Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate AZOBR_RS00065 AZOBR_RS00065 glycerol-3-phosphate transporter membrane protein
Query= uniprot:A3DHA2 (303 letters) >FitnessBrowser__azobra:AZOBR_RS00065 Length = 276 Score = 124 bits (310), Expect = 3e-33 Identities = 66/202 (32%), Positives = 116/202 (57%), Gaps = 5/202 (2%) Query: 101 LMFLNSAIMTIPIVIIQVIVGVFAAYAFAKLRFPLRDKLFFVFIVVMLMPLQVTLVPNYI 160 +M NS +M + I + ++ + + +AYA A RFPLR F++ + +++P++V ++P Y Sbjct: 70 IMMWNSLVMALVIALGKIAISIISAYAVAFFRFPLRMVFFWMIFITLMLPVEVRIIPTYE 129 Query: 161 LLRKLDMIGSFLSVILPGGFSAFGVVLLRQYMRGIPDECCEAAMIDGAGYLKTFTKIILP 220 ++ L +I S+ + +P SA +L RQ+ IPDE EAA IDGAG L+ F ++LP Sbjct: 130 VVANLGLIDSYAGLTIPLIASATATLLFRQFFLTIPDELVEAAKIDGAGALRFFLDVVLP 189 Query: 221 QCKSIIASLAILAFIDNWNMVEQPLIFLSDSAKYPLSVYLA-YINEG----DLGLAFASG 275 ++ IA+L ++ FI WN PL+ + + + + + I G D L A+ Sbjct: 190 LSRTNIAALFVILFIYGWNQYLWPLLITNSAEMETVVIGITKMIGNGEAATDWNLIMATT 249 Query: 276 VLYMIPTVLIYLYGEKYFVEGI 297 VL M+P V + + +++FV+G+ Sbjct: 250 VLAMLPPVAVVVLMQRWFVKGL 271 Lambda K H 0.331 0.147 0.425 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: 198 Number of extensions: 11 Number of successful extensions: 2 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: 303 Length of database: 276 Length adjustment: 26 Effective length of query: 277 Effective length of database: 250 Effective search space: 69250 Effective search space used: 69250 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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