Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Synpcc7942_2494 Synpcc7942_2494 putative branched-chain amino acid ABC transporter, permease protein
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__SynE:Synpcc7942_2494 Length = 307 Score = 127 bits (320), Expect = 4e-34 Identities = 98/306 (32%), Positives = 150/306 (49%), Gaps = 45/306 (14%) Query: 151 GLNIVVGL-AGLLDLGYVAFYAVGAYSYALLSS--------YFGLSFWVLLPLSGIFAAL 201 GL++ + L AG L L AFYA+G Y A+LS+ Y + + + L+ I AA+ Sbjct: 22 GLSVYLPLMAGQLSLASPAFYALGGYLAAILSTKGLTASPEYSVGALLLEMGLAAIAAAV 81 Query: 202 WGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKATLFGIPFDA 261 ++G+PVLRLRG YLAI T+A EI+R+V +N + +T G GI IP+ PF + Sbjct: 82 LAFLVGYPVLRLRGIYLAIATIALVEIVRVVALNLS-ITGGAVGIFGIPQ------PFSS 134 Query: 262 TAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEALREDEIACR 321 G ++ L L ++ RL+++ G A+REDE+A Sbjct: 135 AVG------------------YLWIALPLLLIAVAACWRLQQVRTGLVLAAIREDELAAS 176 Query: 322 SLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSL 381 ++ +NT K+ AF GA+ A G+ A +P F S LA V++GG S Sbjct: 177 AIAVNTTRYKVLAFVLGAVLASLVGAVSAHFLNTWNPRQGTFDASITFLAFVLIGGSRSA 236 Query: 382 TGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELY------RMLIFGLAMVVVMLFKPR 435 G + +V+ ELLR + + P P L R+LIFGL +V+ ++ P+ Sbjct: 237 FGPVLGGMVLTALPELLRAIGSV-----PGLWPGLSRLLQDGRLLIFGLLLVLGSIYFPQ 291 Query: 436 GFVGSR 441 G + R Sbjct: 292 GLIKPR 297 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: 417 Number of extensions: 27 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: 307 Length adjustment: 30 Effective length of query: 433 Effective length of database: 277 Effective search space: 119941 Effective search space used: 119941 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: 50 (23.9 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