Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate 5210165 Shew_2609 inner-membrane translocator (RefSeq)
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__PV4:5210165 Length = 297 Score = 155 bits (391), Expect = 1e-42 Identities = 92/306 (30%), Positives = 170/306 (55%), Gaps = 18/306 (5%) Query: 2 EYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLG 61 E +Q +INGL +G +YG++ + + +VY ++NFA GE ++GA+V Sbjct: 4 ELLIQLIINGLIVGLLYGVVGMCFVLVYKSTQIVNFAQGEFLLVGAWVCWAF-------- 55 Query: 62 ITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQIL 121 +T+ L V + ++ F AV+G ++ I RP+ P ++ ++ IG+SIF Q+ + + Sbjct: 56 LTYFQLPFFVGFLFTLCFMAVFGVLLQMIVLRPMIGEPIISVIMVTIGLSIFFQSLTKWI 115 Query: 122 QGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACE 181 G + + + G +++ L + VI I +M F + G A RA Sbjct: 116 FGVSPQSYPQVFDTQSIAIFG-LNIELAYLMSTVIAILIMAAFFLFFKYSKHGLAMRATA 174 Query: 182 QDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVL 241 D+++A LG++V +V ++++ + A ++A AG+++ ++ GV D G+K F A +L Sbjct: 175 FDQQVAQSLGISVKQVFAMSWGIAATVSATAGVVIGMVNGVSDSL--STIGIKVFPAVIL 232 Query: 242 GGIGSLPGAMLGGVVIGLIEAFWSGYMGSEW------KDVATFTILVLVLIFRPTGLLGR 295 GG+ S+ GA++GGVVIG++E + + S+W D+A F +L+++L F+P GL G Sbjct: 233 GGLDSIVGAIVGGVVIGVLENI-AEFFDSQWLHIGNMYDIAPFYVLLVILWFKPYGLFGT 291 Query: 296 PEIEKV 301 +IE++ Sbjct: 292 RDIERI 297 Lambda K H 0.329 0.144 0.425 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: 297 Number of extensions: 16 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: 301 Length of database: 297 Length adjustment: 27 Effective length of query: 274 Effective length of database: 270 Effective search space: 73980 Effective search space used: 73980 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 (21.8 bits) S2: 48 (23.1 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