Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Dsui_1111 Dsui_1111 ABC-type branched-chain amino acid transport system, permease component
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__PS:Dsui_1111 Length = 355 Score = 137 bits (344), Expect = 7e-37 Identities = 103/333 (30%), Positives = 166/333 (49%), Gaps = 34/333 (10%) Query: 110 IALIALLLYPMVVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAF 169 I ++A L+ PMV S ++ I LI+ + A GLNI+ G AG L LG AF Sbjct: 32 ILVVAALVVPMVA--------SEYWIKAILIPFLIFSLAALGLNILTGYAGQLSLGSAAF 83 Query: 170 YAVGAYS-YALLSSYFGLSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLA--FG 226 AVGA++ Y + G+ + G+ AA G++ G P LR++G YLA+ TLA F Sbjct: 84 MAVGAFAAYNFMGRIEGMPVLLAFVGGGLSAAAVGILFGLPSLRIKGFYLAVATLAAQFF 143 Query: 227 EIIRLVLINWTDVTKGTFGISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIFLFYL 286 + L W + + G+ + + + G FD PIS L+ L Sbjct: 144 IVWALTKFGWFSMDSSS-GVITAQEIQILGYRFDT-----------PIS-------LYLL 184 Query: 287 ILALCMLTAYVTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAG 346 +L + + A + R +GRAW A+R+ ++A +GI + TKL AFA + + G AG Sbjct: 185 VLTIVAVMALAAKNMVRSSVGRAWMAVRDMDVAAEVIGIRIMHTKLLAFAISSFYCGVAG 244 Query: 347 SFFA-ARQGFVSPESFVFLESAVILAIVVLGGMGSLTG--IAIAAIVMVGGTELLREMSF 403 + +A A G V PE F S IL ++++GG+GS+ G + A IV++ + F Sbjct: 245 ALYAYAYLGTVEPEGFNLDLSFKILFMIIIGGVGSIMGSFLGAAFIVLLPIFLDVLIQDF 304 Query: 404 LKLIFGPDFTPELYRMLIFGLAMVVVMLFKPRG 436 L + P + L ++++FG ++ ++ +P G Sbjct: 305 LTGLLPPSISSNL-QLMVFGGLIIFFLIVEPHG 336 Lambda K H 0.330 0.145 0.432 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: 460 Number of extensions: 26 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 463 Length of database: 355 Length adjustment: 31 Effective length of query: 432 Effective length of database: 324 Effective search space: 139968 Effective search space used: 139968 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 (21.8 bits) S2: 50 (23.9 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