Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate GFF1729 PGA1_c17530 phosphoglycerate kinase Pgk
Query= BRENDA::P36204 (654 letters) >FitnessBrowser__Phaeo:GFF1729 Length = 396 Score = 350 bits (897), Expect = e-101 Identities = 186/387 (48%), Positives = 247/387 (63%), Gaps = 2/387 (0%) Query: 9 VDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPKGEPS 68 +DL GKRV++RVD NVPV+DG V DDTRI+ PTIK L G ILL+H GRPKG+ Sbjct: 9 MDLAGKRVLVRVDINVPVEDGRVTDDTRIQRVAPTIKDILAAGGTPILLAHFGRPKGKVV 68 Query: 69 PEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGETKNDP 128 E SL P+ L G V F G + AV+ L G VLLLENTRFH GE KND Sbjct: 69 AEMSLRPLVPALEAAFGAPVTFAADCRGPAAEAAVQGLPAGGVLLLENTRFHAGEEKNDT 128 Query: 129 ELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTYNPEKP 188 +LA A L DI+ NDAF AHRAHAS +A+ +P+ AG LM+ E+ L P++P Sbjct: 129 DLAAEMAKLGDIYCNDAFSAAHRAHASTEALARLLPACAGRLMQAELTALETALGQPQRP 188 Query: 189 YVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKIDLAKE 248 V+GGAKVS K+ ++ NL+ K D ++IGG M TFL A G +VG S E D D A+E Sbjct: 189 VTAVVGGAKVSTKLELLGNLVGKVDNLVIGGGMANTFLAAQGIDVGKSLCEHDMADTARE 248 Query: 249 LLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELFKQKL 308 +L KA+++G +I+LPVD V+A++ + G + + V D P M LD GP+T+ L Sbjct: 249 ILSKAEDQGCKIILPVDVVVAREFKAGADNETVAA-DACPADAMILDAGPQTVAAVADTL 307 Query: 309 SDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGA-ITVVGGGDSAAAVNKFGLED 367 S +KT++WNGPMG FEI F T A A+LT+ GA ++V GGGD+ AA+N+ G Sbjct: 308 STSKTLIWNGPMGAFEIAPFDAATNAAAQQAASLTKSGALVSVAGGGDTVAALNQAGAAA 367 Query: 368 KFSHVSTGGGASLEFLEGKELPGIASI 394 F+++ST GGA LE++EGK LPG+A++ Sbjct: 368 DFTYISTAGGAFLEWMEGKTLPGVAAL 394 Lambda K H 0.317 0.137 0.386 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: 597 Number of extensions: 29 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: 654 Length of database: 396 Length adjustment: 34 Effective length of query: 620 Effective length of database: 362 Effective search space: 224440 Effective search space used: 224440 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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