Align ABC transporter for L-Arginine, putative ATPase component (characterized)
to candidate GFF1259 PS417_06395 amino acid transporter
Query= reanno::BFirm:BPHYT_RS07685 (263 letters) >FitnessBrowser__WCS417:GFF1259 Length = 254 Score = 361 bits (927), Expect = e-105 Identities = 183/253 (72%), Positives = 212/253 (83%), Gaps = 1/253 (0%) Query: 11 KLAVQDIHKRYGDNEVLKGVSLNANKGDVISIIGASGSGKSTFLRCINFLERPNAGQIVV 70 KL V+ +HK YGDNEVLKGVSL A GDVIS+IGASGSGKSTFLRCINFLE PN G + + Sbjct: 3 KLTVEGLHKSYGDNEVLKGVSLKAKTGDVISLIGASGSGKSTFLRCINFLETPNDGAMTL 62 Query: 71 DGEMVKTKTDRAGNLEVADHKQLQRIRTKLAMVFQHFNLWAHMNVLENIVEAPIHVLGLK 130 DG+ ++ +DR G + VAD +LQR+RT+LAMVFQHFNLW+HM+VLENI AP VLG Sbjct: 63 DGQPIRMVSDRHG-MRVADDAELQRLRTRLAMVFQHFNLWSHMSVLENITMAPRRVLGCS 121 Query: 131 RKEAEDRAREYLEKVGLAPRLEKQYPSHLSGGQQQRVAIARALAMNPDVMLFDEPTSALD 190 +K+AEDRAR YL+KVGL R+ QYP+ LSGGQQQRVAIARALAM P+VMLFDEPTSALD Sbjct: 122 KKDAEDRARRYLDKVGLPARVADQYPAFLSGGQQQRVAIARALAMEPEVMLFDEPTSALD 181 Query: 191 PELVGEVLKVMQKLAEEGRTMIVVTHEMGFARNVSNHVMFLHQGRTEEEGLPAEVLSAPR 250 PELVGEVLKV+Q LAEEGRTMI+VTHEM FAR VS+ V+FLHQG EE+G P EVL P+ Sbjct: 182 PELVGEVLKVIQGLAEEGRTMIMVTHEMSFARKVSSQVLFLHQGLVEEQGPPEEVLGNPK 241 Query: 251 SERLKQFLSGSLK 263 SERL+QFLSG+LK Sbjct: 242 SERLQQFLSGNLK 254 Lambda K H 0.318 0.133 0.374 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: 256 Number of extensions: 5 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: 263 Length of database: 254 Length adjustment: 24 Effective length of query: 239 Effective length of database: 230 Effective search space: 54970 Effective search space used: 54970 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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