Align ABC transporter for Glycerol, permease component 2 (characterized)
to candidate H281DRAFT_04157 H281DRAFT_04157 sorbitol ABC transporter membrane protein /mannitol ABC transporter membrane protein
Query= reanno::acidovorax_3H11:Ac3H11_794 (270 letters) >FitnessBrowser__Burk376:H281DRAFT_04157 Length = 291 Score = 142 bits (357), Expect = 1e-38 Identities = 79/259 (30%), Positives = 137/259 (52%), Gaps = 4/259 (1%) Query: 12 FLIAYLLFALLPIYWMVNMSFKTNAEILSTFSFFPQHFTWDNYKTIFTDESWYSGYINSL 71 + +A LLF PI+WM +FKT + S+ FF T+D+++ +F +++S NS+ Sbjct: 36 WFVALLLF--FPIFWMTITAFKTEQQAYSSSLFFTP--TFDSFREVFARSNYFSFAWNSI 91 Query: 72 IYVSINMVITLTVALPAAYAFSRYSFLGDKHVFFWLLTNRMTPPAVFLLPFFQLYTTVGL 131 + V+ L +A+PAAYA + + + V W+L+ +M P L+P + L+ GL Sbjct: 92 LISVGVTVLCLILAVPAAYAMAFFPTRRTQKVLLWMLSTKMMPSVGVLVPIYLLWKNSGL 151 Query: 132 MDTHIAVALAHLLFSVPLAVWILEGFMSGIPREIDETAYIDGYSFPRFFMTIFLPLIKAG 191 +DT + + + L ++P+AVW+ + + IPR+I E IDG + + + + +P+ G Sbjct: 152 LDTVSGLVIVYTLINLPIAVWMSFTYFAEIPRDILEAGRIDGAATWQEIVYLLMPMALPG 211 Query: 192 VGVAAFFCFMFSWVELLLARTLTSVNAKPIVATMTRTVSASGMDWATLAAAGVLTIVPGA 251 + A + SW E + L+S NA P+ + S G+ WA L+AA +L + P Sbjct: 212 LASTALLLVILSWNEAFWSINLSSSNAAPLTVFIASYSSPEGLFWAKLSAASLLAVAPIL 271 Query: 252 IVIWFVRHYIAKGFAMGRV 270 IV W + + +G G V Sbjct: 272 IVGWLSQKQLVRGLTFGAV 290 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: 294 Number of extensions: 27 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: 291 Length adjustment: 26 Effective length of query: 244 Effective length of database: 265 Effective search space: 64660 Effective search space used: 64660 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