Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate WP_086509149.1 BZY95_RS06450 amino acid ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_5404 (365 letters) >NCBI__GCF_002151265.1:WP_086509149.1 Length = 366 Score = 478 bits (1229), Expect = e-139 Identities = 222/355 (62%), Positives = 284/355 (80%) Query: 11 PPPGSSIGVVAWMRANMFSSWINTLLTLFAFYLIYLIVPPLVQWAILDANWVGTTRADCT 70 P PG+++G +AW+R N+FS +NT+ TL YL+Y+++ P +QWA ++A+WVGT+R DC+ Sbjct: 12 PAPGNTVGPIAWLRINLFSGPVNTVFTLLGLYLLYVLLTPTIQWAFINADWVGTSRDDCS 71 Query: 71 KEGACWVFIQQRFGQFMYGYYPADLRWRVDLTVWLAVIGVAPLFISRFPRKAIYGLSFLV 130 +EGACWVF+ R QF+YG YP WRV++ + +A L I R P K L+ LV Sbjct: 72 REGACWVFVNARLTQFIYGLYPRTELWRVNIVFATFAVLIAWLAIPRLPLKRWVALATLV 131 Query: 131 LYPISAWCLLHGGVFGLDAVATSQWGGLMLTLVIATVGIVGALPLGIVLALGRRSNMPAI 190 +P+ A+ LL+GG FGL V T +WGGLMLTL++A VG+V ALP+GI+LALGRRS MP + Sbjct: 132 AFPVFAFFLLYGGYFGLRVVETHRWGGLMLTLILAVVGMVAALPIGILLALGRRSQMPIV 191 Query: 191 RVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNFDKLLRALIGVILFQSAYIAEVVR 250 + CV FIEFWRGVPLIT+LFM+SVMLPLFLP G++ D+L+RALIG+ LFQSAY+AEV+R Sbjct: 192 KSFCVVFIEFWRGVPLITILFMASVMLPLFLPTGVSVDRLVRALIGITLFQSAYMAEVIR 251 Query: 251 GGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVIIIGL 310 GGLQAIP+GQ EAAAA+G+GYW MGL++LPQALK++IPGIVNTFI+LFKDT+LV+IIGL Sbjct: 252 GGLQAIPRGQEEAAAALGMGYWMRMGLIVLPQALKMMIPGIVNTFISLFKDTTLVMIIGL 311 Query: 311 FDLLNSVKQAAADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERKLDTGHKR 365 FDLL V+ A +D +WLG A EGYVFAA +FWIFCF MSRYS +LERKL TGHKR Sbjct: 312 FDLLGIVQAALSDSRWLGFALEGYVFAAFMFWIFCFSMSRYSQYLERKLHTGHKR 366 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: 644 Number of extensions: 30 Number of successful extensions: 1 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: 366 Length adjustment: 30 Effective length of query: 335 Effective length of database: 336 Effective search space: 112560 Effective search space used: 112560 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 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