Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_057508273.1 ABB28_RS08815 lipid A export permease/ATP-binding protein MsbA
Query= uniprot:Q1MCU2 (292 letters) >NCBI__GCF_001431535.1:WP_057508273.1 Length = 582 Score = 83.2 bits (204), Expect = 1e-20 Identities = 76/247 (30%), Positives = 119/247 (48%), Gaps = 35/247 (14%) Query: 15 LKVEHLSMKF--GGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMIT 72 L EH+ +++ A++D SF A+ G +TA++G +G+GKT++ + FY+P+ G IT Sbjct: 341 LAFEHVMLRYREDAGTALDDISFVARPGTVTAVVGRSGSGKTSLIRLVPRFYEPSGGRIT 400 Query: 73 FNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTI 132 + + Y L L +VA Q + LF T+ N+ M+AS I Sbjct: 401 LDGVALDDYPLADL-------RRQVAMVGQKVMLFDD-TIGSNIAYG-----MQASQEQI 447 Query: 133 LGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGD----LPYGAQRRLEIARAMCT 188 R AAEA A W A L + D P G+ L G ++RL IARA+ Sbjct: 448 ----------RAAAEA---ANAWEFIARLPQQLDTPVGENGALLSGGQRQRLAIARAILR 494 Query: 189 GPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYG 248 +L LDE A L+ + L+ + E T L+I H +S + E +D V+V++ G Sbjct: 495 DAPILILDEATAALDNESERLVQDALQRLMPERTT--LVIAHRLSTI-EHADQVLVMDQG 551 Query: 249 QKISDGT 255 + + GT Sbjct: 552 RIVERGT 558 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: 308 Number of extensions: 12 Number of successful extensions: 2 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: 582 Length adjustment: 31 Effective length of query: 261 Effective length of database: 551 Effective search space: 143811 Effective search space used: 143811 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: 50 (23.9 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