Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= TCDB::G3LHY9 (356 letters) >NCBI__GCF_900167125.1:WP_078717009.1 Length = 370 Score = 178 bits (451), Expect = 2e-49 Identities = 91/267 (34%), Positives = 156/267 (58%), Gaps = 17/267 (6%) Query: 4 ITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQPSH 63 I L+H+ + D + L +V + G +LGPSGCGKTTLL +++G PS Sbjct: 8 IRLEHVAKEF------DGETVLHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSS 61 Query: 64 GRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRVRDI 123 G I+ DG+ + ++ R + VFQ ++ M+V+DN+AF LR G+ + ++ RV Sbjct: 62 GEIILDGRSMRDVPPDGRRVNTVFQSYALFPHMSVFDNVAFGLRMSGIPKVEIGERVAKA 121 Query: 124 LEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLRSQL 183 L M+ LA A R+ L+ Q+Q++++ R +V + +L DEPL+ +D ++ +R++L Sbjct: 122 LRMVGLAGQAGRRPTSLSGGQQQRVAIARAVVNRPL-VLLLDEPLSALDYKLRVQMRTEL 180 Query: 184 KRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYFIGS 243 K+L ++ G T ++VTHDQ EA + +++VVVM +G + Q+GTP E++E+P + FV F+G Sbjct: 181 KQLRREMGITFIFVTHDQEEAFSMSDRVVVMNEGCVAQVGTPVEVYEQPVNMFVARFVGE 240 Query: 244 PGM----------NFMPARIEGSTVKV 260 + + A +EG T ++ Sbjct: 241 TNVFEGVAGQSDGGILQALVEGRTCEL 267 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: 331 Number of extensions: 14 Number of successful extensions: 2 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: 370 Length adjustment: 29 Effective length of query: 327 Effective length of database: 341 Effective search space: 111507 Effective search space used: 111507 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 Apr 09 2024. 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