Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_069331237.1 C8J29_RS14155 sn-glycerol-3-phosphate import ATP-binding protein UgpC
Query= reanno::Smeli:SMc04256 (361 letters) >NCBI__GCF_003046325.1:WP_069331237.1 Length = 349 Score = 295 bits (756), Expect = 9e-85 Identities = 162/362 (44%), Positives = 234/362 (64%), Gaps = 14/362 (3%) Query: 1 MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60 M +S+RD+ ++ + V+ ++L+I GEF+V++G SGCGKSTLL +AGL +++ G+I Sbjct: 1 MAEISLRDVRKSYSGLEVIHGVDLEIADGEFVVIVGPSGCGKSTLLRMVAGLEEITAGEI 60 Query: 61 FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120 I R V EP++R I MVFQ+YALYP MTV +N+++GL++AK+ AEIE+RV R++++ Sbjct: 61 AIGGRVVNRLEPRERDIAMVFQNYALYPHMTVRENMAYGLRIAKLSKAEIEERVARSAKM 120 Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180 L++ LL RKP +LSGGQRQRVA+GRALVR+ FL DEPLSNLDAKLR ++R++IK L Sbjct: 121 LELGQLLDRKPRQLSGGQRQRVAMGRALVRNPAAFLLDEPLSNLDAKLRVQMRLQIKELQ 180 Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240 ++++ T IYVTHDQ+EA+TLADR+ VM +GV +Q+A P IY+ P FVAGFIGSP+MN Sbjct: 181 RTVRTTSIYVTHDQVEAMTLADRLVVMNAGVAEQIATPAEIYDRPATTFVAGFIGSPAMN 240 Query: 241 FFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEPTH 300 R G A +V G+ ++LG+RPEH + A EP Sbjct: 241 MLP-----------ARGLGDALEVAGQRLAVPAPAGRDLILGIRPEH--LHPAGPEEPGF 287 Query: 301 QAVVDIEEPMGADNLLWLTFA-GQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAESEN 359 + V E +GAD + A G + +R G+ ++++ D +FDA + Sbjct: 288 ELHVQAVEWLGADAFAHGSLADGTDLVLRTPGKAPVRERDRLKVAPDAAALHLFDAGTGR 347 Query: 360 RL 361 RL Sbjct: 348 RL 349 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: 372 Number of extensions: 10 Number of successful extensions: 2 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: 349 Length adjustment: 29 Effective length of query: 332 Effective length of database: 320 Effective search space: 106240 Effective search space used: 106240 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