Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized)
to candidate WP_152416156.1 C447_RS11610 ATP-binding cassette domain-containing protein
Query= reanno::pseudo3_N2E3:AO353_16275 (244 letters) >NCBI__GCF_000336675.1:WP_152416156.1 Length = 233 Score = 131 bits (329), Expect = 1e-35 Identities = 84/215 (39%), Positives = 116/215 (53%), Gaps = 7/215 (3%) Query: 4 IKNVNKWY---GDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVVV 60 + +V K Y G + L S + G V GPSGSGKSTL+ V AL+ G V V Sbjct: 3 LTDVRKTYDLGGTVEALAGVSLSLADGSYTAVMGPSGSGKSTLLNLVGALDTPTDGTVEV 62 Query: 61 DGTSIADPKTD-LPKLR-SRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATKKGL 118 G + D +R + +G VFQ F L P EN+ + + G S+E ++ Sbjct: 63 AGNDLGAATDDERAAIRGTEIGFVFQTFNLLPRSDAVENVALPLV-FAGWSRERRHERAT 121 Query: 119 QLLERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDV 178 +LL+RVGL H P QLSGGQ+QRVAIARALA DP V+L DEPT +D E V+++ Sbjct: 122 ELLDRVGLGDRRHHRPTQLSGGQRQRVAIARALAPDPAVVLADEPTGNVDTETGAGVMNL 181 Query: 179 MVQLANEGMTMMCVTHEMGFARKVADRVIFMDQGK 213 + + G T++ VTH A ADR++ + G+ Sbjct: 182 LAAANDRGTTILLVTHSREIAEH-ADRIVTVRDGR 215 Lambda K H 0.321 0.136 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: 125 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: 244 Length of database: 233 Length adjustment: 23 Effective length of query: 221 Effective length of database: 210 Effective search space: 46410 Effective search space used: 46410 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: 46 (22.3 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