Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate WP_043920091.1 jaqu_RS16540 sugar ABC transporter permease
Query= uniprot:A8LLL5 (334 letters) >NCBI__GCF_000877395.1:WP_043920091.1 Length = 319 Score = 122 bits (307), Expect = 9e-33 Identities = 91/277 (32%), Positives = 135/277 (48%), Gaps = 21/277 (7%) Query: 54 WIFLFPALFVLLLYLGYPVVETLRLSL-------LERVPGGGYQWVGLDNYAQMASEPKF 106 WIF+ P +F+LL +P++ T+RLS L R P +WVGL NY ++ ++ Sbjct: 35 WIFVAPTIFLLLAVNIFPLIWTIRLSFTNYRANRLNREP----EWVGLRNYERILTDSDT 90 Query: 107 WEAMRNNMFWLIVVPALSTAFGLLAAQLTDR-IKWGNVAKSIIFMPMAISFVGASVIWKL 165 W +M+ +LI AL G A L +R K +II +PM +S W Sbjct: 91 WASMQATAHFLIWTIALQVLIGFALAWLINRQFKGSAFWTTIIVLPMMLSPAVVGNFWSF 150 Query: 166 VYDGRPIEQEQIGILNAIIVGLGG-DPVTFLTIPFWN--NFFLMIVLVWVQTGFAMVILS 222 +Y Q QI + N +I L G DP +F + N + ++IV W+ T F M+I Sbjct: 151 LY------QPQIRLFNYVIAFLSGQDPSSFDILGSVNLAPWAIVIVDTWMWTPFVMLICL 204 Query: 223 AALRGIPEETIEAAIIDGASPLQIFFKIKVPQIMPTVVVVWTTITLVVLKVFDIVFAMTN 282 A LR IP+ EAA +D ASP++ FF I VP ++P +++ + K+FD+V +T Sbjct: 205 AGLRSIPDYLYEAAAVDRASPIRQFFTITVPMVLPFLMLAVLFRGIENFKMFDLVVQLTG 264 Query: 283 GQWETQVLANYMFDKLFRANDWGVGSASAMVIMLLVT 319 G + K W G ASA I+L VT Sbjct: 265 GGPGNITTLTSIDLKREAFEKWRTGYASAYAIILFVT 301 Lambda K H 0.329 0.143 0.455 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: 311 Number of extensions: 21 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: 334 Length of database: 319 Length adjustment: 28 Effective length of query: 306 Effective length of database: 291 Effective search space: 89046 Effective search space used: 89046 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 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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