Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate WP_078211033.1 BXU11_RS03565 ABC transporter ATP-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >NCBI__GCF_002017945.1:WP_078211033.1 Length = 233 Score = 155 bits (393), Expect = 5e-43 Identities = 89/233 (38%), Positives = 137/233 (58%), Gaps = 11/233 (4%) Query: 14 IIQMQGVNKWY----GQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQG 69 +I+++ ++K Y + HVLK IN N+K+GE + + G SGSGKST + L L+E G Sbjct: 1 MIEIKDLHKSYKMGSSELHVLKGINFNIKEGELVAIMGSSGSGKSTLLNILGILDEADSG 60 Query: 70 RIVVDGVELTNDLKQIEAIRRE--VGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAE 127 ++D V + + I + R +G VFQ FNL + T L N + P++ + + +++ Sbjct: 61 SYILDTVPIKKLNETIASKYRNQFLGFVFQSFNLINYKTALDNVAM-PLYYQGIKRKERN 119 Query: 128 EIAMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKE 187 EIAM YL +V + +H P +LSGGQ+QRVAIARAL PK++L DEPT ALD + E Sbjct: 120 EIAMKYLGKVGLATHSHHLPNELSGGQKQRVAIARALASNPKVLLADEPTGALDTKTSYE 179 Query: 188 VLDTMIGLAEDGMTMLCVTHEMGFARTVANRVIFMD----KGEIVEQAAPNDF 236 V++ + G+ ++G T+L VTHE A V+ D ++VEQ + + Sbjct: 180 VMELIQGINDEGKTILIVTHEPDIAAMCKRNVVLKDGLIIDDKLVEQVRASSY 232 Lambda K H 0.322 0.137 0.407 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: 141 Number of extensions: 5 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: 254 Length of database: 233 Length adjustment: 23 Effective length of query: 231 Effective length of database: 210 Effective search space: 48510 Effective search space used: 48510 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: 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