Align Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale)
to candidate CA265_RS01140 CA265_RS01140 ABC transporter
Query= uniprot:Q88GX0 (260 letters) >FitnessBrowser__Pedo557:CA265_RS01140 Length = 229 Score = 135 bits (339), Expect = 1e-36 Identities = 83/224 (37%), Positives = 131/224 (58%), Gaps = 11/224 (4%) Query: 20 LIRIEGLNKHYGA----FHVLRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLEVAQQG 75 ++ I ++K Y + VL +I+ + G + + GPSGSGK+TL+ L+ A G Sbjct: 4 ILNIRNVSKIYQSAGRELTVLDNINFSITAGSTVAITGPSGSGKTTLLGLCAGLDRASSG 63 Query: 76 SIQVDGIDLAATTR-EAAQVRSD-IGMVFQHFNLFPHMSVLDNCLLAPTSVRGLSRKDAE 133 +++++GI L E A VR+ +G +FQ+F L P ++ L+N ++ P +RG K+ Sbjct: 64 TVELNGIALEKLNEDERAAVRNQYVGFIFQNFQLLPTLTALEN-VMVPLELRGA--KNIR 120 Query: 134 ERARMYLSKVGIESQAHKYPSQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPEMVAE 193 A L KVG+ ++H YP QLSGG+QQRV++ARA +P I+ DEPT LD E + Sbjct: 121 AHALELLDKVGLADRSHHYPVQLSGGEQQRVSLARAFSNQPAILFADEPTGNLDAETSEK 180 Query: 194 VLDVLVQL-AGTGMTMLCVTHEMGFARQVAERVLFLEGGQIIED 236 V+ +L L G T++ VTH++ A + A R + ++GG II D Sbjct: 181 VIKLLFDLNKDAGTTLIIVTHDLELAARTA-RSIKIKGGVIISD 223 Lambda K H 0.322 0.137 0.395 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: 123 Number of extensions: 7 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: 260 Length of database: 229 Length adjustment: 24 Effective length of query: 236 Effective length of database: 205 Effective search space: 48380 Effective search space used: 48380 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 (21.9 bits) S2: 46 (22.3 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