Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_089323080.1 CHB58_RS05345 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_900188395.1:WP_089323080.1 Length = 405 Score = 438 bits (1127), Expect = e-127 Identities = 224/401 (55%), Positives = 298/401 (74%), Gaps = 8/401 (1%) Query: 2 EKMTIRDVD---LKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLS 58 +KM+++DV LKG RV +RVDFNVP+++GV+ +D RIRAALPTI Y ++ GAK+IL S Sbjct: 9 KKMSLKDVPVEKLKGSRVFVRVDFNVPLENGVIMNDKRIRAALPTINYLIDHGAKIILCS 68 Query: 59 HLGRPKGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTR 118 HL RPKG FSL PVA+RLS LL K+V FVP +G+EVK A+E LKEGEV LLEN R Sbjct: 69 HLDRPKGRDK-RFSLKPVAERLSRLLEKDVFFVPDCIGEEVKSAIENLKEGEVALLENVR 127 Query: 119 FHPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKF 177 F+P ETKND E AK A ADI+VNDAFGTAHR HAS GI +F+ +VAGFL+EKEI++ Sbjct: 128 FYPEETKNDEEFAKKLAEFADIYVNDAFGTAHRKHASTYGITKFVDLAVAGFLLEKEIEY 187 Query: 178 LSKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSR 237 L NP++P V+++GGAKVS K+ VI NL++ D++LIGG M +TFLKA G EVG S Sbjct: 188 LRMALDNPKRPLVLIIGGAKVSSKLQVIENLLKVVDKMLIGGGMAYTFLKAAGYEVGKSL 247 Query: 238 VEEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIG 297 VEED +D A+E+++ A GV++ +PVD++ A++ + + K+ + IPE MGLDIG Sbjct: 248 VEEDFVDSAREIMKMADSNGVKLYIPVDSMNAEEFKENTKVKLTTFKE-IPEDMMGLDIG 306 Query: 298 PETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSA 357 P T++LF++ ++DA+T+VWNGPMGVFE++ F GT + +A ++K A+T+VGGGDS Sbjct: 307 PATVKLFEEAMADAETIVWNGPMGVFEMEKFRFGTMAIGKVVA--SKKEALTIVGGGDSV 364 Query: 358 AAVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIADKK 398 AA+ GLE HVSTGGGA LEFL GKELPG+ ++ DK+ Sbjct: 365 AALELLGLEHSVDHVSTGGGAFLEFLAGKELPGVVALTDKE 405 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: 40 Number of successful extensions: 5 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: 405 Length adjustment: 35 Effective length of query: 619 Effective length of database: 370 Effective search space: 229030 Effective search space used: 229030 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