Align Sugar ABC transporter permease (characterized, see rationale)
to candidate WP_007675527.1 BN137_RS07340 carbohydrate ABC transporter permease
Query= uniprot:A0A165KQ00 (289 letters) >NCBI__GCF_000319285.1:WP_007675527.1 Length = 280 Score = 120 bits (301), Expect = 3e-32 Identities = 87/291 (29%), Positives = 142/291 (48%), Gaps = 13/291 (4%) Query: 1 MTAKPSLLPSVGRFLVYAVLALATAFFLLPLYAMLVTSFKYAEEIRSTSLLALPGSLNWS 60 M LL VG +L A+ +AT LLP + ML+TSFK +E S P Sbjct: 1 MATNNRLLRRVGFYLGLALFLIAT---LLPFFVMLMTSFKSPKEAISLHPTLFP-----Q 52 Query: 61 AWGTAWQSACTGVDCNGLRPFFMNSVAMAVPAVLISTVWGALNGYVLSLWKFRGSDALFG 120 W A +F NS+ ++V A ++ G L Y LS +F+G + Sbjct: 53 HWTLAHYLDIFNPIIFPFVTYFRNSLVVSVIASGVAVFIGILGAYALSKLRFKGRMTI-N 111 Query: 121 MLLFGVFMPFQVVLL-PMSQVLGWLGLSSSITGLVLVHCLAGLAGTTLFFRNYYAAIPKE 179 + V+M ++L+ P+ +++ LG+ + +++ L ++Y+ IP E Sbjct: 112 ASFYAVYMFSGILLVVPLFKIITALGIYDTQLAIIVTMVTQTLPTAVFMLKSYFDTIPDE 171 Query: 180 LVNAARMDGASFFQIFWRIVLPLSTPIVMVTLIWQFTNIWNDFLFGVVF-SGTDSKPVTV 238 + AA MDG + QI +RI +PL+ ++ ++ F WND+LF +F S + + V Sbjct: 172 IEEAAMMDGLNRLQIIFRITVPLAVSGLVSVFVYCFMVAWNDYLFASIFLSSASNFTLPV 231 Query: 239 GLNNLANTSSSVKAYNVDMAAAIIAGLPTMVIYVLAGKFFVRGLTAGAVKG 289 GLN L +T + + MAA+++ LP +V+Y L+ +F GLT G VKG Sbjct: 232 GLNTLFSTPDYI--WGRMMAASLVTALPVVVMYALSERFIKSGLTDGGVKG 280 Lambda K H 0.327 0.139 0.436 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: 205 Number of extensions: 9 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: 289 Length of database: 280 Length adjustment: 26 Effective length of query: 263 Effective length of database: 254 Effective search space: 66802 Effective search space used: 66802 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