Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate WP_041097951.1 SUTH_RS06285 sn-glycerol-3-phosphate import ATP-binding protein UgpC
Query= TCDB::P0AAG3 (241 letters) >NCBI__GCF_000828635.1:WP_041097951.1 Length = 336 Score = 135 bits (341), Expect = 8e-37 Identities = 78/224 (34%), Positives = 127/224 (56%), Gaps = 7/224 (3%) Query: 2 ITLKNVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITVD 61 ++++ V K +G +V+ ++ GE VV+ GPSG GKSTL++ V GLE + GEI +D Sbjct: 4 VSIRKVHKSFGAVKVIQGIDVDIADGEFVVMVGPSGCGKSTLLRMVAGLETISSGEIAID 63 Query: 62 GIVVNDKKTDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPAREKALKLL 121 G VVN DL + MVFQ++ L+PH+S+ +N+ +K+ + A + Sbjct: 64 GRVVN----DLEPKDRNIAMVFQNYALYPHMSVRQNMAYG-LKIRRMSSADIEAHVKRAA 118 Query: 122 ERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINEVLDVMVE 181 E + L + ++ P +LSGGQ+QRVA+ RA+ +P LFDEP S LD ++ ++ + Sbjct: 119 EILELGPYLDRKPRELSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDAKLRVQMRAELQA 178 Query: 182 LANE-GMTMMVVTHEMGFARKVANRVIFMDEGKIVE-DSPKDAF 223 L T + VTH+ A +A R+I M+ G+ + +P D + Sbjct: 179 LHRRLATTSLYVTHDQVEAMTMAQRMIVMNAGRAEQIGAPLDVY 222 Lambda K H 0.320 0.135 0.383 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: 166 Number of extensions: 7 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: 241 Length of database: 336 Length adjustment: 26 Effective length of query: 215 Effective length of database: 310 Effective search space: 66650 Effective search space used: 66650 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: 47 (22.7 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