Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate Echvi_1333 Echvi_1333 ABC-type (unclassified) transport system, ATPase component
Query= uniprot:G8ALJ1 (236 letters) >FitnessBrowser__Cola:Echvi_1333 Length = 243 Score = 122 bits (305), Expect = 8e-33 Identities = 73/234 (31%), Positives = 123/234 (52%), Gaps = 4/234 (1%) Query: 1 MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60 +L+ + Y + + + +E+ GEIV L+G NGAGK+T I G + G++ Sbjct: 2 ILRGENLIKIYKGRKVVNNISVEVEQGEIVGLLGPNGAGKTTSFYMIVGLIKPNSGKVFL 61 Query: 61 EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQ-MGSITAKPGSFANE-LERVLT 118 + ++IT +P Y +LGI + +F ++SV EN+ + +T P + E +E +L Sbjct: 62 DKEEITPLPMYRRAKLGIGYLAQEASVFRKLSVEENIMAVLEMTNLPKAAQKEKMEELLE 121 Query: 119 LFPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKD 178 F R +SGGE++ I RAL P+ +LLDEP G+ P+ V++I V Sbjct: 122 EFSLTHVR-KNLGMVLSGGERRRTEIARALAVDPKFVLLDEPFAGVDPIAVEEIQTIVAK 180 Query: 179 INREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYL 232 + + + + + + + N L + R Y+M GK+ +GT EL A+E+VR YL Sbjct: 181 L-KNKNIGILITDHNVNETLSITDRAYLMFEGKLLKAGTAEELAADEQVRKVYL 233 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: 130 Number of extensions: 5 Number of successful extensions: 3 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: 243 Length adjustment: 23 Effective length of query: 213 Effective length of database: 220 Effective search space: 46860 Effective search space used: 46860 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