Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_011382978.1 AMB_RS02755 nitrate/sulfonate/bicarbonate ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21106 (365 letters) >NCBI__GCF_000009985.1:WP_011382978.1 Length = 553 Score = 157 bits (396), Expect = 9e-43 Identities = 91/212 (42%), Positives = 134/212 (63%), Gaps = 5/212 (2%) Query: 1 MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60 M + LK + K YGA V+ IDLE++D EFIA++G SG GK+T + ++AGL + G + Sbjct: 1 MPILELKGVAKSYGASSVLRDIDLEIEDGEFIAILGFSGSGKTTLVSLMAGLIKPDAGEV 60 Query: 61 EIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAE--EIKTRVAEAA 118 + G+ V D P R + VFQSY+L P +TV N+ ++ A E K RVA+ Sbjct: 61 LLRGKPV-DGPGADRGV--VFQSYSLMPWLTVEGNIALAVDAVMPDASKAERKARVAKYI 117 Query: 119 AILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKK 178 ++ L+H ERRPS+LSGG RQRVA+ RA+ PD+ L DEPLS LDA R +++ EI+ Sbjct: 118 GMVGLSHAAERRPSELSGGMRQRVAVARALAMSPDILLLDEPLSALDALTRAKLQDEIEA 177 Query: 179 LHARMQATMIYVTHDQVEAMTLSDRIVIMRDG 210 + + + T+I +T+D EA+ L+DRI+ + G Sbjct: 178 IWEQEKKTVILITNDVDEALLLADRIIPLNPG 209 Score = 132 bits (331), Expect = 3e-35 Identities = 79/219 (36%), Positives = 127/219 (57%), Gaps = 8/219 (3%) Query: 14 GALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIGGRKVNDLPPR 73 G L VV G DL++ EFI+L+G SGCGKST L M AGL +VS G + + GR+V++ P Sbjct: 307 GPLTVVDGFDLKMHQGEFISLIGHSGCGKSTVLTMTAGLTDVSEGGVILDGREVSEAGP- 365 Query: 74 ARNISMVFQSYALYPHMTVAENMGFSLKIA---GRPAEEIKTRVAEAAAILDLAHLLERR 130 + ++VFQ+ +L+P +T +N+ + PAE + V+ + L ++++ Sbjct: 366 --DRAVVFQAPSLFPWLTALQNVALGVDRVYPHASPAERLDI-VSYYLERVGLGDSMDKK 422 Query: 131 PSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARMQATMIYV 190 S +S G RQRV + RA P + L DEP LD+ R +++ + ++ R + T I V Sbjct: 423 ASDMSNGMRQRVGIARAFALSPKLLLLDEPFGMLDSLTRWELQEVLMEVWTRTRVTAICV 482 Query: 191 THDQVEAMTLSDRIVIMRDGHIEQVGTPEDV-FRRPATK 228 THD EA+ L+D++V+M +G ++G +V RP T+ Sbjct: 483 THDVDEAILLADKVVMMTNGPNARIGKVLNVDIPRPRTR 521 Lambda K H 0.320 0.137 0.397 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: 495 Number of extensions: 21 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 365 Length of database: 553 Length adjustment: 33 Effective length of query: 332 Effective length of database: 520 Effective search space: 172640 Effective search space used: 172640 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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