Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate Ac3H11_2880 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2880 Length = 350 Score = 173 bits (438), Expect = 7e-48 Identities = 117/347 (33%), Positives = 185/347 (53%), Gaps = 25/347 (7%) Query: 3 ESITRPAASTGAPLPAGTLGRLTTQERLRALGMLPVLVLLCIGFSVLTENFAGWQNLSII 62 E+ P A A G +L LG + LVLLCI ++L NFA + N+ + Sbjct: 11 ENAAAPQAGGSRHAAAAATGASAWWGKLHGLGPVIGLVLLCIAGTLLNSNFATYDNVMNV 70 Query: 63 AQQASINMVLAAGMTFVILTGGIDLSVGSILSISA--VVAMLVSLMPQLG------MLSV 114 + + ++A GM FVI++GGIDLSVGS+ ++ A V+ + ++ P LG ++ + Sbjct: 71 LTRTAFIGIIAVGMCFVIISGGIDLSVGSMAALIAGSVILFMNAMAPVLGSPMAAVVVGM 130 Query: 115 PAALLCGLLFGIVNGALVAFMKLPPFIVTLGTLTAVR---------GLARLVGNDSTIYN 165 A++ G +FG+V+G L+ ++ PFIVTLGTL R G L + S IY+ Sbjct: 131 LLAVVLGAVFGLVHGLLITKGRIEPFIVTLGTLGIFRAYLTYFSNGGAITLENDLSDIYS 190 Query: 166 PDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKV 225 P + +LGVP V I V V +L RT G + A+G N + A+ + + V Sbjct: 191 P------VYYANLLGVPIPVWIFLLVAIVGGVILNRTAYGRYVQAIGSNEQVAQYAAVDV 244 Query: 226 WVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIAAVILGGTSFVGGTGSI 285 + + Y + G+ G+ ++ RL +A+ G +EL+AIAAVI+GGT GG GSI Sbjct: 245 HKIKILTYMLLGVCVGIATLLYVPRLGSASP-TTGLLWELEAIAAVIVGGTVLKGGAGSI 303 Query: 286 VGTLVGALIIAVLSNGLVLLGVSDIW-QYIIKGLVIIGAVALDSYRR 331 GT+VGA++++V+SN L L + ++ ++G VII + +R Sbjct: 304 TGTVVGAILLSVISNILNLTSIISVYLNAAVQGFVIIAVAFMQRGKR 350 Lambda K H 0.325 0.141 0.409 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: 399 Number of extensions: 21 Number of successful extensions: 4 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: 337 Length of database: 350 Length adjustment: 29 Effective length of query: 308 Effective length of database: 321 Effective search space: 98868 Effective search space used: 98868 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 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