Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate GFF2520 PGA1_c25590 putative glycine betaine/L-proline transport system, ATP binding subunit
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >FitnessBrowser__Phaeo:GFF2520 Length = 350 Score = 314 bits (804), Expect = 2e-90 Identities = 154/264 (58%), Positives = 202/264 (76%), Gaps = 1/264 (0%) Query: 7 SKIEVKNVFKIFGNRSKEALELIR-QNKTKDQVLAETGCVVGVNDLSLSIGTGEIFVIMG 65 +KI+++N++KIFG L ++R Q K Q+L E V+G+ D+S+ I GEI VIMG Sbjct: 4 TKIQIRNLYKIFGANPGTVLPMVRNQGMGKSQLLEEHKHVLGLQDISIDIQAGEISVIMG 63 Query: 66 LSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALREFRRHKISMVFQSFGLLPHK 125 LSGSGKSTL+RH NRLI+PT+G IL+DG+D++ LD LRE R+ +SMVFQ F LLPHK Sbjct: 64 LSGSGKSTLIRHLNRLIEPTAGEILLDGQDVMDLDPVQLREMRQRSMSMVFQKFALLPHK 123 Query: 126 SVLDNVAYGLKVRGESKQVCAERALHWINTVGLKGYENKYPHQLSGGMRQRVGLARALAA 185 +VL+N L+VRG+ + C A W++ VGL G+EN+YP QLSGGM+QRVG+ARAL A Sbjct: 124 TVLENAETALRVRGDDRATCEAAARKWLDRVGLSGFENRYPSQLSGGMQQRVGIARALTA 183 Query: 186 DTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFITHDLDEAVRIGNRIAILKDG 245 DTDI+L+DEAFSALDPLIR +MQD LLELQ LHKTIVFITHDLDEA+++ + + ILKDG Sbjct: 184 DTDIMLLDEAFSALDPLIRTDMQDLLLELQTELHKTIVFITHDLDEALKLADHLVILKDG 243 Query: 246 KLIQVGTPREILHSPADEYVDRFV 269 ++Q G P+ I+ +PAD Y++ FV Sbjct: 244 AVVQQGPPQGIVMNPADPYIEAFV 267 Lambda K H 0.321 0.138 0.387 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: 309 Number of extensions: 10 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: 276 Length of database: 350 Length adjustment: 27 Effective length of query: 249 Effective length of database: 323 Effective search space: 80427 Effective search space used: 80427 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: 48 (23.1 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