Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate AZOBR_RS31200 AZOBR_RS31200 sugar ABC transporter permease
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__azobra:AZOBR_RS31200 Length = 325 Score = 157 bits (396), Expect = 5e-43 Identities = 114/322 (35%), Positives = 172/322 (53%), Gaps = 28/322 (8%) Query: 28 LLHRLGMLPVLVVLYLLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVI 87 ++HR LP+LV +L G L + NFAS N+L A + A GMTFVI Sbjct: 1 MIHRF--LPLLVTSAVLVVGFLLCAAQ--FPNFASLRVVGNLLTDNAFLGITAVGMTFVI 56 Query: 88 LTAGIDLSVGSVLAVSAVL-GMQVSLGA---APGWAIPMFIFSGLVMGMVNGAMVALLNI 143 L+ GIDLSVG+V+ + VL + + G +A+ + + G G GA++ + + Sbjct: 57 LSGGIDLSVGAVIGFTTVLLAVLIEQGGWHPVSAFAVALAVAGGF--GAAMGAVIHVFQM 114 Query: 144 NAFVVTLGTMTAFRGAAYLLADGTTVLNNDIPSFEWIGN-------GDFLHVPWLIW--- 193 F+VTL M RG ++L+ + +N+ P + +G+ G L +P L+ Sbjct: 115 PPFIVTLAGMFVARGLGFVLSTDSIPINH--PLYAELGDLALRFDGGGKLTLPALLMLGV 172 Query: 194 VAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAM 253 VA AVV W T G ++YA+GGN Q+A L G+ VG + VY++SGL +GLAG + Sbjct: 173 VAAAVVCAHW-----TRFGANLYALGGNRQSAELMGVPVGRTTVAVYALSGLLAGLAGIV 227 Query: 254 SASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILG- 312 + +G ELD I AVV+GGT L GG G + GT +G LI G++ +T G Sbjct: 228 FSLYTGAGYSLAATGVELDTITAVVIGGTQLTGGYGYVIGTFIGVLIQGLIQTYITFDGS 287 Query: 313 LSSFWQYVAKGAVIVLAVILDK 334 LSS+W +A G ++ + ++L K Sbjct: 288 LSSWWTKIAIGVLLFVFILLQK 309 Lambda K H 0.324 0.138 0.417 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: 353 Number of extensions: 32 Number of successful extensions: 5 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: 344 Length of database: 325 Length adjustment: 28 Effective length of query: 316 Effective length of database: 297 Effective search space: 93852 Effective search space used: 93852 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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