Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_012335137.1 M446_RS26260 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU1 (463 letters) >NCBI__GCF_000019365.1:WP_012335137.1 Length = 475 Score = 489 bits (1259), Expect = e-143 Identities = 263/456 (57%), Positives = 320/456 (70%), Gaps = 9/456 (1%) Query: 13 AGLVRKGLTEALFAAVLSFGMFVLYVGLKTDQN-ISNELIIVQRWGLLAIFVAVAAIGRF 71 AG+V+ ALFA V + G+ V V +T + L + RWGL+A+ + +GR Sbjct: 24 AGIVKDA---ALFALV-TLGLCVPVVSYRTALGGETGGLYLTPRWGLVALLCGLVFVGRI 79 Query: 72 AMVVFIRPNIDRRKLSKAREGELDISTEKSFFHRHFLKIALIALL----LYPMVVVAIKG 127 A V + RR L+ + + + +AL A L P++ V G Sbjct: 80 AQRVVLANREARRALTPSPRQATEAVGAAPNAAQRIRGLALPAFLGVALALPLLAVLGTG 139 Query: 128 PQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLS 187 Y + I +L YVML WGLNIVVGLAGLLDLGYVAFYAVGAY+YALLS+ FG S Sbjct: 140 GLNESRYWIDLAILVLTYVMLGWGLNIVVGLAGLLDLGYVAFYAVGAYTYALLSTTFGFS 199 Query: 188 FWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGIS 247 FW+ LPL+G+ AA WG++LGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTD + G GIS Sbjct: 200 FWICLPLAGLLAACWGMLLGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDFSGGAAGIS 259 Query: 248 SIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIG 307 SIP+ T FG+PF A GFA + S + +FL+YLILAL +LT VT+R+RR+P+G Sbjct: 260 SIPRVTFFGLPFSADEDGFAATLGIAFSPMHRVVFLYYLILALALLTNGVTLRMRRLPLG 319 Query: 308 RAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESA 367 RAWEALREDEIACRSLGINT TKLTAFA GAMF GFAGSFFA RQGFVSPESF FLESA Sbjct: 320 RAWEALREDEIACRSLGINTTNTKLTAFALGAMFGGFAGSFFAVRQGFVSPESFNFLESA 379 Query: 368 VILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMV 427 +ILAIVVLGGMGS G+AIAA+ MV G ELLR + FLK +FG F P YR+L+FGLAMV Sbjct: 380 IILAIVVLGGMGSQIGVAIAAVAMVAGPELLRNLGFLKAVFGEGFDPSEYRLLLFGLAMV 439 Query: 428 VVMLFKPRGFVGSREPTAFLRERKAISGSFIKEGHG 463 ++M+++PRG + R P+ L+ERKAI+GS +KEGHG Sbjct: 440 LMMIWRPRGLISERAPSVVLKERKAIAGSLVKEGHG 475 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: 752 Number of extensions: 42 Number of successful extensions: 2 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: 475 Length adjustment: 33 Effective length of query: 430 Effective length of database: 442 Effective search space: 190060 Effective search space used: 190060 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