Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate WP_038857748.1 AFK65_RS05695 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::acidovorax_3H11:Ac3H11_792 (358 letters) >NCBI__GCF_001277175.1:WP_038857748.1 Length = 371 Score = 201 bits (510), Expect = 3e-56 Identities = 120/327 (36%), Positives = 186/327 (56%), Gaps = 26/327 (7%) Query: 26 PLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTRASPQERNIAQV 85 PL ++ G ++GPSGCGK+T+L +++GL + G + D + V SP ER I V Sbjct: 22 PLDLQINSGEFVVVVGPSGCGKSTLLRLVAGLEEITDGDMYIDDQRVNDDSPSERGIGMV 81 Query: 86 FQFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAGLAADAKQ 145 FQ +Y MTV +N+AF L KVPE +I +RV A +L++ L++R L+ +Q Sbjct: 82 FQSYALYPHMTVYQNMAFALEMAKVPEKEIDERVRESARILQLEHLLDRRPKDLSGGQRQ 141 Query: 146 KISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTHDQVEALT 205 ++++GR +VR + + LFDEPL+ +D L+ Q+R ++ +H + T++YVTHDQVEA+T Sbjct: 142 RVAIGRAIVR-EPSLFLFDEPLSNLDASLRVQMRMEIAALHRRIHATILYVTHDQVEAMT 200 Query: 206 FADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLPAHRDGENLSVAGH--- 262 AD++VV+ +G+ QVG+ AL++ PA+ FV FIGSP MN +P G+ L V H Sbjct: 201 LADRIVVLNQGQIEQVGTPLALYDTPANVFVAQFIGSPKMNLIP----GKMLRVMEHACE 256 Query: 263 -------RLASPVGRAL--PAGALQVGIRPEYLALAQPQQAGALPGTVVQVQDIGTYQML 313 RL PV A+Q+GIRPE++ + +A + G V+ V+ +G ++ Sbjct: 257 VELENGLRLTLPVQAVAGQEGDAVQLGIRPEHVEIMTLAKAD-VEGEVLFVEHMGNETLV 315 Query: 314 TAKVG--------EHTVKARFTPETRL 332 G HT + PE L Sbjct: 316 YVNGGYGAEPLVMRHTERLEVRPEHHL 342 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: 323 Number of extensions: 14 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: 371 Length adjustment: 29 Effective length of query: 329 Effective length of database: 342 Effective search space: 112518 Effective search space used: 112518 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 24 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