Align Histidine transport ATP-binding protein HisP (characterized)
to candidate CA265_RS07485 CA265_RS07485 macrolide ABC transporter ATP-binding protein
Query= SwissProt::P02915 (258 letters) >FitnessBrowser__Pedo557:CA265_RS07485 Length = 252 Score = 135 bits (341), Expect = 6e-37 Identities = 86/229 (37%), Positives = 130/229 (56%), Gaps = 14/229 (6%) Query: 22 LKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEGAIIVNGQNINLVRDKDGQLK 81 LK VSL G+ ++++G SGSGKST + + L+ PS G ++NG N++ + D D + Sbjct: 25 LKSVSLDINKGEFVALMGPSGSGKSTLMNILGCLDTPSSGTYVLNGTNVSHMSD-DALAE 83 Query: 82 VADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSKHDARERALKYLAKVG 141 V +NQ + VFQ FNL T L+NV P+ G SK D RA + L VG Sbjct: 84 V--RNQ------EIGFVFQTFNLLPRSTSLDNVA-LPLIYAGTSKKDRDARAARALENVG 134 Query: 142 IDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALDPELVGEVLRIMQQLAE 201 + R K P LSGGQ+QRV++ARAL P ++L DEPT LD + E++ +++++ Sbjct: 135 LGNRMDHK-PNELSGGQRQRVAVARALINNPSIILADEPTGNLDTKTSIEIMGLLEEIHS 193 Query: 202 EGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVFGNPQSPRLQ 250 +G T+++VTHE A+H + ++ + G IE + + SPRLQ Sbjct: 194 KGNTIILVTHEEDIAQH-AHRIVRMRDGLIENDYLNTDI--KNVSPRLQ 239 Lambda K H 0.319 0.136 0.383 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: 141 Number of extensions: 9 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: 258 Length of database: 252 Length adjustment: 24 Effective length of query: 234 Effective length of database: 228 Effective search space: 53352 Effective search space used: 53352 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: 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