Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_086511668.1 BZY95_RS20100 ABC transporter ATP-binding protein
Query= TCDB::G3LHY9 (356 letters) >NCBI__GCF_002151265.1:WP_086511668.1 Length = 365 Score = 396 bits (1018), Expect = e-115 Identities = 198/361 (54%), Positives = 257/361 (71%), Gaps = 9/361 (2%) Query: 1 MARITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQ 60 MA+ITL + H+Y +P +DY+++E++H W+ GGAYALLGPSGCGK+TLLNIISGLL Sbjct: 1 MAQITLKSLAHSYSPSPSGPEDYAIREMEHVWHQGGAYALLGPSGCGKSTLLNIISGLLT 60 Query: 61 PSHGRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRV 120 PS G++LFD + V L+ + RNIAQVFQFPV+YDTMTVYDNLAFPLRN G A + RV Sbjct: 61 PSDGQVLFDDRVVNELAPEERNIAQVFQFPVVYDTMTVYDNLAFPLRNVGTPAAKIRERV 120 Query: 121 RDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLR 180 ++ +++DL S +RKA+ LTAD+KQK+S+GRGLVR+DV+AILFDEPLTVIDP +KW LR Sbjct: 121 AEVADVLDLTSLLKRKARNLTADEKQKVSMGRGLVRDDVSAILFDEPLTVIDPQLKWKLR 180 Query: 181 SQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYF 240 +LK +H++F TM+YVTHDQ EA TFA+K+ VMY+GQ+VQ GTP ELFE P+HTFVGYF Sbjct: 181 RKLKEIHERFNITMIYVTHDQLEASTFADKIAVMYEGQVVQFGTPRELFETPAHTFVGYF 240 Query: 241 IGSPGMNFMPARIEGSTVKVGDETLTLEYAPKT----SGTAKTELGIRPEFIRL----GR 292 IGSPGMN M V+ G LTL A + S + +LGIRPEF+ + G Sbjct: 241 IGSPGMNLMEVARTEEGVRTGTVDLTLPPALRNAIHRSRSRNIKLGIRPEFVEVLTEPGE 300 Query: 293 EGMPITISKVEDIGRQKIVRARFADQPIAIVVPEDADIP-ADARVTFDPSAISIYADSWR 351 P+ I V+D+G +IV FA P + ED +P A V F + +++Y D +R Sbjct: 301 ASYPVEIDNVQDLGTYRIVSFTFAGMPFRARLGEDQPLPRRHAYVRFPEAWLNLYIDEFR 360 Query: 352 V 352 V Sbjct: 361 V 361 Lambda K H 0.321 0.137 0.405 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: 416 Number of extensions: 16 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: 356 Length of database: 365 Length adjustment: 29 Effective length of query: 327 Effective length of database: 336 Effective search space: 109872 Effective search space used: 109872 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