Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_011801377.1 PNAP_RS09960 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000015505.1:WP_011801377.1 Length = 400 Score = 295 bits (756), Expect = 2e-84 Identities = 167/379 (44%), Positives = 241/379 (63%), Gaps = 13/379 (3%) Query: 14 KRVIMRVDFNVPVK-DGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRP-KGEPSPEF 71 KRV +R D NVP G + +DTRIRA+LP I+ AL+ GA V++ SHLGRP +G P Sbjct: 18 KRVFIRADLNVPQDASGRITEDTRIRASLPCIRMALDAGAAVMVTSHLGRPAEGGFKPGD 77 Query: 72 SLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGETKNDPELA 131 SLAPVA+RLSELLG+ V V + V D V ++ G+++LLEN R + GE ND L+ Sbjct: 78 SLAPVAERLSELLGRPVSLVSSWV-DGVP-----VEPGQLVLLENCRLNAGEKSNDEALS 131 Query: 132 KFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFLSKVTYNPEKPYV 190 + A+L D+ V+DAFGTAHRA A+ GIAQF P + AG L+ EI ++ PE+P V Sbjct: 132 RKLAALCDVFVHDAFGTAHRAEATTHGIAQFAPIACAGPLLAAEIDAINSALAQPERPLV 191 Query: 191 VVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKIDLAKELL 250 ++GG+KVS K+ ++ +L K D++++GG + TF+ A G +G S E ++ A+ ++ Sbjct: 192 AIVGGSKVSSKLTILQSLASKVDQLIVGGGIANTFMLAAGLNIGKSLAEPGLVEEARAVI 251 Query: 251 EKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELFKQKLSD 310 E K +G E+ +P D V A+ V + D + + + LDIGP+T +L Sbjct: 252 EAMKARGAEVPIPTDVVCAKSFAADAVATVKQAGD-VEDDDLILDIGPDTAARLAAQLKS 310 Query: 311 AKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNKFGLEDKFS 370 A T+VWNGP+GVFE + F++GT+ +A AIA E A ++ GGGD+ AA+ ++G+E Sbjct: 311 AGTIVWNGPVGVFEFEAFSKGTEGIARAIA---ESSAFSIAGGGDTLAAIAQYGIEKDVG 367 Query: 371 HVSTGGGASLEFLEGKELP 389 ++STGGGA LE LEGK LP Sbjct: 368 YISTGGGAFLEVLEGKTLP 386 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: 563 Number of extensions: 30 Number of successful extensions: 7 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: 400 Length adjustment: 34 Effective length of query: 620 Effective length of database: 366 Effective search space: 226920 Effective search space used: 226920 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 10 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