Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate WP_042615044.1 ABB28_RS00970 carbohydrate ABC transporter permease
Query= uniprot:D8IPH9 (270 letters) >NCBI__GCF_001431535.1:WP_042615044.1 Length = 278 Score = 85.1 bits (209), Expect = 1e-21 Identities = 74/250 (29%), Positives = 116/250 (46%), Gaps = 7/250 (2%) Query: 15 IVLVLVAVFPLLWALLNSVKTLLDIVT-PTPRFLFTPTLENYRQVIGSPEVLVGLTNSAV 73 +VL LV++ PLLW + SV + T P P T NY ++ + V NS + Sbjct: 20 LVLALVSLAPLLWMVSVSVMPAGEATTFPPPLTPSHVTFANYHELFARTGMGVNFANS-L 78 Query: 74 IVGSAVLLGTFM-GVPAAYVIARYHVPGKRDIQFFLLSLRFLPPVAVAIPLIAIWVDLGL 132 +V A+ LG+ + A Y A+ G+ + L++ +P +PL + LGL Sbjct: 79 LVSVAITLGSLLLNTMAGYAFAKLRFVGRDRLFQVLMAALVIPAQVAMLPLFLLMKQLGL 138 Query: 133 YDTRFSMIVTYLLTTLSTITWLSIPVFQRMPREIEEAATLDGYGPYAVFWKIALPNCATT 192 ++ +IV L T +L + +P E+ EAA +DG G +F++I LP Sbjct: 139 VNSFGGVIVPALATVFGI--FLVRQYARSIPDELLEAARMDGAGEMRIFFQIVLPMLKPV 196 Query: 193 LLGGIIFSFVLVWNELMIAL-ALTSSNSATLPVVASAFTSMGQEVPWGVINASTVLLALP 251 L+ IF+F+ WN+ M L LT TLP VA A S + ++ A V+ +P Sbjct: 197 LVTLSIFTFMGAWNDFMWPLIVLTDQEHYTLP-VALATLSREHIMDVEMMMAGAVVTVIP 255 Query: 252 PLIFVGVLSR 261 L +L R Sbjct: 256 VLALFLLLQR 265 Lambda K H 0.327 0.142 0.434 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: 212 Number of extensions: 11 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: 270 Length of database: 278 Length adjustment: 25 Effective length of query: 245 Effective length of database: 253 Effective search space: 61985 Effective search space used: 61985 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 (21.7 bits) S2: 47 (22.7 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