Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_038857067.1 AFK65_RS10835 ABC transporter ATP-binding protein
Query= TCDB::G3LHY9 (356 letters) >NCBI__GCF_001277175.1:WP_038857067.1 Length = 360 Score = 213 bits (542), Expect = 6e-60 Identities = 127/347 (36%), Positives = 197/347 (56%), Gaps = 19/347 (5%) Query: 1 MARITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQ 60 MA+++L HI+ Y KD++L+ D E+ +GPSGCGK+T L +I+GL Sbjct: 1 MAQLSLQHIQKIYDNQVHVVKDFNLEIADKEF-----IVFVGPSGCGKSTTLRMIAGLEA 55 Query: 61 PSHGRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRV 120 S G +L DG + ++ ++RNIA VFQ +Y MTVYDN+AF L+ + VA A ++ RV Sbjct: 56 ISGGDLLIDGVRMNDVPAKARNIAMVFQNYALYPHMTVYDNMAFGLKMQKVAPAIIEERV 115 Query: 121 RDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLR 180 +++ L + +RK L+ Q+Q+++LGR +VR + L DEPL+ +D ++ +R Sbjct: 116 AWAAQILGLKEYLKRKPGALSGGQRQRVALGRAIVR-EAGVFLMDEPLSNLDAKLRVQMR 174 Query: 181 SQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYF 240 +++ +LH++ TM+YVTHDQTEA+T A ++V+M DG + Q+G P E++ P++ FV F Sbjct: 175 AEISKLHQKLNTTMIYVTHDQTEAMTMATRIVIMKDGIVQQVGAPKEVYNHPANMFVAGF 234 Query: 241 IGSPGMNFMPARIEGSTVKVGDETLTLEYAP------KTSGTAK--TELGIRPEFI---R 289 IGSP MNF+ I+G ETL L SG + LGIRPE I Sbjct: 235 IGSPAMNFIRGAIDGEYFVT--ETLKLPLPVNKLARLNDSGYQRKAVVLGIRPEDIFPGA 292 Query: 290 LGREGMPITISKVEDIGRQKIVRARFADQPIAIVVPEDADIPADARV 336 G + + I+ E G + ++ A + + D D AD R+ Sbjct: 293 TGDDAIEAKITVAELTGAEFMLYATVGGHEMVVRAGADKDYQADQRI 339 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: 319 Number of extensions: 15 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: 360 Length adjustment: 29 Effective length of query: 327 Effective length of database: 331 Effective search space: 108237 Effective search space used: 108237 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