Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate Pf6N2E2_5970 L-arabinose transport system permease protein (TC 3.A.1.2.2)
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5970 Length = 322 Score = 175 bits (444), Expect = 1e-48 Identities = 98/299 (32%), Positives = 165/299 (55%), Gaps = 5/299 (1%) Query: 38 VLVLLCIGFSVLT----ENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLSVGSIL 93 V++L IG VL +NF N+ + S + A M + + +G DLSVGS++ Sbjct: 25 VMLLAAIGIFVLCTLMIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSVI 84 Query: 94 SISAVVAMLVSLMPQLGMLSVPAALLCGLLFGIVNGALVAFMKLPPFIVTLGTLTAVRGL 153 + + VVA +V L + AAL+ GL+ G++NG ++A +++ I TL T+ VRGL Sbjct: 85 ACAGVVAAVVMRDTNSVFLGISAALVMGLIVGLINGIVIAKLRVNALITTLATMQIVRGL 144 Query: 154 ARLVGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGG 213 A + N + F GNG++ GVP ++I ++L T G A+GG Sbjct: 145 AYIFANGKAVGVSQESFFVFGNGQMFGVPVPILITIVCFLFFGWLLNYTTYGRNTMAIGG 204 Query: 214 NAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIAAVIL 273 N EAA L+G+ V + ++AV G++ L GV+ ++R+ + + +GQ +EL I+A +L Sbjct: 205 NQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMTSGQPM-IGQGFELTVISACVL 263 Query: 274 GGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALDSYRRK 332 GG S GG G I + G LI+A++ N + L + +QY+I+G +++ AV +D +++ Sbjct: 264 GGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAVVIDRLKQR 322 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: 302 Number of extensions: 24 Number of successful extensions: 2 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: 322 Length adjustment: 28 Effective length of query: 309 Effective length of database: 294 Effective search space: 90846 Effective search space used: 90846 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