Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate SM_b20232 SM_b20232 sugar ABC transporter permease
Query= uniprot:A8LLL5 (334 letters) >FitnessBrowser__Smeli:SM_b20232 Length = 314 Score = 122 bits (307), Expect = 9e-33 Identities = 81/280 (28%), Positives = 144/280 (51%), Gaps = 15/280 (5%) Query: 51 IRPWIFLFPALFVLLLYLGYPVVETLRLSLLERVPGGGYQWVGLDNYAQMASEPKFWEAM 110 I ++F+ P L ++LG P+ +L LS+ E GGY +VG NY +M ++P FW+ Sbjct: 27 IAGYLFVLPDALGLFIFLGVPMALSLVLSVFEVNGFGGYSFVGARNYLRMWNDPLFWKGA 86 Query: 111 RNNMFWLIVVPALSTAFGLLAAQLTDRI-KWGNVAKSIIFMPMAISFVGASVIWKLVYDG 169 R + ++ L GL A L R ++ + +S+ F P +S V +++W+ + Sbjct: 87 RVTALYAAMLVPLLYVCGLGLALLVQRTDRFNAIMRSMFFAPHMVSLVVVALVWQFMV-- 144 Query: 170 RPIEQEQIGILNAIIVGLGGDPVTFLTIPFWNNFFLMIVLVWVQTGFAMVILSAALRGIP 229 ++IG+++ + L ++ L P + +++V VW GF M+I L+ IP Sbjct: 145 ----VDKIGVVSRLTAALDIGGISLLGDPNFALITIVLVSVWFLMGFYMLIFLGGLQDIP 200 Query: 230 EETIEAAIIDGASPLQIFFKIKVPQIMPT---VVVVWTTITLVVLKVFDIVFAMTNG--Q 284 + EAA+IDGA + F+ I +P + PT V++V + + FDI++ MT G Sbjct: 201 RQYYEAAMIDGAGAIARFWFITLPLLKPTSFFVIMVSMVAAVAGAQAFDIIYVMTKGGPA 260 Query: 285 WETQVLANYMFDKLFRANDWGVGSASA---MVIMLLVTPI 321 T VL Y++ + F +G +A A +V +++VT + Sbjct: 261 NATSVLIVYIYQQAFGFGAFGYAAAMASILVVALMIVTAV 300 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: 270 Number of extensions: 21 Number of successful extensions: 4 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: 314 Length adjustment: 28 Effective length of query: 306 Effective length of database: 286 Effective search space: 87516 Effective search space used: 87516 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