Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate GFF1860 Psest_1899 ABC-type sugar transport systems, ATPase components
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__psRCH2:GFF1860 Length = 390 Score = 204 bits (518), Expect = 4e-57 Identities = 126/325 (38%), Positives = 189/325 (58%), Gaps = 19/325 (5%) Query: 1 MARITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQ 60 MA + L +++ +YG + + +LK++ + + G L+GPSGCGK+TL+N I+GL Sbjct: 1 MASLELRNVQKSYG----NSQIATLKDIALKIDAGEFLILVGPSGCGKSTLMNCIAGLEN 56 Query: 61 PSHGRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRV 120 + G IL DG+D++ S + R+IA VFQ +Y TM+V DN+AF L+ R V A ++ V Sbjct: 57 ITGGEILVDGEDISQASPKDRDIAMVFQSYALYPTMSVRDNIAFGLKMRKVPAAKIEEEV 116 Query: 121 RDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLR 180 + +++ + RK L+ Q+Q++++GR L R LFDEPL+ +D ++ +R Sbjct: 117 ARVAKLLQIEPLLERKPSQLSGGQQQRVAMGRALARRP-KIYLFDEPLSNLDAKLRVEMR 175 Query: 181 SQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYF 240 +++K +H++ T VYVTHDQ EA+T +KV VM DG I Q GTP E++ P++ FV F Sbjct: 176 TEIKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGVIQQFGTPHEIYNNPANLFVASF 235 Query: 241 IGSPGMNFMPARI---EGSTVKV-GDETLTLEY-APKTSGTAKTE----LGIRPEFIRLG 291 IGSP MNF+P RI +G V V E + E P TS + LGIRPE I L Sbjct: 236 IGSPPMNFVPLRIRQRDGRWVGVLNSEQGSCELPLPITSDDGLRDRELILGIRPEQIGLA 295 Query: 292 REG-----MPITISKVEDIGRQKIV 311 G + + I VE G +V Sbjct: 296 PAGSADFSLAVDIEVVEPTGPDTLV 320 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: 317 Number of extensions: 6 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: 390 Length adjustment: 30 Effective length of query: 326 Effective length of database: 360 Effective search space: 117360 Effective search space used: 117360 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 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