Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_085637757.1 MGEO_RS11955 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::pseudo5_N2C3_1:AO356_00010 (365 letters) >NCBI__GCF_002115805.1:WP_085637757.1 Length = 365 Score = 313 bits (803), Expect = 4e-90 Identities = 169/363 (46%), Positives = 242/363 (66%), Gaps = 10/363 (2%) Query: 4 LKIENLKKGFEGLSIIKGIDLEVKDKEFVVFVGPSGCGKSTLLRLIAGLEDVTSGTIELD 63 L I+NL K + I+K I++ ++ +F+V VGPSGCGKSTLL IAGLE +T G+I + Sbjct: 5 LDIKNLYKSYGTTEILKDINVSIEPGDFLVLVGPSGCGKSTLLNCIAGLEPITGGSINIG 64 Query: 64 GRDITEVTPAKRDLAMVFQTYALYPHMTVRKNLSFALDLAGEKKPDVERKVAEAARILEL 123 G+D+T V+P RD+AMVFQ+YALYP MTV KN++F + + G + +RK+A+ A+ L++ Sbjct: 65 GKDMTHVSPKDRDIAMVFQSYALYPTMTVAKNITFGMKVRGVDQATQDRKLAQVAQQLQI 124 Query: 124 GSLLDRKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQTRLELSRLHKEL 183 LL+R+P QLSGGQRQRVA+GRA+VR+PK+FLFDEPLSNLDA LRV+ R E+ LH L Sbjct: 125 EPLLNRRPGQLSGGQRQRVAMGRALVRDPKLFLFDEPLSNLDAKLRVEMRTEIKSLHHNL 184 Query: 184 QATMIYVTHDQVEAMTLATKVVVLNAGRIEQIGSPLELYHHPANLFVAGFLGTPKMGFLQ 243 A+M+YVTHDQ+EAMTLATK+VV+ G I+QIGSP E+Y+ PANLFVA F+G+P M + Sbjct: 185 GASMVYVTHDQIEAMTLATKIVVMKGGVIQQIGSPAEIYNRPANLFVADFMGSPAMNLIP 244 Query: 244 ATVH-AVHASGVEVRFASGTTLLIPRDSSALSVGQSVTIGIRPEHLT----LGAEGQVLV 298 A H A + +E+ SG +++ D+ + + V +G+RPE + GAE Sbjct: 245 AKAHRADEGTRIEITRKSGEPIVL-TDTKNRDLPEDVILGVRPEDIADPDLRGAEAAQAA 303 Query: 299 --TTDVTERLGSDTFCHVNVDSGESLTVRVQGDCEVPYAARRYLTLDVAHCHLF-DESGL 355 D+ E G+DTF + + G+ +T R+ + + L+ D+ F E+GL Sbjct: 304 ECLIDMVEPAGADTFAVMQL-GGKHVTARLHAETTAKPGQPKRLSFDLGKVSYFAPETGL 362 Query: 356 SVS 358 ++ Sbjct: 363 RLN 365 Lambda K H 0.319 0.136 0.381 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: 358 Number of extensions: 16 Number of successful extensions: 1 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: 365 Length of database: 365 Length adjustment: 30 Effective length of query: 335 Effective length of database: 335 Effective search space: 112225 Effective search space used: 112225 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