Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Pf6N2E2_2924 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2924 Length = 418 Score = 354 bits (908), Expect = e-102 Identities = 217/440 (49%), Positives = 278/440 (63%), Gaps = 36/440 (8%) Query: 20 LTEALFAAVLSFGMFVLYVGLKTDQNISNELIIVQRWGLLAIFVAVAAIGRFAMVVFIRP 79 L ALF+A+L + + +GLK N + +LA +AV ++ F V+F Sbjct: 5 LKSALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSPAILAT-IAVCSLLMFLRVLF--- 60 Query: 80 NIDRRKLSKAREGELDISTEKSFF------HRHFLKIALIALLLYPMVVVAIKGPQGSLT 133 + + K+ G I + S F R + ++ L++P G +G++ Sbjct: 61 STQISAMWKSSPGLPVIPAKASNFLTLPTTQRWIVLALIVGALVWPFF-----GSRGAV- 114 Query: 134 YVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLP 193 + ILIYVML GLNIVVGLAGLLDLGYV FYAVGAYSYALLS YFGLSFW+ LP Sbjct: 115 ---DIATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLP 171 Query: 194 LSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKAT 253 ++G+ AA +G +LGFPVLRLRGDYLAIVTL FGEIIRL L N TD+T G GIS+I K T Sbjct: 172 IAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPT 231 Query: 254 LFGIPFDATAGGFAKLFH----LPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRA 309 FG+ F+ A + FH L +S IFL+ + L L + +V RL RMPIGRA Sbjct: 232 FFGLTFERKAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRA 291 Query: 310 WEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVI 369 WEALREDEIACR+LG+N KL+AF GA FAGFAGSFFAARQG V+PESF F+ESA+I Sbjct: 292 WEALREDEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAII 351 Query: 370 LAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMVVV 429 LAIVVLGGMGS G+ +AAIVM+ E++RE S YRML+FG MV++ Sbjct: 352 LAIVVLGGMGSQLGVILAAIVMILLPEMMREFS-------------EYRMLMFGALMVLM 398 Query: 430 MLFKPRGFVGSREPTAFLRE 449 M+++P+G + + P LR+ Sbjct: 399 MIWRPQGLLPMQRPHMELRK 418 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: 638 Number of extensions: 40 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: 418 Length adjustment: 32 Effective length of query: 431 Effective length of database: 386 Effective search space: 166366 Effective search space used: 166366 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 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