Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate 350090 BT0562 putative ABC transporter ATP-binding protein (NCBI ptt file)
Query= uniprot:D8IUY7 (241 letters) >FitnessBrowser__Btheta:350090 Length = 489 Score = 98.2 bits (243), Expect = 3e-25 Identities = 58/191 (30%), Positives = 110/191 (57%), Gaps = 6/191 (3%) Query: 5 ILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHI 64 I+ V+++S +YG ++A+K + V +GE+ LIG +GAGK+T + +T L A + + Sbjct: 7 IVVVKEISKSYGKVEALKEVSFAVEQGEVFGLIGPDGAGKSTLFRILTTLLLADKGTATV 66 Query: 65 EYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADIDKWF 124 L K+ ++ K+ +P ++ +S++ENL A Q D+ K Sbjct: 67 NGLDVVTDYKQ----IRTKVGYMPGRFSLYQDLSVEENLEFFATVFHTLIQENYDLIK-- 120 Query: 125 AVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVIR 184 ++ +++ + AG LSGG +Q LA++ +L+ P +L LDEP+ G+ P+ ++ ++++R Sbjct: 121 DIYQQIEPFKKRRAGALSGGMKQKLALSCSLIHKPDILFLDEPTTGVDPVSRKEFWQMLR 180 Query: 185 NVSAQGITILL 195 N+ QGITI++ Sbjct: 181 NLRKQGITIIV 191 Score = 74.3 bits (181), Expect = 4e-18 Identities = 60/224 (26%), Positives = 105/224 (46%), Gaps = 17/224 (7%) Query: 1 MTTNILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITG----TLP 56 M +++V+QL+ ++G AV I +V GE+ +GANGAGKTT ++ + G T Sbjct: 243 MAAPVIEVEQLTKSFGHFTAVDHISFQVQRGEIFGFLGANGAGKTTAMRMLCGLSRPTSG 302 Query: 57 ASRVEGHIEYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQEN--LLMGAYTSDDKG 114 +V G+ + + E VK + + + ++ + + EN L G Y + Sbjct: 303 VGKVAGYDIF--------REAEQVKRHIGYMSQKFSLYEDLKVWENIRLFAGIYGMKEM- 353 Query: 115 QIAADIDKWFAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPI 174 +I D+ ER + L G +Q LA + ++ PK++ LDEP+ G+ P Sbjct: 354 EIEEKTDELLERLGFADERDT-LVKNLPLGWKQKLAFSVSIFHEPKIVFLDEPTGGVDPA 412 Query: 175 MVEKIFEVIRNVSAQGITILLVEQNAKLALEAAHRGYVMESGLI 218 + +E+I + +GIT+ + A E +R +M G I Sbjct: 413 TRRQFWELIYQAADRGITVFVTTHYMDEA-EYCNRISIMVDGQI 455 Lambda K H 0.317 0.134 0.365 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: 235 Number of extensions: 7 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 241 Length of database: 489 Length adjustment: 29 Effective length of query: 212 Effective length of database: 460 Effective search space: 97520 Effective search space used: 97520 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 (21.6 bits) S2: 49 (23.5 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