Align ABC transporter permease (characterized, see rationale)
to candidate SMc02359 SMc02359 high-affinity branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__Smeli:SMc02359 Length = 296 Score = 172 bits (436), Expect = 9e-48 Identities = 115/305 (37%), Positives = 172/305 (56%), Gaps = 22/305 (7%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 M +Q +I+ L LG YAL+ALG ++YGI++L+NFA+GE++M+ T + G Sbjct: 1 MAFAIQFVIDVLSLGGAYALMALGLVIIYGILRLVNFAYGELIMVAGYTMFLASGS---- 56 Query: 61 MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120 G P W+++ ++A +A + + A+RP+R+ A LIT+ S LLQ A+ Sbjct: 57 --GLP-WIVM---AVLAVGMAILFGIITDYAAFRPVRAKSVTAVLITSFAFSNLLQNAAL 110 Query: 121 IIWKPNYKPYPTMLP---SSPFEIGGAFITPTQILILGVTAVAL-ASLVYLVNHTNLGRA 176 + P + P LP S IGGA ITP + LI ++AL A + +L+ T LG A Sbjct: 111 LFISPRPRNVP--LPDIFSQTVSIGGA-ITPVRNLITIAASIALLAGVAFLMRRTTLGIA 167 Query: 177 MRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAF 236 MRA A N +A ++GV +++IS+ F + LA + GI++ GT +G P L AF Sbjct: 168 MRAAATNFTMARMLGVPANLIISSAFALSGFLAGVVGILWIGRIGTVVPGIGLEPLLVAF 227 Query: 237 TAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLR 296 A V GG+ +L GAVVGG LL LI+ + TL+ LL + D F F ++I+IL R Sbjct: 228 IATVIGGMRSLPGAVVGGFLLALIDTTLN---YTLSQDLL--KFRDAFTFSLVILILLWR 282 Query: 297 PSGLL 301 P GL+ Sbjct: 283 PDGLI 287 Lambda K H 0.327 0.142 0.419 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: 219 Number of extensions: 11 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: 309 Length of database: 296 Length adjustment: 27 Effective length of query: 282 Effective length of database: 269 Effective search space: 75858 Effective search space used: 75858 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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