Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate PfGW456L13_386 Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1)
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_386 Length = 254 Score = 235 bits (600), Expect = 6e-67 Identities = 123/247 (49%), Positives = 168/247 (68%), Gaps = 11/247 (4%) Query: 15 IQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVVD 74 + ++ ++K YG VLK ++LN + G+ I L G SGSGKST +RC+N LE G + +D Sbjct: 4 LTVENLHKSYGNHEVLKGVSLNARTGDVISLIGASGSGKSTFLRCINFLETPNDGAMSLD 63 Query: 75 GVEL----------TNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKR 124 + D +++ IR + MVFQHFNL+ H+T+L N T+AP V + K+ Sbjct: 64 SQPIKMVHDHHGMRVADANELQRIRTRLAMVFQHFNLWSHMTVLDNITMAPRRVLGVSKK 123 Query: 125 KAEEIAMHYLERVRIPEQ-AHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPE 183 AE+ A YL++V +P + A +YP LSGGQQQRVAIARAL M+P+IMLFDEPTSALDPE Sbjct: 124 DAEDRARRYLDKVGLPARVADQYPAFLSGGQQQRVAIARALSMEPEIMLFDEPTSALDPE 183 Query: 184 MVKEVLDTMIGLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQND 243 +V EVL + GLAE+G TM+ VTHEM FAR V+N+V+F+ +G + EQ AP D NP+++ Sbjct: 184 LVGEVLKVIQGLAEEGRTMIMVTHEMSFARKVSNQVLFLHQGRVEEQGAPEDVLGNPKSE 243 Query: 244 RTKLFLS 250 R K FLS Sbjct: 244 RLKQFLS 250 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: 202 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: 254 Length adjustment: 24 Effective length of query: 230 Effective length of database: 230 Effective search space: 52900 Effective search space used: 52900 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: 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