Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate 7024902 Shewana3_2076 inner membrane ABC transporter permease protein YjfF (RefSeq)
Query= SwissProt::P39328 (341 letters) >FitnessBrowser__ANA3:7024902 Length = 320 Score = 105 bits (262), Expect = 2e-27 Identities = 79/254 (31%), Positives = 130/254 (51%), Gaps = 12/254 (4%) Query: 58 DILNRAAPVALLAIGMTLVIATGGIDLSVGAVMAIAGATTAAMTVAGFSLPIV-LLSALG 116 ++L A + + A+GMTLVI +GGIDLSVGAV+A++G T+ + P++ + L Sbjct: 38 NLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALSGVVTSLLITEYQWHPLLAFVVILP 97 Query: 117 TGILAGLWNGILVAILKIQPFVATLILMVAGRGVAQLITAGQIV-------TFNSPDLSW 169 G L G G ++ + K+QPF+ TL M RG+A ++ I ++ Sbjct: 98 LGTLFGALMGTIIHVYKLQPFIVTLAGMFLARGLATTLSEESIAIDHPFYDAVAEMSIAL 157 Query: 170 FGSGSLLFLPTPVIIAVLTLILFWLLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLT 229 G+G+ L +I +L ++ ++ T G + A+G N +A+ G++ + Sbjct: 158 PGNGA---LDLSSLIFILFFVIIAVVMHYTRFGTNVYAIGGNQHSAELMGISIAKTTISI 214 Query: 230 YVLSGLCAAIAGIIVAADIRGADANNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGA 289 Y +S A +AGI+ A A + +ELDAI AVVIGG L GG +L +V+G Sbjct: 215 YAISSFLATLAGIVFTFYTFSGYALGA-IGVELDAIAAVVIGGTLLTGGSGFVLGTVLGV 273 Query: 290 LIIQGMNTGILLSG 303 +++ + T I G Sbjct: 274 ILMGVIQTYITFDG 287 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: 285 Number of extensions: 22 Number of successful extensions: 3 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: 320 Length adjustment: 28 Effective length of query: 313 Effective length of database: 292 Effective search space: 91396 Effective search space used: 91396 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