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:Q1MCU2 (292 letters) >FitnessBrowser__Cola:Echvi_1333 Length = 243 Score = 102 bits (254), Expect = 8e-27 Identities = 79/262 (30%), Positives = 129/262 (49%), Gaps = 33/262 (12%) Query: 14 LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73 +L+ E+L + G +N+ S E ++G+I L+GPNGAGKTT F I G KP G + Sbjct: 2 ILRGENLIKIYKGRKVVNNISVEVEQGEIVGLLGPNGAGKTTSFYMIVGLIKPNSGKVFL 61 Query: 74 NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLL-VAQHNKLMKASGYTI 132 +++ + LP +R K + Q +F L+V EN++ V + L KA+ Sbjct: 62 DKEE-----ITPLPMYRRAK-LGIGYLAQEASVFRKLSVEENIMAVLEMTNLPKAA---- 111 Query: 133 LGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPEL 192 ++E E + LE+ L + L G +RR EIARA+ P+ Sbjct: 112 ---------QKEKMEEL------LEEFSLTHVRKNLGMVLSGGERRRTEIARALAVDPKF 156 Query: 193 LCLDEPAAGLNP---RESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQ 249 + LDEP AG++P E T+ A LK+ IL+ +H+++ + I+D ++ G+ Sbjct: 157 VLLDEPFAGVDPIAVEEIQTIVAKLKN----KNIGILITDHNVNETLSITDRAYLMFEGK 212 Query: 250 KISDGTPDHVKNDPRVIAAYLG 271 + GT + + D +V YLG Sbjct: 213 LLKAGTAEELAADEQVRKVYLG 234 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: 164 Number of extensions: 11 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: 292 Length of database: 243 Length adjustment: 25 Effective length of query: 267 Effective length of database: 218 Effective search space: 58206 Effective search space used: 58206 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: 47 (22.7 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