Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_085637757.1 MGEO_RS11955 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= BRENDA::Q8NMV1 (376 letters) >NCBI__GCF_002115805.1:WP_085637757.1 Length = 365 Score = 284 bits (727), Expect = 2e-81 Identities = 156/313 (49%), Positives = 210/313 (67%), Gaps = 16/313 (5%) Query: 21 VKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIA 80 +K N+ I G+FLVLVGPSGCGKST L +AGLE +T G+I IG KD+THV+P+DRDIA Sbjct: 20 LKDINVSIEPGDFLVLVGPSGCGKSTLLNCIAGLEPITGGSINIGGKDMTHVSPKDRDIA 79 Query: 81 MVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQ 140 MVFQ+YALYP MTV +N+ F +K+ G Q ++++ + A L + L R+P LSGGQ Sbjct: 80 MVFQSYALYPTMTVAKNITFGMKVRGVDQATQDRKLAQVAQQLQIEPLLNRRPGQLSGGQ 139 Query: 141 RQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEAL 200 RQRVAMGRA+VR+P++FL DEPLSNLDAKLRV+ RT+I +L LG + VYVTHDQ EA+ Sbjct: 140 RQRVAMGRALVRDPKLFLFDEPLSNLDAKLRVEMRTEIKSLHHNLGASMVYVTHDQIEAM 199 Query: 201 TMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSGHARI 260 T+ +I V+K G +QQ+G+P E+Y+RPAN+FVA F+GSPAMNL K A G RI Sbjct: 200 TLATKIVVMKGGVIQQIGSPAEIYNRPANLFVADFMGSPAMNL--IPAKAHRADEG-TRI 256 Query: 261 KLS---------PETLAAMTPEDNGRITIGFRPEAL-EIIPEGESTDLSIPIKLDFVEEL 310 +++ +T PED + +G RPE + + G + +D VE Sbjct: 257 EITRKSGEPIVLTDTKNRDLPED---VILGVRPEDIADPDLRGAEAAQAAECLIDMVEPA 313 Query: 311 GSDSFLYGKLVGE 323 G+D+F +L G+ Sbjct: 314 GADTFAVMQLGGK 326 Lambda K H 0.316 0.135 0.380 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: 387 Number of extensions: 10 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: 376 Length of database: 365 Length adjustment: 30 Effective length of query: 346 Effective length of database: 335 Effective search space: 115910 Effective search space used: 115910 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 (21.6 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