Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate GFF3463 PS417_17730 ribonucleotide-diphosphate reductase subunit alpha
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__WCS417:GFF3463 Length = 502 Score = 396 bits (1018), Expect = e-115 Identities = 213/502 (42%), Positives = 322/502 (64%), Gaps = 14/502 (2%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73 +LK + I KR+PGV A+ +++ +V EI +L+GENGAGKSTL+KIL GV D G+IL+ Sbjct: 4 LLKLENICKRYPGVQALKSINLQVERGEIHALLGENGAGKSTLMKILGGVEHQDEGQILI 63 Query: 74 NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSR---VDE 130 +G+ +F + DA GI ++ QE +L +T ENIFL +E LS+R + + Sbjct: 64 DGQAQQFATYRDAIAAGIGIVFQEFSLIPYLTAVENIFLGHE--------LSNRFGLLRK 115 Query: 131 NYMYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVE 190 M S+ L +G V++L+ A++Q VEI KAL + R++ +DEPT++LT Sbjct: 116 REMVEASEALFKRLGVTIDLQCAVKHLSVAEQQFVEIAKALALDARLLVLDEPTATLTPS 175 Query: 191 ETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIK 250 E E LFEI+ LK +G++V+F+SH L+E+ ++ DRI V+RDG +G + D+D +++ Sbjct: 176 EAELLFEIMRELKRQGVAVIFISHHLEEIFQVCDRISVLRDGGNVGVTDVADSDIDHLVE 235 Query: 251 MMVGREVEF-FPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTE 309 MMVGR + FP G + LEV++++ + F++ KGE+LGFAGLVG+GRTE Sbjct: 236 MMVGRRLACSFPPKPTRERGPLLLEVKDIQLVRNGPHNRFQLHKGEILGFAGLVGSGRTE 295 Query: 310 TMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVL 369 L + G S D+++ G K+ + +P A+ GIGL+PE RK +GL+ ++++NI L Sbjct: 296 LALGMMGALPSVSKDVWLRGEKITLDDPAQALAHGIGLLPESRKSEGLITDFSIRENISL 355 Query: 370 PSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATN 429 +L K ++D+ +E E +K+LSIK PS NLSGGNQQKVV+A+W+ + Sbjct: 356 NNLPKYQNASGLIDKNRECASVEGLMKQLSIKAPSSESRVFNLSGGNQQKVVIARWINHH 415 Query: 430 ADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEI 489 D+L+FDEPTRGIDVGAKA+I+ ++R L QG A+IMISSELPEI+ + DR+ V +G I Sbjct: 416 CDVLVFDEPTRGIDVGAKAQIYALMRSLTEQGYAIIMISSELPEIIGMCDRVAVFHKGAI 475 Query: 490 TAVLDNREKRVTQEEIMYYASG 511 +L+ V +E+M +A+G Sbjct: 476 VKLLE--ASAVNPQEVMRHATG 495 Score = 72.8 bits (177), Expect = 3e-17 Identities = 49/229 (21%), Positives = 107/229 (46%), Gaps = 7/229 (3%) Query: 35 FEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVEFHSPVDAFKKGISVI 94 F++++ EI+ G G+G++ L + G L + ++ + GE++ P A GI ++ Sbjct: 275 FQLHKGEILGFAGLVGSGRTELALGMMGALPSVSKDVWLRGEKITLDDPAQALAHGIGLL 334 Query: 95 HQELN---LCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSKELLDLIGAKF-SP 150 + L + ++ ENI L + + S +D+N + L+ + K S Sbjct: 335 PESRKSEGLITDFSIRENISLNNLP---KYQNASGLIDKNRECASVEGLMKQLSIKAPSS 391 Query: 151 DALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEMLKSRGISVV 210 ++ V NL+ +Q V I + + ++ DEPT + V +++ ++ L +G +++ Sbjct: 392 ESRVFNLSGGNQQKVVIARWINHHCDVLVFDEPTRGIDVGAKAQIYALMRSLTEQGYAII 451 Query: 211 FVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVGREVEF 259 +S L E++ + DR+ V G + L+ + +++ G E+ Sbjct: 452 MISSELPEIIGMCDRVAVFHKGAIVKLLEASAVNPQEVMRHATGGSSEY 500 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: 645 Number of extensions: 32 Number of successful extensions: 7 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: 502 Length adjustment: 35 Effective length of query: 485 Effective length of database: 467 Effective search space: 226495 Effective search space used: 226495 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