Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_097070282.1 CRO22_RS11435 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >NCBI__GCF_900217815.1:WP_097070282.1 Length = 289 Score = 142 bits (357), Expect = 1e-38 Identities = 93/297 (31%), Positives = 156/297 (52%), Gaps = 19/297 (6%) Query: 6 QQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAGLP 65 Q ++NGL LG+ Y L+A+G T+++ ++ ++NFAHG +++LGGF I + V+ LP Sbjct: 3 QIIVNGLFLGASYALIALGLTLIFSLMNVLNFAHGQMYVLGGF---ITYTVVAQFH--LP 57 Query: 66 VAVLLLVMLVVAMLMTSLWNWTIERVAYRPL--RGSFRLAPLITAIGMSITLSNFIQVTQ 123 V L+ V + + ER + P+ R + ++ A G++ L + Sbjct: 58 FVVGLICSAVALAALGAF----AERFLFAPVIRRSKREESTMLLAAGIAFFLDAVTLLVF 113 Query: 124 GPRNKPIPPMVSSVYQFG-NISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATEQD 182 G + + IP +V V+ + I + +I+I + L+ F + + GRA RA QD Sbjct: 114 GEKQRGIPKIVQGVFNWDFRIVMPYDRILIGCLAVALIAAFILFMRLSRTGRAMRALAQD 173 Query: 183 RKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAVLGG 242 R A L+GV+V + I F +GA LA + G + + GV + G +KAF ++GG Sbjct: 174 RMAAELMGVDVGRYSMIGFALGAMLAGLVGGLLVSIVGV-NLGMGGPTSIKAFMMIMIGG 232 Query: 243 IGSLPGAVFGGLLIGLIE----SLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRP 295 G + GA+ GG ++G++E SL +AY I Y + F L L F+P G++G+P Sbjct: 233 AGVISGAIAGGFILGMLESVGLSLLAAYGDITY--LVIFVSLLIFLAFRPQGLMGKP 287 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: 304 Number of extensions: 29 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: 289 Length adjustment: 26 Effective length of query: 274 Effective length of database: 263 Effective search space: 72062 Effective search space used: 72062 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 Sep 24 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