Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_084143515.1 METAC_RS0107790 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= uniprot:Q1MCU1 (463 letters) >NCBI__GCF_000427445.1:WP_084143515.1 Length = 468 Score = 477 bits (1227), Expect = e-139 Identities = 253/459 (55%), Positives = 321/459 (69%), Gaps = 9/459 (1%) Query: 8 AGKPDAGLVRKGLTEALF----AAVLSFGMFVLYVGLKTDQNISNELIIVQRWGLLAIFV 63 A P+A +R L AL AA ++ G+ + +T+ + SN L++ +RW +A Sbjct: 12 APAPEASPLRDRLRSALIGAAKAAGVALGLAFPLLAYRTETDFSNALVLQERWAAVAAIA 71 Query: 64 AVAAIGRFAMVVFIRPNIDRRKLS-KAREGELDISTEKSFFHRHFLKIALIALLLYPMVV 122 A + R ++ + P + S + R E +S R L +L+ +P+VV Sbjct: 72 LAAFVVR--LICLLIPGRTKAASSPRRRRAEFAAIVARS--RRLISAAGLASLIAFPLVV 127 Query: 123 VAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSS 182 + + GP SL ++D++GIQILIY+ L WGLNIVVGLAGLLDLGYVAFYAVGAYSYALLS+ Sbjct: 128 LVLLGPARSLKWIDSYGIQILIYMTLGWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLST 187 Query: 183 YFGLSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKG 242 FG SFW LP++G+ AALWGV LGFPVLRLRGDYLAIVTLAFGEIIR+VL NWTD+T G Sbjct: 188 NFGWSFWASLPIAGLLAALWGVALGFPVLRLRGDYLAIVTLAFGEIIRIVLTNWTDLTNG 247 Query: 243 TFGISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLR 302 G+SSIP+ + FG+PF A GFA F L S Y IFLFYL LAL +LT +VT+RLR Sbjct: 248 EAGVSSIPRVSFFGLPFIAGPEGFAAHFGLAYSPIYRVIFLFYLALALALLTNFVTLRLR 307 Query: 303 RMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFV 362 RMP+GRAWEALREDEIACRSLGINTV KL AFA GA+ G AG+ FAARQGFVSP SF Sbjct: 308 RMPLGRAWEALREDEIACRSLGINTVAVKLAAFALGALVGGLAGAVFAARQGFVSPSSFT 367 Query: 363 FLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIF 422 F+ESA ILAIVVLGG GS G+A+AA+ ++GG+ELLRE+ +L+ I G F P YRMLI Sbjct: 368 FIESATILAIVVLGGAGSQLGVALAALFIIGGSELLRELDWLQHIVGEGFDPTQYRMLII 427 Query: 423 GLAMVVVMLFKPRGFVGSREPTAFLRERKAISGSFIKEG 461 G A++V+M +KPRG + +R P+ FL E + + + +EG Sbjct: 428 GFALIVIMNWKPRGLIANRTPSVFLAEPRLAAPALAEEG 466 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: 705 Number of extensions: 32 Number of successful extensions: 1 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: 468 Length adjustment: 33 Effective length of query: 430 Effective length of database: 435 Effective search space: 187050 Effective search space used: 187050 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