Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_084931850.1 HA51_RS03335 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::Smeli:SM_b21106 (365 letters) >NCBI__GCF_002095475.1:WP_084931850.1 Length = 360 Score = 317 bits (811), Expect = 4e-91 Identities = 177/368 (48%), Positives = 229/368 (62%), Gaps = 16/368 (4%) Query: 1 MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60 MA V L + KRYG V+H +DL + D F LVGPSGCGKST LR++AGLE +S G I Sbjct: 1 MASVELVNVAKRYGKQSVLHPLDLTIPDGSFTVLVGPSGCGKSTLLRLLAGLESLSDGTI 60 Query: 61 EIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAI 120 + K+ND P R+I+MVFQSYALYPH+TVAEN+ F +++ EE ++++ A I Sbjct: 61 MMDKVKINDRDPADRDIAMVFQSYALYPHLTVAENLAFHMQVKKVKREEQQSKIERIAGI 120 Query: 121 LDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLH 180 L + LL+R P LSGGQRQRVAMGRA+VR P VFLFDEPLSNLDA+LR ++R EIK LH Sbjct: 121 LGIDKLLQRYPRALSGGQRQRVAMGRAMVRNPQVFLFDEPLSNLDAQLRMELRAEIKSLH 180 Query: 181 ARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMN 240 R + TM+YVTHDQVEAMTL+D+IV+MR+G I Q G P ++ RPA FVA FIGSPPMN Sbjct: 181 QRFKTTMVYVTHDQVEAMTLADQIVVMREGRIVQQGAPLAIYDRPADTFVARFIGSPPMN 240 Query: 241 MEEAVLTDGK---LAFASGATLPLPPRFRSL--VREGQKVTFGLRPDDVYPSGHGLHAGD 295 + A L + PLPPR++++ REG VT G RP D+ + A Sbjct: 241 LLPAQLISREGIPGVQCHDLWQPLPPRWQTVGREREGDNVTLGARPHDLIETESRALAS- 299 Query: 296 ADAVHEIELPVTITEPLGNETLVFTQFNGRDWVSRMLNPRPLRPGEAVPMSFDLARAHLF 355 V + E G TL+ ++G ++ G+ + + F+ R HLF Sbjct: 300 ----------VKVVEITGESTLLHLDWHGHALHMQVAGRHHAVSGDEMRIGFNAERIHLF 349 Query: 356 DGETGRAL 363 D ETG L Sbjct: 350 DAETGLRL 357 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: 401 Number of extensions: 22 Number of successful extensions: 4 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: 360 Length adjustment: 29 Effective length of query: 336 Effective length of database: 331 Effective search space: 111216 Effective search space used: 111216 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