Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Echvi_1333 Echvi_1333 ABC-type (unclassified) transport system, ATPase component
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__Cola:Echvi_1333 Length = 243 Score = 127 bits (319), Expect = 2e-34 Identities = 79/245 (32%), Positives = 131/245 (53%), Gaps = 12/245 (4%) Query: 5 VMTGQPLLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQAR 64 ++ G+ L+++ Y + + + V V +GEIV L+G NGAGK+T I G + Sbjct: 2 ILRGENLIKI------YKGRKVVNNISVEVEQGEIVGLLGPNGAGKTTSFYMIVGLIKPN 55 Query: 65 TGSVVFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVE 124 +G V + +IT +P + A+L I + +F +++V EN+ + NL A+ E Sbjct: 56 SGKVFLDKEEITPLPMYRRAKLGIGYLAQEASVFRKLSVEENIMAVLEMTNLPKAAQK-E 114 Query: 125 KIFTLFPRLKERHAQR--GGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGI 182 K+ L H ++ G LSGGE++ I RAL PK +LLDEP G+ P+ V+ I Sbjct: 115 KMEELLEEFSLTHVRKNLGMVLSGGERRRTEIARALAVDPKFVLLDEPFAGVDPIAVEEI 174 Query: 183 FEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242 + KL + + + + + N L ++ RAY+M GK+ +G+ +EL A+ +VR YL Sbjct: 175 QTIVAKLKN-KNIGILITDHNVNETLSITDRAYLMFEGKLLKAGTAEELAADEQVRKVYL 233 Query: 243 EGGRH 247 G+H Sbjct: 234 --GKH 236 Lambda K H 0.320 0.137 0.387 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: 153 Number of extensions: 7 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: 247 Length of database: 243 Length adjustment: 24 Effective length of query: 223 Effective length of database: 219 Effective search space: 48837 Effective search space used: 48837 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