Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_012976935.1 AZL_RS23490 metal-dependent hydrolase
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_000010725.1:WP_012976935.1 Length = 632 Score = 217 bits (552), Expect = 6e-61 Identities = 112/250 (44%), Positives = 163/250 (65%), Gaps = 2/250 (0%) Query: 7 EVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTF 66 EVVL+ G+++RFGGL A D+ T++ G++ +IGPNGAGK+T FN ++ + P +G Sbjct: 382 EVVLEARGVTRRFGGLVANRDISFTVRAGEILAVIGPNGAGKSTLFNQLSCVDHPTSGEI 441 Query: 67 ELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKG 126 G+ + +A AG++R+FQ+++L M+ LENV +G H+R G+ A R Sbjct: 442 LFRGERIDGRTARAMAGAGLSRSFQHVKLLPTMSVLENVAIGAHLRGSKGVAAAALRLN- 500 Query: 127 FKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAA 186 +AEEA + A+ L VG+G+ +A +L+ G QR LEIARAL DP L+ LDEPAA Sbjct: 501 -RAEEARLLDEARRQLVRVGLGQHLHAEAGSLALGQQRILEIARALCADPCLLLLDEPAA 559 Query: 187 GMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQK 246 G+ EK L EL+ R+R++ ILL+EHD+ VMGL DRV V+++G++IAEG P +Q Sbjct: 560 GLRFLEKQALAELLVRLRSEGMAILLVEHDMDFVMGLVDRVYVMEFGERIAEGPPETIQT 619 Query: 247 NEKVIEAYLG 256 N V+EAYLG Sbjct: 620 NPAVLEAYLG 629 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: 409 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: 632 Length adjustment: 31 Effective length of query: 229 Effective length of database: 601 Effective search space: 137629 Effective search space used: 137629 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