Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate HSERO_RS05320 HSERO_RS05320 ribonucleotide-diphosphate reductase subunit alpha
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__HerbieS:HSERO_RS05320 Length = 502 Score = 383 bits (983), Expect = e-110 Identities = 208/501 (41%), Positives = 315/501 (62%), Gaps = 11/501 (2%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73 +L+ GI K F V + VD EV E+ +L+GENGAGKSTL+KIL G+++PDAGEI + Sbjct: 1 MLQLTGIKKNFGPVTVLRGVDLEVRAGEVHALLGENGAGKSTLMKILCGIVRPDAGEIRI 60 Query: 74 NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133 +G+ F S A G+ V+ QE +L + +N+FLA E R+ + M Sbjct: 61 DGQPCRFDSYRAAIAGGVGVVFQEFSLIPYLDAVDNMFLAREL-----RSRWGWLQRAAM 115 Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193 R++E++ +G D V L+ AQ+Q VEI KAL + RI+ +DEPT++LT E E Sbjct: 116 RRRAQEIIGQLGVAIPLDVPVCKLSVAQQQFVEIAKALALDARILVLDEPTATLTPAEVE 175 Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253 LF ++ L+++G++++F+SH L+E+ I DRI V+RDG + E D +++MMV Sbjct: 176 HLFAVMRSLRAQGVAIIFISHHLEEIFEICDRITVLRDGAYVATCATAEVDQARLVEMMV 235 Query: 254 GREVE--FFPHGIE--TRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTE 309 GR +E F P + GE+ LEV L+ + + F++R+GE+LGFAGLVG+GRTE Sbjct: 236 GRRIENCFPPKPAKGGEGEGEVVLEVHALQLRRQAPVSQFQLRRGEILGFAGLVGSGRTE 295 Query: 310 TMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVL 369 T+L + G + S + ++G + +P A++ GIGL+PE RK QGL+ ++ N+ L Sbjct: 296 TVLAMLGAHAALSCKLSMHGVPLRFADPAQALQAGIGLLPESRKEQGLITSFSILHNVSL 355 Query: 370 PSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATN 429 + K GL LD R+E++ +E ++R+ +K P + LSGGNQQKVV+A+W+ Sbjct: 356 NNYGKYRLGGLFLDRRREQQATEAAMQRVRVKAPGAQVRVDTLSGGNQQKVVIARWINHA 415 Query: 430 ADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEI 489 +LIFDEPTRGIDVGAK+EI++++RE AQG +++MISSELPE++ ++DR+ V G I Sbjct: 416 MKVLIFDEPTRGIDVGAKSEIYQLMREFTAQGYSILMISSELPEVVGMADRVCVFRGGGI 475 Query: 490 TAVLDNREKRVTQEEIMYYAS 510 A L+ + V EEIM +A+ Sbjct: 476 VATLEG--EAVNAEEIMTHAT 494 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: 620 Number of extensions: 27 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 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