Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate 208026 DVU2529 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >MicrobesOnline__882:208026 Length = 393 Score = 318 bits (814), Expect = 4e-91 Identities = 177/397 (44%), Positives = 256/397 (64%), Gaps = 14/397 (3%) Query: 3 KMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGR 62 KMT D+DLKGKRV++R D NVP+K+G + D RIRAALP+I+ A+E GA+V+++SHLGR Sbjct: 5 KMT--DLDLKGKRVLLREDLNVPLKEGRITSDKRIRAALPSIRMAMEAGARVLIVSHLGR 62 Query: 63 P-KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHP 121 P +GE FSLAPVA LS LG++V+ V + D V ++ EG+ +L EN RF Sbjct: 63 PVEGEFDEAFSLAPVAAHLSRELGRDVRLVKDYI-DGV-----DVAEGDCVLCENVRFLK 116 Query: 122 GETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFLSK 180 GE KN EL + A+L DI V DAFG AHRA AS +A+F P + AG L+ E+ L + Sbjct: 117 GEKKNTEELGRRLAALCDIFVMDAFGAAHRAQASTHAVARFAPVACAGPLLAAELDALER 176 Query: 181 VTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEE 240 P+ P V ++GG+KVS K+ ++ NL + DR+++GG + F+KA G EVG S E Sbjct: 177 ALDAPKHPLVGIIGGSKVSTKLTLLDNLSHRVDRLIVGGGIANNFIKAAGYEVGKSLYEP 236 Query: 241 DKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPET 300 + ++ A L+ A+ G EI +P+D V+ ++ G V ++ + P+ M LDIGP T Sbjct: 237 ELVEEAARLMAAARAAGGEIPVPLDVVVGPELADGAPATVRKVSEVGPDE-MILDIGPAT 295 Query: 301 IELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAV 360 +++ L A T+VWNGP+G FE + F GT+ + A+A + A ++ GGGD+ AAV Sbjct: 296 ATRYREILLAAGTIVWNGPVGAFEWEQFGAGTRALCEAVA---DSPAFSIAGGGDTVAAV 352 Query: 361 NKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIADK 397 K+G+ + ++STGGGA LEFLEGKELP +A + ++ Sbjct: 353 EKYGVASRVGYISTGGGAFLEFLEGKELPAVAILQER 389 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: 635 Number of extensions: 35 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 654 Length of database: 393 Length adjustment: 34 Effective length of query: 620 Effective length of database: 359 Effective search space: 222580 Effective search space used: 222580 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