Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate WP_054656298.1 CES79_RS03760 amino acid ABC transporter permease
Query= uniprot:B2TBJ8 (250 letters) >NCBI__GCF_002217945.1:WP_054656298.1 Length = 247 Score = 112 bits (281), Expect = 5e-30 Identities = 75/230 (32%), Positives = 117/230 (50%), Gaps = 10/230 (4%) Query: 1 MHFDFDFLFDTIKQLLAAVPTTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYIL 60 M+FD+ + F +L A VP TL + S+IL + + ++++S FA YI Sbjct: 1 MNFDWHYFFSLFIKLPAYVPITLLMAILSMILAIFIGGFLTSLQLSTIAPLRGFAHFYIS 60 Query: 61 VFRGSPLLIQMFLVYYGMGQFGVIRESFLWPVLR--EPYMCAVLSLALCTAGYTAEIIRG 118 +FRG P L+Q+F+++YG+ Q ++P LR ++ V+ L A Y AEI R Sbjct: 61 LFRGMPTLVQLFIIFYGLPQ--------IFPALRGLSAFVAVVVGLGFKQASYLAEIFRA 112 Query: 119 GLMAVPVGQIEAGYSIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVW 178 + +V GQIEAG S+ +S L V+ P A LPA V LVK T+LA + + Sbjct: 113 AVNSVDKGQIEAGQSLNISRTKLFLNVVLPQATINALPATGNTFVSLVKETSLAFTLGLT 172 Query: 179 EVTGVAQQIIQQTYRTTEVFICAALIYLFLNFVIVRLLGMLETRLSRHLR 228 E+ G + I Q+++ E ++ +IY L + L +LE L R Sbjct: 173 ELFGDGKLIAGQSFKYFETYLAVGIIYWLLITIYTWLQHLLENSLQTPYR 222 Lambda K H 0.331 0.143 0.431 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: 137 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: 250 Length of database: 247 Length adjustment: 24 Effective length of query: 226 Effective length of database: 223 Effective search space: 50398 Effective search space used: 50398 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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