaps = 6/494 (1%) Query: 20 ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILV 79 ++ ++ +S+ FPGV+AL V L G V AL+GENGAGKSTL+KIL G+Y + GEIL Sbjct: 4 LISVKRLSKRFPGVRALHEVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDTGEILY 63 Query: 80 DGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRT-IDWQTMNSRS 138 +G+P F S + A GV IHQE L + LT+A+N+F+G PR R +D +N+++ Sbjct: 64 EGQPVDFQSPREAQAVGVGIIHQELQLMNHLTIAQNMFIGREPRGRLGLFLDEDKLNAQA 123 Query: 139 KALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFR 198 +L + +DP + L++A++ +V IA+ALS ++R++IMDEPT+AL+ EI +LFR Sbjct: 124 HDILARMHVTLDPRALVSSLTVARQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAELFR 183 Query: 199 IVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRK-TPQDEIVRMMVGR 257 I+R LK++G I++ISHK DEL +IAD V R V V+ K T I+ MMVGR Sbjct: 184 IIRDLKKRGVGIIYISHKMDELKQIADRVTVL--RDGEYVATVAVKDTTVQAIIGMMVGR 241 Query: 258 DVENVFPKIDVAIGGPV-LEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSL 316 + + P +A G V LE+ + RD+SF LRKGEILG GL+GAGR+E+++++ Sbjct: 242 TLTDAAPSQHIANQGEVALEVTRLNAGPLVRDVSFALRKGEILGFAGLMGAGRTEVARAV 301 Query: 317 FGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLAR 376 FG SG++V++G + TI +P DA+ GI Y+ E+R R GLA M + N+ + +L + Sbjct: 302 FGADPIESGEIVVKGVKATIRNPSDAVARGIGYLSEDRKRFGLATGMSVESNIVMSNLRK 361 Query: 377 -TSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVII 435 S FLR A + L +R + + V LSGGNQQK+VI KWL V+ Sbjct: 362 FLSLNFFLRRTQIRKTAAHFINLLAIRTPSATQEVRLLSGGNQQKIVIAKWLERDCDVLF 421 Query: 436 LDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFE 495 DEPT+GID+G+K+ ++ + LA +G +I+M+SSELPEI+ MSDR++VM EG G Sbjct: 422 FDEPTRGIDVGAKSEIYKLLRSLADQGKAIVMISSELPEILRMSDRIVVMCEGRITGELA 481 Query: 496 RAELSPEALVRAAT 509 A + E +++ AT Sbjct: 482 AAGATQERIMQLAT 495 Score = 83.6 bits (205), Expect = 2e-20 Identities = 70/248 (28%), Positives = 119/248 (47%), Gaps = 20/248 (8%) Query: 273 PVLEIRNYSHR----TEFRDISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMV 328 P++ ++ S R ++ F L GE+ + G GAG+S L + L G+ +G+++ Sbjct: 3 PLISVKRLSKRFPGVRALHEVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDTGEIL 62 Query: 329 LEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLARTSRRGF------ 382 EGQ + SP++A G+ + +E L + I QNM + R R G Sbjct: 63 YEGQPVDFQSPREAQAVGVGIIHQELQ---LMNHLTIAQNMFIGREPR-GRLGLFLDEDK 118 Query: 383 LRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKG 442 L A LAR + LD RA V +L+ QQ V I K L+ +V+I+DEPT Sbjct: 119 LNAQAHDILARMHVT-LDPRAL-----VSSLTVARQQMVEIAKALSFDSRVLIMDEPTSA 172 Query: 443 IDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPE 502 ++ A + I +L G+ II +S ++ E+ ++DRV V+++G + + + Sbjct: 173 LNDAEIAELFRIIRDLKKRGVGIIYISHKMDELKQIADRVTVLRDGEYVATVAVKDTTVQ 232 Query: 503 ALVRAATG 510 A++ G Sbjct: 233 AIIGMMVG 240 Lambda K H 0.320 0.137 0.382 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 561 Number of extensions: 28 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 512 Length of database: 503 Length adjustment: 34 Effective length of query: 478 Effective length of database: 469 Effective search space: 224182 Effective search space used: 224182 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory