Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate WP_085637757.1 MGEO_RS11955 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= uniprot:Q6MNM2 (347 letters) >NCBI__GCF_002115805.1:WP_085637757.1 Length = 365 Score = 299 bits (766), Expect = 7e-86 Identities = 166/359 (46%), Positives = 228/359 (63%), Gaps = 20/359 (5%) Query: 4 IQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISID 63 + N+ KS+G+ ++LK I++ I PG+FLVLVGPSGCGKSTLL +AGLE G+I+I Sbjct: 5 LDIKNLYKSYGTTEILKDINVSIEPGDFLVLVGPSGCGKSTLLNCIAGLEPITGGSINIG 64 Query: 64 GKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQI 123 GK + + P++RDIAMVFQSYALYP MTVA+N+ FG+K++ + A +++ ++++ LQI Sbjct: 65 GKDMTHVSPKDRDIAMVFQSYALYPTMTVAKNITFGMKVRGVDQATQDRKLAQVAQQLQI 124 Query: 124 KHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHNS 183 + LL+R+P +LSGGQRQRVA+GRAL R + LFDEPLSNLDA LR +MR EIK LHHN Sbjct: 125 EPLLNRRPGQLSGGQRQRVAMGRALVRDPKLFLFDEPLSNLDAKLRVEMRTEIKSLHHNL 184 Query: 184 KSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMNFL- 242 ++M+YVTHDQ+EA TL +I V+K GVI+QIG+P+EIY+RP N F+A F+GSP MN + Sbjct: 185 GASMVYVTHDQIEAMTLATKIVVMKGGVIQQIGSPAEIYNRPANLFVADFMGSPAMNLIP 244 Query: 243 -------EGAVL-------EKIPWPEARK----ADQILGIRPDAFALNQGPLGTQEVALG 284 EG + E I + + D ILG+RP+ A + G + Sbjct: 245 AKAHRADEGTRIEITRKSGEPIVLTDTKNRDLPEDVILGVRPEDIA-DPDLRGAEAAQAA 303 Query: 285 DFQIDISENLGGQQMLHGTLAGNNVRILVDSMDNFSMKQTLPLKIDLTKAHLFDKKTGL 343 + ID+ E G L G +V + + Q L DL K F +TGL Sbjct: 304 ECLIDMVEPAGADTFAVMQLGGKHVTARLHAETTAKPGQPKRLSFDLGKVSYFAPETGL 362 Lambda K H 0.318 0.136 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: 335 Number of extensions: 12 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: 347 Length of database: 365 Length adjustment: 29 Effective length of query: 318 Effective length of database: 336 Effective search space: 106848 Effective search space used: 106848 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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