Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate 202699 SO3602 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)
Query= reanno::acidovorax_3H11:Ac3H11_792 (358 letters) >FitnessBrowser__MR1:202699 Length = 376 Score = 157 bits (398), Expect = 3e-43 Identities = 110/315 (34%), Positives = 170/315 (53%), Gaps = 15/315 (4%) Query: 23 ALLPLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTRASPQERNI 82 AL PL ++ ++G LLGPSG GKTT+L I++GL G + F RDVT+ ++R + Sbjct: 17 ALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGHIHFGNRDVTQVHVRDRRV 76 Query: 83 AQVFQFPVIYDTMTVAENLAFPL----RNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAG 138 VFQ ++ MTVA+N+AF L + ++ +I++RV + EM+++ + Sbjct: 77 GFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSAAEIQKRVSHLLEMVQLGHLAQRYPEQ 136 Query: 139 LAADAKQKISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTH 198 L+ KQ+I+L R L +L DEP +D ++ +LRR L+ +H ELK T ++VTH Sbjct: 137 LSGGQKQRIALARALA-TQPEVLLLDEPFGALDAKVRKELRRWLRSLHDELKFTSVFVTH 195 Query: 199 DQVEALTFADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLPAHRDGENLS 258 DQ EAL +D+VVVM+ G QV + L+ +P FV F+G+ +N A+ + Sbjct: 196 DQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFDFLGN--VNRFEANWQQNRWT 253 Query: 259 VAGHRLASPVGRALPA-GALQVGIRPEYLALA-QPQQAGALPGTVVQVQDIGT-YQMLTA 315 + P L GAL V R LALA +P +P T+V + IG ++ A Sbjct: 254 NGDAFIVPPEQTPLQQNGALYV--RSHELALADKPNSQAHIPFTIVAITPIGAEVRVELA 311 Query: 316 KVG---EHTVKARFT 327 +G E +A+FT Sbjct: 312 PIGWQSEELWEAKFT 326 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: 301 Number of extensions: 9 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: 376 Length adjustment: 30 Effective length of query: 328 Effective length of database: 346 Effective search space: 113488 Effective search space used: 113488 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