Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__Putida:PP_2455 Length = 524 Score = 327 bits (838), Expect = 7e-94 Identities = 187/486 (38%), Positives = 291/486 (59%), Gaps = 25/486 (5%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73 +L A G+ K + V + V + E+++L GENGAGKSTL K+++G+ P G + Sbjct: 16 VLAASGLGKTYAQPV-LGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGHMTY 74 Query: 74 NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133 G+ S +A + G+ ++ QELNL +TVAEN+FL + + Sbjct: 75 RGQAYAPGSRGEAERLGVRMVMQELNLLPTLTVAENLFL-------------DNLPSRFG 121 Query: 134 YTRSKELLDLIGAKFS--------PDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTS 185 + K L L A + PD V L +QMVEI + L+ + ++ +DEPT+ Sbjct: 122 WISHKRLRQLATAAMARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTA 181 Query: 186 SLTVEETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDV 245 LT E LF IE L++RG+++V++SHRL+E+ R++ RIVV+RDGK + + + Sbjct: 182 MLTAREVALLFTQIERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSS 241 Query: 246 DTIIKMMVGREVEFFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGA 305 ++ +MVGRE+ + G L+V L DKV+ VSFEVR GE+ G +GL+GA Sbjct: 242 AELVNLMVGRELGEHIDLGRRQLGAPLLKVDKLCRGDKVREVSFEVRAGEIFGISGLIGA 301 Query: 306 GRTETMLLVFGVNQKESGDIYVNG--RKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTV 363 GRTE + L++G ++ +SG I + + V I +P+ A++ GI LI EDRK +GL+L ++ Sbjct: 302 GRTELLRLIYGADRADSGGIALGQPPQAVSIDSPKAAVRAGIALITEDRKGEGLLLTQSI 361 Query: 364 KDNIVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLA 423 NI L +L +SR G VLD E+ ++E ++ + I++ Q+ LSGGNQQKVV+ Sbjct: 362 SANIALGNLGAVSRAG-VLDSEAEKALAERQIQAMRIRSAGAQQVVGELSGGNQQKVVIG 420 Query: 424 KWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVV 483 +WL + +L+FDEPTRGIDVGAK +I+ ++ ELA QGKA++++SS+L E++ + DRI V Sbjct: 421 RWLERDCQVLLFDEPTRGIDVGAKFDIYGLLAELARQGKALVVVSSDLRELMLICDRIAV 480 Query: 484 MWEGEI 489 + G + Sbjct: 481 LSAGRL 486 Score = 72.4 bits (176), Expect = 4e-17 Identities = 59/225 (26%), Positives = 107/225 (47%), Gaps = 8/225 (3%) Query: 30 VDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNG--ERVEFHSPVDAF 87 V V FEV EI + G GAG++ L++++ G + D+G I + + V SP A Sbjct: 280 VREVSFEVRAGEIFGISGLIGAGRTELLRLIYGADRADSGGIALGQPPQAVSIDSPKAAV 339 Query: 88 KKGISVIHQELN---LCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSKELLDLI 144 + GI++I ++ L +++ NI L + L S E + R + + + Sbjct: 340 RAGIALITEDRKGEGLLLTQSISANIALGNLGAVSRAGVLDSEA-EKALAERQIQAMRIR 398 Query: 145 GAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEMLKS 204 A +V L+ +Q V I + L ++ +++ DEPT + V ++ ++ L Sbjct: 399 SA--GAQQVVGELSGGNQQKVVIGRWLERDCQVLLFDEPTRGIDVGAKFDIYGLLAELAR 456 Query: 205 RGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTII 249 +G ++V VS L E+M I DRI V+ G+ I + + D ++ Sbjct: 457 QGKALVVVSSDLRELMLICDRIAVLSAGRLIDTFARDHWSQDQLL 501 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: 639 Number of extensions: 25 Number of successful extensions: 9 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 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