Align GlpP, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate GFF508 PGA1_c05200 putative ABC transporter, inner membrane component
Query= TCDB::G3LHZ0 (288 letters) >FitnessBrowser__Phaeo:GFF508 Length = 287 Score = 437 bits (1124), Expect = e-127 Identities = 212/286 (74%), Positives = 244/286 (85%), Gaps = 1/286 (0%) Query: 3 KTWNNKAWFLVLPVLLLVAFSAVIPLMTVVNYSVQDTFGNNEFFWAGTDWFVQTLHSDRF 62 KT N KAWF VLPVLLLVAF+A+IP+MTVVNYSVQ+TFG+N FFW G DWF Q L SDRF Sbjct: 2 KTENQKAWFFVLPVLLLVAFNALIPMMTVVNYSVQETFGDNVFFWQGLDWFQQILRSDRF 61 Query: 63 WESLQRNLLFSFIILALEIPLGIFIALNMPKSGPGVPVCLVLMALPLLIPWNVVGTIWQV 122 +L R +F+F+IL +EIPLGI IAL+MP+ G VPVCLVLMALP+LIPWNVVG +W + Sbjct: 62 HAALGRQFMFTFLILIIEIPLGIAIALSMPRKGFWVPVCLVLMALPMLIPWNVVGAMWNI 121 Query: 123 FGRVDIGLLGHTLE-AIGLDYNYVRDPIDAWVTVIVMDVWHWTSLVVLLCYAGLVSIPDA 181 F DIGLLG+ L +G++Y+ +DPI AWVT+I MDVWHWTSLVVLL YAGLVSIPDA Sbjct: 122 FTLPDIGLLGYFLNHTLGINYDMTQDPIAAWVTIITMDVWHWTSLVVLLSYAGLVSIPDA 181 Query: 182 YYQAAKIDGASRWSVFRYIQLPKMKRVLLIAVLLRFMDSFMIYTEPFVVTGGGPGNSTTF 241 YYQAAKIDGAS W+VFR+IQLPKMK VL IA+LLRFMDSF IYTEPFV+TGGGPGNSTT Sbjct: 182 YYQAAKIDGASNWAVFRFIQLPKMKTVLTIAILLRFMDSFNIYTEPFVLTGGGPGNSTTL 241 Query: 242 LSIDLVKMAVGQFDLGPAAAMSIIYFLIILLLSWVFYTVMTSSDEN 287 LSIDLVK+A+GQFDLGPAAAMS+IYF I LL+SW+FYTVMT D+N Sbjct: 242 LSIDLVKIALGQFDLGPAAAMSLIYFAITLLVSWLFYTVMTKDDQN 287 Lambda K H 0.329 0.143 0.464 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: 366 Number of extensions: 13 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: 288 Length of database: 287 Length adjustment: 26 Effective length of query: 262 Effective length of database: 261 Effective search space: 68382 Effective search space used: 68382 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 47 (22.7 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