Align ABC transporter (characterized, see rationale)
to candidate WP_086510097.1 BZY95_RS11680 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= uniprot:A0A166QFW2 (381 letters) >NCBI__GCF_002151265.1:WP_086510097.1 Length = 368 Score = 451 bits (1161), Expect = e-131 Identities = 242/361 (67%), Positives = 282/361 (78%), Gaps = 4/361 (1%) Query: 1 MIKLKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDL 60 M + LD +NK G I++DV L I GEFVVFVGPSGCGKSTLLRLIAGL+SI G+L Sbjct: 1 MASVTLDKINKVFGSTHIIKDVDLAIGEGEFVVFVGPSGCGKSTLLRLIAGLESITDGEL 60 Query: 61 LIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQI 120 I + VN+L PRERGVGMVFQSYALYPHM+VY+N++FGLKLAKT K ++ ERV+ TA+I Sbjct: 61 SIGDQVVNELPPRERGVGMVFQSYALYPHMTVYENMAFGLKLAKTAKETVHERVMATARI 120 Query: 121 LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180 LQL++LL+RKPK LSGGQRQRVAMGRAMAREP ILLFDEPLSNLDASLRVQMRNEIARLH Sbjct: 121 LQLEELLERKPKALSGGQRQRVAMGRAMAREPRILLFDEPLSNLDASLRVQMRNEIARLH 180 Query: 181 DRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN 240 RLGSTM+YVTHDQVEAMTLADKIVVL+GGRVEQVGSP+ELY+RPA++FVAGF+GSP MN Sbjct: 181 KRLGSTMVYVTHDQVEAMTLADKIVVLDGGRVEQVGSPQELYQRPATKFVAGFIGSPTMN 240 Query: 241 FLSARLQTPGETSLVDTLVWGIT--SLPFDSSNLAAGTPLSLGIRPEHVSLKAADGTAGV 298 FL ARL T G+T +LP D+S A G L+LGIRPEH+ L A G+ G Sbjct: 241 FLPARLLGADATG-CRIGATGLTELALPQDASGHAQGAALTLGIRPEHLRLSEAQGSEGF 299 Query: 299 VVTAVEYLGSETYVHLETGQDEP-LICRCEVSAGWQAGDRVELLLDLDNLHLFDADGVAL 357 + VEYLG+E YV+LE + E LI R E W+ G RV L D +++HLFDA G AL Sbjct: 300 EIVNVEYLGNEVYVYLEPKEGETLLIQRGEAPTTWRVGQRVTLAPDPEHVHLFDAGGRAL 359 Query: 358 S 358 S Sbjct: 360 S 360 Lambda K H 0.320 0.137 0.394 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: 428 Number of extensions: 14 Number of successful extensions: 3 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: 381 Length of database: 368 Length adjustment: 30 Effective length of query: 351 Effective length of database: 338 Effective search space: 118638 Effective search space used: 118638 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: 50 (23.9 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