Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate HSERO_RS22220 HSERO_RS22220 D-ribose transporter ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__HerbieS:HSERO_RS22220 Length = 505 Score = 389 bits (1000), Expect = e-112 Identities = 213/501 (42%), Positives = 315/501 (62%), Gaps = 10/501 (1%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73 +L GI KRF GVVA+ +V F V E+++L+GENGAGKSTL+KILTG+ +PD G I + Sbjct: 12 VLSLSGIGKRFQGVVALQDVGFTVRPGEVMALLGENGAGKSTLVKILTGIHQPDEGSIHL 71 Query: 74 NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133 G V F S DA + GI+ +HQE + + ++VAENI++ + + G R R+D M Sbjct: 72 GGREVRFASAQDAMRGGITAVHQETVMFEELSVAENIWIGRQPLCGTPR----RIDWRRM 127 Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193 ++ L + A V++L+ AQR VEI +AL ++ +++ MDEPT++L+ E Sbjct: 128 EDEARALFARLEVDLPVRARVKDLSVAQRHFVEIARALSQQAQVVIMDEPTAALSHHEIG 187 Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253 L+ II L+ G +V+F+SH+ DE+ ++DR V+RDG+ I + + ++ +MV Sbjct: 188 ELYRIIGQLRRAGTAVIFISHKFDEIYAVADRYTVLRDGRFIASGELADITEQQLVALMV 247 Query: 254 GREV-EFFPHGIETRPGEIA--LEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTET 310 GREV + F + A LEV++L + +VSF VR GE+LGF GLVGAGR+E Sbjct: 248 GREVGQVFSRAASNTEDQTAPVLEVKHLSHPSEFDDVSFAVRPGEILGFYGLVGAGRSEV 307 Query: 311 MLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLP 370 M +FG++ + G ++++GR+V++ +P AI G+ +PEDR+ QG +L + + NI LP Sbjct: 308 MHALFGLSPEAQGAVWIDGREVKLCSPAQAIAHGLAYVPEDRQRQGALLSLPIFQNITLP 367 Query: 371 SLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNA 430 L I + L R+E +I+ ++L +K +Q LSGGNQQKVVLAKWLAT Sbjct: 368 VLPGIGFF-LRRHRRREIDIARRLCEQLELKASHFHQHVAQLSGGNQQKVVLAKWLATQP 426 Query: 431 DILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEIT 490 +LI DEPT+GID+G+KA +HR I EL AQG AVI++SSELPE++ +SDRIVVM +G + Sbjct: 427 RVLILDEPTKGIDIGSKAAVHRFIGELVAQGLAVILVSSELPEVMGMSDRIVVMHQGRVQ 486 Query: 491 AVLDNREKRVTQEEIMYYASG 511 V E + E + ASG Sbjct: 487 QVFSRAE--ASAEALAAAASG 505 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: 616 Number of extensions: 30 Number of successful extensions: 8 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: 505 Length adjustment: 35 Effective length of query: 485 Effective length of database: 470 Effective search space: 227950 Effective search space used: 227950 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