Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate GFF2975 HP15_2919 amino acid ABC transporter, permease protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5404 (365 letters) >FitnessBrowser__Marino:GFF2975 Length = 223 Score = 89.7 bits (221), Expect = 6e-23 Identities = 64/202 (31%), Positives = 100/202 (49%), Gaps = 5/202 (2%) Query: 157 GLMLTLVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVM 216 G+ TL+I+ G++ LGI L + +R +IE +RG P++ + Sbjct: 22 GIPYTLLISFGGLLIGFALGIFFGLLSINKKWFLRWPATAYIEIFRGTPILVQVLFIFYG 81 Query: 217 LPLFLPEGMNFDKLLRALIGVILFQSAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMG 276 LP + G D L + + L AYI+EVVRGG+Q+I KGQ EA ++GL ++ Sbjct: 82 LPDLI--GGPIDPLTAGIAAIALNSGAYISEVVRGGVQSIDKGQTEAGLSLGLSRTQTFW 139 Query: 277 LVILPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNSVKQAAADPKWLGMATEGYVF 336 V+ PQA + +IP + N I KDTSL +IG+ +L V+Q A E Y Sbjct: 140 SVVWPQAFRRMIPPLGNQAIVSIKDTSLFSVIGVGEL---VRQGQIYIANTFTAFEVYFV 196 Query: 337 AALVFWIFCFGMSRYSMHLERK 358 A+++ +S +ER+ Sbjct: 197 VAILYLAITLSLSIILRFVERR 218 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: 237 Number of extensions: 15 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: 365 Length of database: 223 Length adjustment: 26 Effective length of query: 339 Effective length of database: 197 Effective search space: 66783 Effective search space used: 66783 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: 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