Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_011842820.1 RSPH17029_RS20290 sn-glycerol-3-phosphate import ATP-binding protein UgpC
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_000015985.1:WP_011842820.1 Length = 349 Score = 301 bits (772), Expect = 1e-86 Identities = 171/357 (47%), Positives = 229/357 (64%), Gaps = 19/357 (5%) Query: 1 MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60 MA++ L V K+Y ++V+ ++L+I GE +V VGPSGCGKSTLLRM+AGLE+IT G + Sbjct: 1 MAEISLRDVRKSYAGIEVIHGVDLEIADGEFVVIVGPSGCGKSTLLRMVAGLEEITAGEI 60 Query: 61 EIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEK 120 I G VVN + P +R IAMVFQ+YALYPHMTVRENM++ L+IAK S+AEI+ V +A Sbjct: 61 AIGGRVVNRLEPRERDIAMVFQNYALYPHMTVRENMAYGLRIAKLSKAEIEERVARSARM 120 Query: 121 LQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLK 180 L+LGQ LDR P+ LSGGQRQRVA+GR++VR+P +L DEPLSNLDA LRV RL+I +L+ Sbjct: 121 LELGQLLDRKPRQLSGGQRQRVAMGRALVRNPAAFLLDEPLSNLDAKLRVQMRLQIKELQ 180 Query: 181 EAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKM 240 + +T +YVTHDQVEAMTLA R+VV+ G Q+ +P E+Y++P FVA FIGSP M Sbjct: 181 RTV-RTTSIYVTHDQVEAMTLADRLVVMNAGVAEQIATPAEIYDRPATTFVAGFIGSPAM 239 Query: 241 NLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAPGGDYVFE 300 N+LP + +G + G R P+ L+ +GVRPE + A P + FE Sbjct: 240 NMLPARGLGDALEVA-----GQRLAVPAPAGRDLI-----LGVRPEHLHAAGP-EEPGFE 288 Query: 301 GKVAITEALGEVTLLYFEAPSGED---PTIGKLQGIHKDLKGQVTRLTAEPAKVHVF 354 V E LG + G D T GK +D ++ + A +H+F Sbjct: 289 LHVQAVEWLGADAFAHGRLADGTDLVLRTPGKAPVRERDR----LKVAPDAAALHLF 341 Lambda K H 0.316 0.135 0.379 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: 20 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: 373 Length of database: 349 Length adjustment: 29 Effective length of query: 344 Effective length of database: 320 Effective search space: 110080 Effective search space used: 110080 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 Apr 10 2024. 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