Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate WP_086511012.1 BZY95_RS16625 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::acidovorax_3H11:Ac3H11_792 (358 letters) >NCBI__GCF_002151265.1:WP_086511012.1 Length = 346 Score = 194 bits (494), Expect = 2e-54 Identities = 116/282 (41%), Positives = 167/282 (59%), Gaps = 21/282 (7%) Query: 27 LKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTRASPQERNIAQVF 86 L + EDG L+GPSGCGK+T+L +++GL + G + GRDVT A P ERNIA VF Sbjct: 23 LNLRIEDGSFTVLVGPSGCGKSTLLRMIAGLETVTRGAISIGGRDVTTAEPSERNIAMVF 82 Query: 87 QFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAGLAADAKQK 146 Q +Y MTVA N+ F +R KVP + +V A +L + L ++ A L+ +Q+ Sbjct: 83 QSYALYPHMTVARNIDFGMRLAKVPTEERMAKVAEAARLLNLEELLERKPAELSGGQRQR 142 Query: 147 ISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTHDQVEALTF 206 +++GR +VR + LFDEPL+ +D L+ ++R +L ++H L T+IYVTHDQVEA+T Sbjct: 143 VAIGRAIVR-NPGVFLFDEPLSNLDAALRNRMRVELAELHQRLDATMIYVTHDQVEAMTL 201 Query: 207 ADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLPAHRDGENLSVAGHRLAS 266 AD +VVM G+ QVG+ L++RP FV FIGSP MN + +GE Sbjct: 202 ADCIVVMNAGQIEQVGTPMNLYQRPETLFVAGFIGSPKMNLI----EGE----------- 246 Query: 267 PVGRALPAGALQVGIRPEYLALAQPQQAGALPGTVVQVQDIG 308 V +A GA +GIRPE+L ++ +AG V V+ +G Sbjct: 247 -VAKA--HGATTLGIRPEHLEVS--HEAGEWRTRVRVVEMLG 283 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: 292 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: 346 Length adjustment: 29 Effective length of query: 329 Effective length of database: 317 Effective search space: 104293 Effective search space used: 104293 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