Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate PfGW456L13_2122 L-arabinose transport system permease protein (TC 3.A.1.2.2)
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2122 Length = 323 Score = 175 bits (444), Expect = 1e-48 Identities = 97/298 (32%), Positives = 165/298 (55%), Gaps = 1/298 (0%) Query: 35 MLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLSVGSILS 94 ML V + + ++L +NF N+ + S + A M + + +G DLSVGS+++ Sbjct: 27 MLLAAVGIFVACTLLIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSVIA 86 Query: 95 ISAVVAMLVSLMPQLGMLSVPAALLCGLLFGIVNGALVAFMKLPPFIVTLGTLTAVRGLA 154 + VVA +V L V AAL+ GL+ G++NG ++A +++ I TL T+ VRGLA Sbjct: 87 CAGVVAAVVMRDTNSVFLGVCAALVMGLIVGLINGIVIAKLRVNALITTLATMQIVRGLA 146 Query: 155 RLVGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGGN 214 + N + F GNG++ GVP ++I ++L T G A+GGN Sbjct: 147 YIFANGKAVGVSQESFFVFGNGQMFGVPVPILITIVCFLFFGWLLNYTTYGRNTMAIGGN 206 Query: 215 AEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIAAVILG 274 EAA L+G+ V + ++AV G++ L GV+ ++R+ + + +GQ +EL I+A +LG Sbjct: 207 QEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMTSGQPM-IGQGFELTVISACVLG 265 Query: 275 GTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALDSYRRK 332 G S GG G I + G LI+A++ N + L + +QY+I+G +++ AV +D +++ Sbjct: 266 GVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAVVIDRLKQR 323 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: 297 Number of extensions: 23 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: 323 Length adjustment: 28 Effective length of query: 309 Effective length of database: 295 Effective search space: 91155 Effective search space used: 91155 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