Align ABC transporter for L-Arginine, putative ATPase component (characterized)
to candidate GFF3439 PS417_17605 amino acid transporter
Query= reanno::BFirm:BPHYT_RS07685 (263 letters) >FitnessBrowser__WCS417:GFF3439 Length = 276 Score = 340 bits (873), Expect = 1e-98 Identities = 179/258 (69%), Positives = 208/258 (80%), Gaps = 4/258 (1%) Query: 7 TEACKLAVQDIHKRYGDNEVLKGVSLNANKGDVISIIGASGSGKSTFLRCINFLERPNAG 66 T A KL V+ IHKRYG++EVLKGVSLNA +GDVIS+IGASGSGKST LRCINFLE+P+AG Sbjct: 22 TAAIKLQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAG 81 Query: 67 QIVVDGEMVKTKTDRAGNLEVADHK-QLQRIRTKLAMVFQHFNLWAHMNVLENIVEAPIH 125 I +DG ++ + RAG A H+ QLQ +RT+LAMVFQHFNLW+HM VLENI AP Sbjct: 82 VITLDGISIEMRQGRAGTR--APHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRR 139 Query: 126 VLGLKRKEAEDRAREYLEKVGLAPRLEKQYPSHLSGGQQQRVAIARALAMNPDVMLFDEP 185 VL + EAE RAR YL+KVGL R+ QYP+ LSGGQQQRVAIARALAM P+++LFDEP Sbjct: 140 VLDVSAAEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEP 199 Query: 186 TSALDPELVGEVLKVMQKLAEEGRTMIVVTHEMGFARNVSNHVMFLHQGRTEEEGLPAEV 245 TSALDPELVGEVLKV+Q LAEEGRTM++VTHEMGFAR VS+ V+FLHQGR EE G A + Sbjct: 200 TSALDPELVGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHG-DARI 258 Query: 246 LSAPRSERLKQFLSGSLK 263 L P SERL+QFLS LK Sbjct: 259 LDQPNSERLQQFLSNRLK 276 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: 232 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: 263 Length of database: 276 Length adjustment: 25 Effective length of query: 238 Effective length of database: 251 Effective search space: 59738 Effective search space used: 59738 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