Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein (TIGR)
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__DvH:206505 Length = 524 Score = 272 bits (695), Expect = 3e-77 Identities = 172/496 (34%), Positives = 269/496 (54%), Gaps = 19/496 (3%) Query: 6 AFRGDRMEILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLK 65 A R D +++ +GI K F V A ++ ++ I +L+GENGAGKSTL+ IL+G L Sbjct: 26 ALRHDVTPVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLA 85 Query: 66 PDAGEILVNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLS 125 D G I V+GE V F SP DA K GI +++Q L D+MTVAEN+ L GQ Sbjct: 86 QDTGIIHVDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLL------GQSGAWL 139 Query: 126 SRVDENYMYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTS 185 S V +M EL G P A V +L+ +RQ VEI K L ++ R++ +DEPT+ Sbjct: 140 SPV---HMSRVVAELAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTA 196 Query: 186 SLTVEETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDV 245 LT ETE+LFE + + G ++VF+SH++ EV+ ++D I ++R G+ + E + E Sbjct: 197 VLTPGETEQLFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPG 256 Query: 246 DT-IIKMMVGREVEFFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVG 304 + + MVGREV PG+ L V L D +K +SFEVRKGEV AG+ G Sbjct: 257 EAELANRMVGREVILEVAAEPLEPGDRVLHVDGLA-GDGLKGLSFEVRKGEVFAIAGVAG 315 Query: 305 AGRTETMLLVFGVNQKESGDIYVNG---RKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRM 361 G+ E + V G+ + G++ + G R+ K P G+ IPEDR+ L + Sbjct: 316 NGQRELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQG---GLAYIPEDRQGLATCLSL 372 Query: 362 TVKDNIVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVV 421 + DN +L + +R G LD + + + D + +++ +LSGGN QK+V Sbjct: 373 DLVDNFLLTARGCFTR-GPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLV 431 Query: 422 LAKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRI 481 + + +++ + PT+G+D+ A E+ + E+ + V+++S +L E+L L+DR+ Sbjct: 432 VGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSHA-GVLLVSGDLNEVLALADRV 490 Query: 482 VVMWEGEITAVLDNRE 497 VM+ G +LD + Sbjct: 491 AVMYRGCFIGLLDRSD 506 Score = 64.3 bits (155), Expect = 1e-14 Identities = 57/231 (24%), Positives = 108/231 (46%), Gaps = 10/231 (4%) Query: 33 VDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVEFHSPVDAFKKGIS 92 + FEV + E+ ++ G G G+ L++ +TG+ +P GE+ + G + G++ Sbjct: 298 LSFEVRKGEVFAIAGVAGNGQRELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQGGLA 357 Query: 93 VI---HQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSKELLDLIGAKFS 149 I Q L C ++ + +N L T +D ++++L + Sbjct: 358 YIPEDRQGLATCLSLDLVDNFLLTARGCF----TRGPFLDRKSADAAARDILAEYNVQPG 413 Query: 150 -PDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEMLKSRGIS 208 +A R+L+ Q + + + ++P +I + PT L + TE ++ + ++S Sbjct: 414 RAEAPARSLSGGNLQKLVVGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSHA-G 472 Query: 209 VVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFD-VDTIIKMMVGREVE 258 V+ VS L+EV+ ++DR+ VM G IG L + + + VD I MM G E Sbjct: 473 VLLVSGDLNEVLALADRVAVMYRGCFIGLLDRSDTNKVDAIGLMMAGVSCE 523 Lambda K H 0.319 0.138 0.381 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: 653 Number of extensions: 45 Number of successful extensions: 10 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: 520 Length of database: 524 Length adjustment: 35 Effective length of query: 485 Effective length of database: 489 Effective search space: 237165 Effective search space used: 237165 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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