Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_011766230.1 AZO_RS12615 metal-dependent hydrolase
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_000061505.1:WP_011766230.1 Length = 597 Score = 220 bits (560), Expect = 6e-62 Identities = 111/250 (44%), Positives = 168/250 (67%), Gaps = 2/250 (0%) Query: 7 EVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTF 66 E++L+ ++++FGGL A +++ + +K G++ LIGPNGAGK+T FN I+G+ TP +G Sbjct: 347 ELILEAKNVTRKFGGLIANNNMSLEVKAGEILALIGPNGAGKSTMFNQISGVDTPTSGEV 406 Query: 67 ELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKG 126 GKP E+A+ G++R+FQ+++L M+ LENV +G H+R G+ A +R Sbjct: 407 LFRGKPVAGHDSREIARMGMSRSFQHVKLLPTMSVLENVAIGGHLRGDKGVLSAAWRMD- 465 Query: 127 FKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAA 186 + EEA + A ++ VG+ + +A +L+ G QR LEIARAL +DP L+ LDEPAA Sbjct: 466 -REEEARLLAEAARQIERVGLAEHMFDEAGSLALGQQRILEIARALCSDPCLLLLDEPAA 524 Query: 187 GMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQK 246 G+ EK L EL+ +++ + ILL+EHD+ VMGL DRV V+++G++IAEG P +VQK Sbjct: 525 GLRFKEKEALGELLKKLKAEGMAILLVEHDMDFVMGLVDRVVVMEFGEKIAEGLPEDVQK 584 Query: 247 NEKVIEAYLG 256 N KV+EAYLG Sbjct: 585 NPKVLEAYLG 594 Lambda K H 0.319 0.137 0.384 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: 388 Number of extensions: 13 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: 260 Length of database: 597 Length adjustment: 31 Effective length of query: 229 Effective length of database: 566 Effective search space: 129614 Effective search space used: 129614 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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