Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate BWI76_RS07270 BWI76_RS07270 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__Koxy:BWI76_RS07270 Length = 255 Score = 196 bits (499), Expect = 3e-55 Identities = 120/263 (45%), Positives = 162/263 (61%), Gaps = 18/263 (6%) Query: 13 TLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMIT 72 +LL V H++ +FGGL A+++ S +G+I LIGPNGAGKTT FN ITG Y G Sbjct: 2 SLLSVCHMTKRFGGLTAVDNVSLSINQGEIYGLIGPNGAGKTTCFNLITGLYPADSGEFA 61 Query: 73 FNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTI 132 G+ Y + ++T A +ARTFQN+RLF+ ++VLEN++V +H + T Sbjct: 62 I---GGEAYFPSNIE--KVT-AAGIARTFQNVRLFNNMSVLENVMVGRHVR-------TR 108 Query: 133 LGL-IGVGPYKREAAEAI---ELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCT 188 GL + +KR AE ELA L+ + A A DL YG QRRLEIARA+ T Sbjct: 109 NGLWAAISRHKRARAEETQTRELAWHLLDYTGISQFAHYRACDLAYGHQRRLEIARALAT 168 Query: 189 GPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYG 248 P LL LDEPAAG+N E L LL IR + G ++L+IEHD+ +VM I D ++VL+YG Sbjct: 169 EPRLLALDEPAAGMNAAEKMALGELLLRIR-DDGKTLLMIEHDVKLVMGICDRLMVLDYG 227 Query: 249 QKISDGTPDHVKNDPRVIAAYLG 271 + ++ GTPD V+ DP VIAA+LG Sbjct: 228 KTLTSGTPDTVRRDPAVIAAWLG 250 Lambda K H 0.318 0.136 0.386 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: 188 Number of extensions: 8 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: 292 Length of database: 255 Length adjustment: 25 Effective length of query: 267 Effective length of database: 230 Effective search space: 61410 Effective search space used: 61410 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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