Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate GFF3855 PGA1_78p00190 sn-glycerol-3-phosphate import ATP-binding protein UgbC
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Phaeo:GFF3855 Length = 361 Score = 436 bits (1120), Expect = e-127 Identities = 227/360 (63%), Positives = 276/360 (76%), Gaps = 6/360 (1%) Query: 3 SVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFI 62 SV +RDL L+FG + VL +LNLDI+ GEFLVLLGSSGCGKSTLLNCIAGLLD+SDGQIFI Sbjct: 7 SVEIRDLDLHFGELQVLHQLNLDIEQGEFLVLLGSSGCGKSTLLNCIAGLLDISDGQIFI 66 Query: 63 KDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQ 122 + +NVTW EP +RGIGMVFQSYALYPQMTVE NLSFGLK A++P AEI KRV RA+E+LQ Sbjct: 67 QGQNVTWAEPSERGIGMVFQSYALYPQMTVEGNLSFGLKNARLPKAEIAKRVARAAEVLQ 126 Query: 123 IQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQS 182 I+PLLKRKP+ LSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLR++LRVE+KRLHQ Sbjct: 127 IEPLLKRKPAALSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRADLRVELKRLHQQ 186 Query: 183 LKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFF 242 L NTMIYVTHDQ+EA+TLADRIA+MK G I QL+ P IYN P+NL+VAGFIGSP+MN Sbjct: 187 LANTMIYVTHDQVEAMTLADRIAIMKGGRIMQLSSPDEIYNRPQNLYVAGFIGSPAMNLI 246 Query: 243 RGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKV-DEARDGEPTHQ 301 G + DG AG +A + Y G V+G+RPEH+ ++ + T + Sbjct: 247 EGVL--IDG--VFHAGSLALPMQRYDYRNGPHHG-AAVIGIRPEHILTGEQITRADATAE 301 Query: 302 AVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAESENRL 361 +VD+ E +G+D L++ T Q++ +R+ G R G +R+ FD G AS+FD +E RL Sbjct: 302 VLVDLVEGLGSDTLVYATHGAQNLRLRMDGASRVSAGDRLRIGFDTGRASLFDPNTEARL 361 Lambda K H 0.320 0.137 0.392 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: 450 Number of extensions: 16 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: 361 Length of database: 361 Length adjustment: 29 Effective length of query: 332 Effective length of database: 332 Effective search space: 110224 Effective search space used: 110224 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