Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate WP_017616633.1 CDO52_RS13840 carbohydrate ABC transporter permease
Query= uniprot:A8LLL4 (385 letters) >NCBI__GCF_002263495.1:WP_017616633.1 Length = 315 Score = 227 bits (578), Expect = 4e-64 Identities = 111/233 (47%), Positives = 158/233 (67%), Gaps = 7/233 (3%) Query: 153 PPEFTFANYENMLLDPNNSEGMARAFFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRA 212 P T NY +L ++EG +FFNT+ +++P+T++ +++AA AAYA AWMEFPGR Sbjct: 90 PSRLTLENYAGLL----DNEGFVASFFNTILISVPSTVLIVVIAALAAYAFAWMEFPGRD 145 Query: 213 LLIALIVGLLVVPLQLALIPLLTLHNAIGIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGL 272 L +VGLLVVPLQ+ALIP+ ++ +GI G L H GFG+P AI+LLRN+ + Sbjct: 146 WLFLGVVGLLVVPLQVALIPIAQVYGPLGIYGSIPGVVLFHVGFGLPFAIFLLRNFFAAI 205 Query: 273 PRDIIENAKVDGATDFQIFTKIVLPLSFPALASFAIFQFLWTWNDLLVAKVFLIDATGQT 332 PRD++E A++DG + IF +++LPL PA+AS AIFQFLW WNDLLVA VF A Sbjct: 206 PRDLLEAARMDGGKELTIFRRVILPLGGPAIASLAIFQFLWVWNDLLVALVFADSANQPM 265 Query: 333 TVMTNQIVELLGTRGGNWEILATAAFVSIAVPLLVFFSMQRFLVRGLLAGSVK 385 TV + G N +++++ AF+S+ VPLLVFF+ QR+ V+G++AG+VK Sbjct: 266 TVALQSEMRQF---GANIDVISSGAFLSMVVPLLVFFAFQRYFVQGVMAGAVK 315 Score = 47.4 bits (111), Expect = 6e-10 Identities = 20/40 (50%), Positives = 29/40 (72%) Query: 14 AVQLSVVGLVVLWLLPTFGLFVSSFRTVEQISSSGWWKAM 53 A+Q+ +V + + WLLPT GLFVSS R+ + +SSGWW + Sbjct: 48 AIQVLLVLVGLFWLLPTLGLFVSSLRSPQDNASSGWWTVL 87 Lambda K H 0.323 0.138 0.419 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: 330 Number of extensions: 16 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 385 Length of database: 315 Length adjustment: 29 Effective length of query: 356 Effective length of database: 286 Effective search space: 101816 Effective search space used: 101816 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 49 (23.5 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