Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate Echvi_2123 Echvi_2123 ABC-type spermidine/putrescine transport systems, ATPase components
Query= reanno::acidovorax_3H11:Ac3H11_792 (358 letters) >FitnessBrowser__Cola:Echvi_2123 Length = 318 Score = 112 bits (280), Expect = 1e-29 Identities = 87/339 (25%), Positives = 161/339 (47%), Gaps = 45/339 (13%) Query: 23 ALLPLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTRAS----PQ 78 AL ++ + GG +++G SG GK+++L I++GL V S G V + + + P Sbjct: 19 ALEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAGVVHLGDQKILNPAQKLVPG 78 Query: 79 ERNIAQVFQFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAG 138 I + Q +Y TV EN+A PL + K+R I E+L + +++ Sbjct: 79 YDEIQLIHQEYKLYPNSTVEENIARPLL--LYDKAYQKERTAEILELLSLRAFKDKKPRQ 136 Query: 139 LAADAKQKISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTH 198 L+ +QK+++GR L + +L DEP + +D K L +LK+I L++T+I+VTH Sbjct: 137 LSGGQQQKVAIGRAL-SIEPEVLLLDEPFSSLDAIQKRDLIEELKEIFDALEVTVIFVTH 195 Query: 199 DQVEALTFADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLPAHRDGENLS 258 D +AL +++++++ +GK +Q G+ +F +PA +V G +N +P Sbjct: 196 DVDDALLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARLFGY--LNLIP--------- 244 Query: 259 VAGHRLASPVGRALPAGALQVGIRPEYLALAQPQQAGALPGTVVQVQDIGTYQMLTAKVG 318 GA + +RP + + ++ VV+ Q + Y +LT K+ Sbjct: 245 ----------------GAEEAYVRPSEVKITSKT---SIKAEVVKQQFLIHYNLLTVKLE 285 Query: 319 EHTVKARFTPETRLPSSGDTAWLQVLGEHTCYYKNEELL 357 + + + +R + GD +L Y+ E+L+ Sbjct: 286 DSELFWKVDDPSRSVNVGDEVFLD--------YQKEQLI 316 Lambda K H 0.320 0.136 0.395 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: 224 Number of extensions: 11 Number of successful extensions: 3 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: 358 Length of database: 318 Length adjustment: 28 Effective length of query: 330 Effective length of database: 290 Effective search space: 95700 Effective search space used: 95700 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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