Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate BWI76_RS03135 BWI76_RS03135 sugar ABC transporter permease
Query= uniprot:A8LLL5 (334 letters) >FitnessBrowser__Koxy:BWI76_RS03135 Length = 290 Score = 128 bits (321), Expect = 2e-34 Identities = 84/270 (31%), Positives = 147/270 (54%), Gaps = 15/270 (5%) Query: 53 PWIFLFPALFVLLLYLGYPVVETLRLSLLE-RVPGGGYQWVGLDNYAQMASEPKFWEAMR 111 PW+ L P+L LLL+ +P+ ++ SL + R+ G Q+VGL+N++++ ++ FW+++ Sbjct: 7 PWLILSPSLLFLLLFTWFPLGRSVYDSLFDTRMVSDGGQYVGLENFSRLFADSVFWQSLV 66 Query: 112 NNMFWLI--VVPALSTAFGLLAAQLTDRIKWGNVAKSIIFMPMAISFVGASVIWKLVYDG 169 NN+ +++ VVP ++ A LLA LT+ + ++ F PM I V A+ +W ++ Sbjct: 67 NNLLYILLTVVPGVTLAL-LLAVALTENHRVNRWLRTAFFFPMIIPMVSAAALWLFIF-- 123 Query: 170 RPIEQEQIGILNAIIVGLGGDPVTFLTIPFWNNFFLMIVL--VWVQTGFAMVILSAALRG 227 +G+L+ + L G P+ + N+ L + L VW G+ M+ A L+ Sbjct: 124 ----MPGLGLLDHYLAKLFG-PMNNNWLGRSNSALLALALIGVWKFAGYYMLFFLAGLQS 178 Query: 228 IPEETIEAAIIDGASPLQIFFKIKVPQIMPTVVVVWTTITLVVLKVFDIVFAMTNGQWE- 286 IP T EAAI++GA+ Q+FFK+ +P + PT+ V TT + + D V MT G + Sbjct: 179 IPASTREAAIMEGATRTQVFFKVTLPLLRPTLSFVITTALIYSITQIDHVAVMTRGGPDN 238 Query: 287 -TQVLANYMFDKLFRANDWGVGSASAMVIM 315 T VL Y+ + + +D G SA+ + + Sbjct: 239 ATTVLLYYIQNLAWDTHDLGKASAATFLTL 268 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: 232 Number of extensions: 16 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: 290 Length adjustment: 27 Effective length of query: 307 Effective length of database: 263 Effective search space: 80741 Effective search space used: 80741 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 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