Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_045585060.1 AL072_RS29555 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= uniprot:Q1MCU1 (463 letters) >NCBI__GCF_001305595.1:WP_045585060.1 Length = 497 Score = 378 bits (971), Expect = e-109 Identities = 222/452 (49%), Positives = 290/452 (64%), Gaps = 46/452 (10%) Query: 9 GKPDAGLVRKGLT-EALFAAVLSFGMFVLYVGLKTDQNISNELIIVQRWGLLAIFVAVAA 67 G+ GL+R+G+ L AVL G+ ++ L + L++V G++A+ Sbjct: 74 GRLGLGLIRQGMALPVLVLAVLCAGIGLV---LPMPTQVLR-LVLVLGGGVIAL------ 123 Query: 68 IGRFAMVVFIRPNIDRRKLSKA-REGELD-ISTEKSFFHRHFLKIALIALLLYPMVVVAI 125 R AM V R KLS+A R+ +D ++ R+ +A+ ++ PM +A Sbjct: 124 --RAAMTVAT----GRSKLSQADRDRRMDRVAARVQHASRYIGPVAVAIAVVLPMTPLAD 177 Query: 126 KGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFG 185 + + + GI +L Y+ML WGLNIVVGLAGLLDLGYVAFYAVGAYSYALL+ YFG Sbjct: 178 R-------MLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLAHYFG 230 Query: 186 LSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFG 245 LSFW+ LPL+G+ AA GV+LGFPVLRLRGDY AIVTL FGEIIR++L+NW T G G Sbjct: 231 LSFWLCLPLAGVLAAFSGVLLGFPVLRLRGDYFAIVTLGFGEIIRIILVNWYQFTGGPNG 290 Query: 246 ISSIPKATLFGI------PFDATAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTI 299 IS IP+ + FGI P D A F ++F L S + +FL+YLILAL ++ T+ Sbjct: 291 ISGIPRPSFFGIAEFSRTPADGMA-AFHEMFGLEFSPLHRIVFLYYLILALALVVNVFTL 349 Query: 300 RLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPE 359 R+R++P+GRAWEALRED+IAC SLGIN KL AFA AMF GFAGSFFA RQGF+SPE Sbjct: 350 RVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGSFFATRQGFISPE 409 Query: 360 SFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRM 419 SF F+ESA+ILAIVVLGGMGS G+ +A ++++G E RE++ YRM Sbjct: 410 SFTFIESAIILAIVVLGGMGSQIGVVVATLLVIGLPEAFRELAD-------------YRM 456 Query: 420 LIFGLAMVVVMLFKPRGFVGSREPTAFLRERK 451 L FG MVV+ML++PRG + R+PT L K Sbjct: 457 LAFGAGMVVIMLWRPRGLLAHRDPTILLHGGK 488 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: 725 Number of extensions: 43 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: 463 Length of database: 497 Length adjustment: 34 Effective length of query: 429 Effective length of database: 463 Effective search space: 198627 Effective search space used: 198627 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: 51 (24.3 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