Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate Synpcc7942_1116 Synpcc7942_1116 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >FitnessBrowser__SynE:Synpcc7942_1116 Length = 402 Score = 455 bits (1171), Expect = e-132 Identities = 226/389 (58%), Positives = 290/389 (74%), Gaps = 3/389 (0%) Query: 10 DLKGKRVIMRVDFNVPVK-DGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPKGEPS 68 DL+GKRV++RVDFNVP+ +G + DDTRIRAALPTI+Y E GAKVIL+SH GRPKG+P Sbjct: 13 DLEGKRVLVRVDFNVPLDGNGKITDDTRIRAALPTIRYLSESGAKVILVSHFGRPKGKPV 72 Query: 69 PEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGETKNDP 128 L PVA+RLSELLG+ V VG + V G+V+LLEN RFH E ND Sbjct: 73 ESMRLTPVAERLSELLGRPVVKTTDAVGAGAEAQVAATSNGQVVLLENVRFHAEEEANDA 132 Query: 129 ELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFI-PSVAGFLMEKEIKFLSKVTYNPEK 187 E AK ASLADI+VNDAFG AHRAHAS G+ +++ P VAG+L+EKE+++L NP++ Sbjct: 133 EFAKALASLADIYVNDAFGAAHRAHASTAGVTEYLSPCVAGYLLEKELQYLQAAIDNPQR 192 Query: 188 PYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKIDLAK 247 P ++GG+KVS KIGVI L++K D++LIGG M+FTF KA G VG S VEEDK+DLA+ Sbjct: 193 PLAAIVGGSKVSSKIGVIETLLDKCDKLLIGGGMIFTFYKAQGLSVGGSLVEEDKLDLAR 252 Query: 248 ELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELFKQK 307 L+ KA+EKGV+++LPVD V+A K P K V ID IP+GWMGLDIGPE+++ F++ Sbjct: 253 SLMAKAQEKGVQLLLPVDVVVADKFAPDANAKTVAID-AIPDGWMGLDIGPESVKQFEEA 311 Query: 308 LSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNKFGLED 367 L+D ++V+WNGPMGVFE D FA GT+ +A ++A LT KGA T++GGGDS AAV K G+ Sbjct: 312 LADCRSVIWNGPMGVFEFDQFAVGTEAIARSLAGLTRKGATTIIGGGDSVAAVEKVGVAS 371 Query: 368 KFSHVSTGGGASLEFLEGKELPGIASIAD 396 + SH+STGGGASLE LEGK LPG+A++ D Sbjct: 372 EMSHISTGGGASLELLEGKVLPGVAALDD 400 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: 702 Number of extensions: 34 Number of successful extensions: 4 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: 402 Length adjustment: 35 Effective length of query: 619 Effective length of database: 367 Effective search space: 227173 Effective search space used: 227173 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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