Align ABC transporter (characterized, see rationale)
to candidate WP_086508166.1 BZY95_RS01120 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= uniprot:A0A166QFW2 (381 letters) >NCBI__GCF_002151265.1:WP_086508166.1 Length = 371 Score = 352 bits (903), Expect = e-101 Identities = 193/362 (53%), Positives = 244/362 (67%), Gaps = 3/362 (0%) Query: 1 MIKLKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDL 60 M +L L + K G+ + RD+ L I GEFVVFVGPSGCGKSTLLR+IAGL+ I G++ Sbjct: 1 MGRLTLAGIGKDYAGVEVSRDIDLTIEDGEFVVFVGPSGCGKSTLLRMIAGLEDISHGEM 60 Query: 61 LIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQI 120 +DG R+N++ P+ER +GMVFQSYALYPHM+V +N++FGLKLA+TDK +R RV A++ Sbjct: 61 RLDGERINEVPPQERDIGMVFQSYALYPHMTVAENMAFGLKLARTDKAEIRRRVEHAAEM 120 Query: 121 LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180 L L +LL+RKPKELSGGQRQRVA+GR + +EP + LFDEPLSNLDA+LRV MR +IA LH Sbjct: 121 LHLGELLERKPKELSGGQRQRVAIGRTLVKEPAVFLFDEPLSNLDAALRVDMRVQIAELH 180 Query: 181 DRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN 240 RLG+TMIYVTHDQVEAMTLAD+IV+L GGR+ QVG+P LY PA+ VA F+GSPR+N Sbjct: 181 RRLGATMIYVTHDQVEAMTLADRIVLLAGGRIAQVGAPLSLYHFPATLEVARFIGSPRIN 240 Query: 241 FLSARLQTPGETSLVDTLVWGIT-SLPFDSSNLAAGTPLSLGIRPE-HVSLKAADGTAGV 298 + + PG L G T ++ D + L AG +L +R E V+ AD Sbjct: 241 VIPVEVLDPGRQRTSVRLPDGATLAVAVDGARLRAGDKATLAVRAEDFVTPADADARLTA 300 Query: 299 VVTAVEYLGSETYVHLET-GQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDADGVAL 357 + E LG ET HL G E L R + + G VEL L + HLF ADG A Sbjct: 301 RLMVAERLGYETLAHLRVEGVSETLTQRLDGLTRLEDGQAVELGLSGERCHLFAADGKAC 360 Query: 358 SR 359 R Sbjct: 361 PR 362 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: 377 Number of extensions: 13 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: 381 Length of database: 371 Length adjustment: 30 Effective length of query: 351 Effective length of database: 341 Effective search space: 119691 Effective search space used: 119691 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