Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate SMc02359 SMc02359 high-affinity branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >FitnessBrowser__Smeli:SMc02359 Length = 296 Score = 160 bits (405), Expect = 3e-44 Identities = 98/300 (32%), Positives = 164/300 (54%), Gaps = 15/300 (5%) Query: 1 MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60 M + +Q +++ L+LG Y L+A+G ++YGI+ ++NFA+G++ M+ G+ +FL S Sbjct: 1 MAFAIQFVIDVLSLGGAYALMALGLVIIYGILRLVNFAYGELIMVAGYT---MFLASGS- 56 Query: 61 FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSN--F 118 GLP +VM V+A+ M L+ + A+RP+R A LIT+ S L N Sbjct: 57 --GLP----WIVMAVLAVGMAILFGIITDYAAFRPVRAKSVTAVLITSFAFSNLLQNAAL 110 Query: 119 IQVTQGPRNKPIPPMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRA 178 + ++ PRN P+P + S G ++ +I I + LL +++ RT LG A RA Sbjct: 111 LFISPRPRNVPLPDIFSQTVSIGGAITPVRNLITIAASIALLAGVAFLMRRTTLGIAMRA 170 Query: 179 TEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAA 238 + MA +LGV + IS F + LA V G +++ G G P + AF A Sbjct: 171 AATNFTMARMLGVPANLIISSAFALSGFLAGVVGILWIGRIGTVVPGIGLEPLLVAFIAT 230 Query: 239 VLGGIGSLPGAVFGGLLIGLIESLWSAYFT---IAYKDVATFAILAFVLIFKPTGILGRP 295 V+GG+ SLPGAV GG L+ LI++ + + + ++D TF+++ +L+++P G++ P Sbjct: 231 VIGGMRSLPGAVVGGFLLALIDTTLNYTLSQDLLKFRDAFTFSLVILILLWRPDGLIRGP 290 Lambda K H 0.329 0.143 0.421 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: 287 Number of extensions: 26 Number of successful extensions: 5 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: 300 Length of database: 296 Length adjustment: 26 Effective length of query: 274 Effective length of database: 270 Effective search space: 73980 Effective search space used: 73980 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: 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