Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Pf1N1B4_3216 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3216 Length = 418 Score = 358 bits (919), Expect = e-103 Identities = 219/442 (49%), Positives = 283/442 (64%), Gaps = 36/442 (8%) Query: 18 KGLTEALFAAVLSFGMFVLYVGLK-TDQNISNELIIVQRWGLLAIFVAVAAIGRFAMVVF 76 + L +ALF+A+L + + +GLK T I+ E+ L+ I AV ++ F V+F Sbjct: 3 RNLKQALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSTATLITI--AVCSVLMFLRVLF 60 Query: 77 IRPNIDRRKLSKAREGELDISTEKSFFHRHFLKIA-----LIALLLYPMVVVAIKGPQGS 131 + K S L + K+ +FL + +I L+ +V G +G+ Sbjct: 61 DQQISSAWKASP----NLPVMPAKA---TNFLTLPTTQRWIIIALIIGALVWPFFGSRGA 113 Query: 132 LTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVL 191 + + +LIYVML GLNIVVGLAGLLDLGYV FYAVGAYSYALLS Y+GLSFW+ Sbjct: 114 V----DIATLVLIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYYGLSFWIC 169 Query: 192 LPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPK 251 LP++G+ AA +G +LGFPVLRLRGDYLAIVTL FGEIIRL L N TD+T G GIS+IPK Sbjct: 170 LPIAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDLTGGPNGISNIPK 229 Query: 252 ATLFGIPFDATAGGFAKLFH----LPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIG 307 TLFG+ FD TA + FH L +S IFL+ + + L + +V RL RMP+G Sbjct: 230 PTLFGLSFDRTAAEGLQTFHEYFGLEYNSINKVIFLYLIAVLLSLFALFVINRLLRMPLG 289 Query: 308 RAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESA 367 RAWEALREDEIACR+LG+N KL+AF GA FAGFAGSFFAARQG V+PESF F+ESA Sbjct: 290 RAWEALREDEIACRALGLNPTVIKLSAFTLGACFAGFAGSFFAARQGLVTPESFTFIESA 349 Query: 368 VILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMV 427 ILAIVVLGGMGS G+ +AA VM+ E++RE S YRML+FG MV Sbjct: 350 TILAIVVLGGMGSQLGVVLAATVMILLPEMMREFS-------------EYRMLMFGALMV 396 Query: 428 VVMLFKPRGFVGSREPTAFLRE 449 ++M+++P+G + + P LR+ Sbjct: 397 LMMIWRPQGLLPMQRPHMELRK 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: 635 Number of extensions: 39 Number of successful extensions: 4 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