Align ABC transporter (characterized, see rationale)
to candidate Echvi_3653 Echvi_3653 ABC-type sulfate/molybdate transport systems, ATPase component
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__Cola:Echvi_3653 Length = 290 Score = 155 bits (393), Expect = 1e-42 Identities = 96/228 (42%), Positives = 142/228 (62%), Gaps = 12/228 (5%) Query: 1 MIKLKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDL 60 MI + L K G L D+ L I+ GEF+ GPSG GK++ LR+I+GL + G L Sbjct: 1 MINIDLQKSLKANGPAMDL-DIKLTISQGEFITLFGPSGSGKTSTLRMISGLLTPDKGHL 59 Query: 61 LIDGRRVND------LEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERV 114 ++G + D + P R +G +FQ Y+L+P+M+V +NI+F LK AK DK L E + Sbjct: 60 SVNGEQWFDASFGKNVSPGRRKLGYLFQDYSLFPNMTVKENIAFALKNAK-DKAYLME-L 117 Query: 115 LKTAQILQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRN 174 L++ +L L L PK LSGGQ+QRVA+ RA+A +PDILL DEPLS LD S+R +++ Sbjct: 118 LESMGLLHLQDTL---PKHLSGGQQQRVALARALALKPDILLLDEPLSALDPSMREKLQE 174 Query: 175 EIARLHDRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELY 222 I +H + T I V+HD E + L+D+I+ L+ G+V + +P+E + Sbjct: 175 YILAIHRKYALTTILVSHDAGEIIKLSDRIIELDHGKVLRQCTPKEFF 222 Lambda K H 0.320 0.137 0.394 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: 226 Number of extensions: 12 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: 381 Length of database: 290 Length adjustment: 28 Effective length of query: 353 Effective length of database: 262 Effective search space: 92486 Effective search space used: 92486 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: 49 (23.5 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