Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate WP_011842475.1 RSPH17029_RS18135 amino acid ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_5404 (365 letters) >NCBI__GCF_000015985.1:WP_011842475.1 Length = 370 Score = 271 bits (692), Expect = 3e-77 Identities = 146/355 (41%), Positives = 217/355 (61%), Gaps = 10/355 (2%) Query: 13 PGSSIGVVAWMRANMFSSWINTLLTLFAFYLIYLIVPPLVQWAILDANWVGTTRADC-TK 71 P + + AW+RAN+FSS +LLTL ++ ++ W +++A + T C Sbjct: 19 PDARLSAPAWLRANLFSSVWQSLLTLVVAVVLIRFFWFVLDWGVVNAVFYTTDPDVCRAA 78 Query: 72 EGACWVFIQQRFGQFMYGYYPADLRWRVDLTVWLAVIGVAPLFISRFPRKAIYGLSFLV- 130 GACW I ++ ++G YP D WR+ V + + + + +S +PR + L FLV Sbjct: 79 TGACWAVIVEKHRPMLFGLYPYDEHWRL---VLMMAVYLGTVVLSLWPR--CWNLRFLVP 133 Query: 131 ---LYPISAWCLLHGGVFGLDAVATSQWGGLMLTLVIATVGIVGALPLGIVLALGRRSNM 187 + +S L+ GGV GL V TS+WGGL LT+++ T ++ +P+ ++LALGRR+ + Sbjct: 134 LWIVSSLSIGILMFGGVLGLRYVPTSEWGGLPLTMLLFTGTVLIGMPVAVLLALGRRAPL 193 Query: 188 PAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNFDKLLRALIGVILFQSAYIAE 247 P R V V FIE RGVPLIT+LF++ + PLFLP G+ +KLLR +G+ +F + Y AE Sbjct: 194 PVARGVSVVFIEALRGVPLITILFVAVNVFPLFLPAGVEVNKLLRITVGIAIFFACYQAE 253 Query: 248 VVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVII 307 V+RGGLQAIP GQYEAAA++ L YW++ +ILPQAL++ +P I N IA K+TS VII Sbjct: 254 VIRGGLQAIPTGQYEAAASLSLSYWQTTRRIILPQALRISLPAITNHIIAAMKNTSFVII 313 Query: 308 IGLFDLLNSVKQAAADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERKLDTG 362 IGLFD+L + DP W E Y+F A V+ F + +S Y+ +E+ + +G Sbjct: 314 IGLFDILTATTAVMQDPLWRKFYIEAYLFVAAVYLFFGYALSLYARQVEKWIASG 368 Lambda K H 0.330 0.144 0.469 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: 532 Number of extensions: 35 Number of successful extensions: 4 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: 365 Length of database: 370 Length adjustment: 30 Effective length of query: 335 Effective length of database: 340 Effective search space: 113900 Effective search space used: 113900 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 2024. 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