Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate WP_015887278.1 NGR_RS05625 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::acidovorax_3H11:Ac3H11_792 (358 letters) >NCBI__GCF_000018545.1:WP_015887278.1 Length = 360 Score = 228 bits (582), Expect = 1e-64 Identities = 124/322 (38%), Positives = 191/322 (59%), Gaps = 6/322 (1%) Query: 24 LLPLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTRASPQERNIA 83 L + + E G LLG SGCGK+T+LNI++GL PS G +L R + A P++R+IA Sbjct: 19 LKSIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIGERSILGAHPKDRDIA 78 Query: 84 QVFQFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAGLAADA 143 VFQ +Y M+VA N+ F L RKVP + ++ V A +L++ L+++ + L+ Sbjct: 79 MVFQSYALYPNMSVARNIGFGLEMRKVPAAEREKAVRDTARLLQIENLLDRKPSQLSGGQ 138 Query: 144 KQKISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTHDQVEA 203 +Q++++GR LVR + LFDEPL+ +D L+ ++R +LK++H LK T++YVTHDQ+EA Sbjct: 139 RQRVAIGRALVR-EPQVFLFDEPLSNLDAKLRMEMRTELKRLHQMLKTTVVYVTHDQIEA 197 Query: 204 LTFADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLPAHRDGENLSVAGHR 263 +T A ++ VM G+ Q+G+ +++RPA +V F+GSP MN L A G L + G Sbjct: 198 MTLATRIAVMRDGRIEQLGTPAEIYDRPATLYVAGFVGSPPMNILDAEGTGSGLRILGSE 257 Query: 264 LASPVGRALPAGA----LQVGIRPEYLALAQPQQAGALPGTVVQVQDI-GTYQMLTAKVG 318 P+G A P G ++VGIRPE L LA G +V+V ++ G ++TA++G Sbjct: 258 NTLPLGGAFPNGTTGRRVKVGIRPEALRLAGDDATGGRLTAIVEVMELTGPELVITARIG 317 Query: 319 EHTVKARFTPETRLPSSGDTAW 340 E + A P T L A+ Sbjct: 318 EQRITACLPPRTSLEPGSTQAF 339 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: 315 Number of extensions: 15 Number of successful extensions: 4 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: 360 Length adjustment: 29 Effective length of query: 329 Effective length of database: 331 Effective search space: 108899 Effective search space used: 108899 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 Apr 09 2024. 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