Align ABC transporter for Glycerol, permease component 2 (characterized)
to candidate GFF1646 PGA1_c16690 binding protein-dependent transport system, inner membrane component
Query= reanno::acidovorax_3H11:Ac3H11_794 (270 letters) >FitnessBrowser__Phaeo:GFF1646 Length = 283 Score = 146 bits (369), Expect = 4e-40 Identities = 78/257 (30%), Positives = 136/257 (52%), Gaps = 2/257 (0%) Query: 16 YLLFALLPIYWMVNMSFKTNAEILSTFS-FFPQHFTWDNYKTIFTDESWYSGYINSLIYV 74 YL FAL P+YW++ ++ +A I S + P T++N+ T+ + + + + NSL Sbjct: 25 YLGFALFPLYWLMKIAITPDALIFSEGTRMLPSAVTFENFATVLFETEFLAYFRNSLTVS 84 Query: 75 SINMVITLTVALPAAYAFSRYSFLGDKHVFFWLLTNRMTPPAVFLLPFFQLYTTVGLMDT 134 T +A A YAFSR+ F G + + +L +M P + + P +++ +GL+++ Sbjct: 85 LGTAFFTTLIAAGAGYAFSRFVFAGKRIIIAVMLITQMFPLLMIIAPIYKIVADLGLLNS 144 Query: 135 HIAVALAHLLFSVPLAVWILEGFMSGIPREIDETAYIDGYSFPRFFMTIFLPLIKAGVGV 194 ++ + + F++P A ++++ F GIP++++E A +DG S + T+ PL G+G Sbjct: 145 LTSLIVVYTAFNIPFATFLMQSFFDGIPKDLEEAAMMDGCSRFQALRTVVFPLTLPGLGA 204 Query: 195 AAFFCFMFSWVELLLARTLTSVN-AKPIVATMTRTVSASGMDWATLAAAGVLTIVPGAIV 253 F F +W ELL A L S N A + VS +DW + AAGVL +VP + Sbjct: 205 TLGFVFTAAWSELLFALMLISKNDAMTFPVGLLTFVSKFSVDWGQMMAAGVLALVPSCLF 264 Query: 254 IWFVRHYIAKGFAMGRV 270 F++ Y+ +G G V Sbjct: 265 FIFIQRYLVQGLTSGAV 281 Lambda K H 0.332 0.141 0.451 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: 216 Number of extensions: 13 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: 270 Length of database: 283 Length adjustment: 25 Effective length of query: 245 Effective length of database: 258 Effective search space: 63210 Effective search space used: 63210 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (22.0 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