Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate GFF509 PGA1_c05210 sn-glycerol-3-phosphate import ATP-binding protein UgbC
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__Phaeo:GFF509 Length = 371 Score = 417 bits (1072), Expect = e-121 Identities = 209/351 (59%), Positives = 251/351 (71%), Gaps = 1/351 (0%) Query: 1 MARITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQ 60 MA+ITL +RH+Y P S DY+LKE+D +W DGGAYALLGPSGCGK+TLLNIISGLL Sbjct: 1 MAKITLSKLRHSYMPTPSSASDYALKEIDLDWTDGGAYALLGPSGCGKSTLLNIISGLLV 60 Query: 61 PSHGRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRV 120 PS G+ILFDGKDVT L RNIAQVFQFPVIYDTMTVYDNLAFPLRNRG EA V RV Sbjct: 61 PSEGQILFDGKDVTKLPPDQRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGRDEATVKERV 120 Query: 121 RDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLR 180 I EM+++ +A GL+ D KQKIS+GRGLVR DVN ++FDEPLTVIDPH+KW LR Sbjct: 121 MAIAEMLEVTDLLTMRAAGLSPDNKQKISMGRGLVREDVNVVMFDEPLTVIDPHLKWKLR 180 Query: 181 SQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYF 240 S+LK LH++ TM+YVTHDQTEALTFA++VVVM G++VQIGTP ELFERP+HTFVG+F Sbjct: 181 SKLKELHQRVKATMIYVTHDQTEALTFADQVVVMQLGEVVQIGTPVELFERPAHTFVGHF 240 Query: 241 IGSPGMNFMPARIEGSTVKVGDETLTLEYAPKTSGTAKTELGIRPEFIRLGREGMPITIS 300 IGSPGMN +P + +G + LE K KTE+GIRPEF+ L G+P T++ Sbjct: 241 IGSPGMNVLPCDLRAGQPYIGAHPVALEGPIKGDAAGKTEVGIRPEFVSLTNSGLPATVT 300 Query: 301 KVEDIGRQKIVRARFADQPI-AIVVPEDADIPADARVTFDPSAISIYADSW 350 KV D+GR +V Q I A+V A ++F +Y D W Sbjct: 301 KVSDVGRHTVVECEAEGQRINAVVEGAGPAKGAAVHLSFRQDQTRLYVDGW 351 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: 436 Number of extensions: 11 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: 356 Length of database: 371 Length adjustment: 29 Effective length of query: 327 Effective length of database: 342 Effective search space: 111834 Effective search space used: 111834 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 17 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