Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate AZOBR_RS31200 AZOBR_RS31200 sugar ABC transporter permease
Query= SwissProt::P39328 (341 letters) >FitnessBrowser__azobra:AZOBR_RS31200 Length = 325 Score = 100 bits (249), Expect = 5e-26 Identities = 87/285 (30%), Positives = 137/285 (48%), Gaps = 12/285 (4%) Query: 58 DILNRAAPVALLAIGMTLVIATGGIDLSVGAVMAIAGATTAAMTVAGFSLPIVLLS-ALG 116 ++L A + + A+GMT VI +GGIDLSVGAV+ A + G P+ + AL Sbjct: 37 NLLTDNAFLGITAVGMTFVILSGGIDLSVGAVIGFTTVLLAVLIEQGGWHPVSAFAVALA 96 Query: 117 TGILAGLWNGILVAILKIQPFVATLILMVAGRGVAQLITAGQIVTFNSP------DLSW- 169 G G ++ + ++ PF+ TL M RG+ +++ I N P DL+ Sbjct: 97 VAGGFGAAMGAVIHVFQMPPFIVTLAGMFVARGLGFVLSTDSI-PINHPLYAELGDLALR 155 Query: 170 FGSGSLLFLPTPVIIAVLTLILFWLLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLT 229 F G L LP +++ V+ + + T G + A+G N ++A+ GV + Sbjct: 156 FDGGGKLTLPALLMLGVVAAAV--VCAHWTRFGANLYALGGNRQSAELMGVPVGRTTVAV 213 Query: 230 YVLSGLCAAIAGIIVAADIRGADANNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGA 289 Y LSGL A +AGI+ + GA + A +ELD I AVVIGG L GG ++ + +G Sbjct: 214 YALSGLLAGLAGIVFSL-YTGAGYSLAATGVELDTITAVVIGGTQLTGGYGYVIGTFIGV 272 Query: 290 LIIQGMNTGILLSGFPPEMNQVVKAVVVLCVLIVQSQRFISLIKG 334 LI + T I G + V+L V I+ + +++ G Sbjct: 273 LIQGLIQTYITFDGSLSSWWTKIAIGVLLFVFILLQKGLLAVWTG 317 Lambda K H 0.327 0.142 0.416 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: 315 Number of extensions: 19 Number of successful extensions: 5 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: 341 Length of database: 325 Length adjustment: 28 Effective length of query: 313 Effective length of database: 297 Effective search space: 92961 Effective search space used: 92961 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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