Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate 5210167 Shew_2611 ABC transporter-related protein (RefSeq)
Query= uniprot:G8ALJ1 (236 letters) >FitnessBrowser__PV4:5210167 Length = 265 Score = 117 bits (293), Expect = 2e-31 Identities = 76/249 (30%), Positives = 129/249 (51%), Gaps = 17/249 (6%) Query: 1 MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60 +L V + +G ++AL V E+ G + S+IG NGAGK+++L +I G R + G I F Sbjct: 5 ILTVDQISLAFGGVKALTDVSFEVERGAVFSIIGPNGAGKTSMLNSISGRYRPQKGTIHF 64 Query: 61 EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMG-------SITAKPGSFANEL 113 + QD+T + LGI ++ + +F MSVL+N+ +G + P +A+ Sbjct: 65 DNQDVTHLRPNARADLGIGRTFQNLALFGHMSVLDNIMVGRHHLMKNNWLTGPLYWASPA 124 Query: 114 ERVLTLFPRLKERI----------SQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLG 163 ++ R E I AGT+S G ++ + + RA+ P+L+LLDEP G Sbjct: 125 QKEELAHRRQVEEIIDFLDISHVRKSIAGTLSYGLRKRVELARAMALNPKLILLDEPMAG 184 Query: 164 LAPLVVKQIFQAVKDINREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLA 223 + + + + + D+N E +TV M+E + + ++H V+ GK +SG ++A Sbjct: 185 MNLEEKEDMARYILDLNEEFGITVVMIEHDMGVVMDISHEVMVLDFGKKLISGLPEAVMA 244 Query: 224 NEEVRSAYL 232 +E VR AYL Sbjct: 245 DEHVRQAYL 253 Lambda K H 0.320 0.136 0.377 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: 129 Number of extensions: 3 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: 236 Length of database: 265 Length adjustment: 24 Effective length of query: 212 Effective length of database: 241 Effective search space: 51092 Effective search space used: 51092 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 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