Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate Ga0059261_0728 Ga0059261_0728 phosphoglycerate kinase (EC 2.7.2.3)
Query= BRENDA::P36204 (654 letters) >FitnessBrowser__Korea:Ga0059261_0728 Length = 397 Score = 311 bits (798), Expect = 3e-89 Identities = 169/386 (43%), Positives = 243/386 (62%), Gaps = 5/386 (1%) Query: 10 DLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPKGEPSP 69 D+ GKRV++R D NVP+ DG V DDTR+RAA+PT+ ++GA V++L+H GRPK PSP Sbjct: 14 DVTGKRVLVREDLNVPMADGHVTDDTRLRAAVPTVSELADKGAIVLVLAHFGRPK-TPSP 72 Query: 70 EFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGETKNDPE 129 E S A + + S++LG+ V+++ GD A L+ G++ +LENTRF GE KNDP+ Sbjct: 73 ELSTAQLVRPFSQVLGRPVRYIDWE-GDIESTAT--LQPGDIAVLENTRFFGGEEKNDPK 129 Query: 130 LAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTYNPEKPY 189 + +A+L D +VNDAF AHRAHAS G+A +P+ AG ME E+ L K NPE P Sbjct: 130 VIDRFAALGDFYVNDAFSAAHRAHASTEGLAHRLPAFAGRQMEAELDALDKALGNPEHPV 189 Query: 190 VVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKIDLAKEL 249 V+GGAKVS K+ V+ +L+ + D ++IGG M TFL A G VG S E D A+E+ Sbjct: 190 AAVVGGAKVSTKLDVLKHLVGQVDHLIIGGGMANTFLAARGVNVGKSLCEHDLTGTAEEI 249 Query: 250 LEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELFKQKLS 309 + A++ I LP D V++++ + E M LD+GP E L Sbjct: 250 FDAAEKANCTIHLPYDVVVSKEFAANPPSLRTCNVHEVAEDEMILDVGPAASEALADVLK 309 Query: 310 DAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGA-ITVVGGGDSAAAVNKFGLEDK 368 + +T+VWNGP+G FE F T +A +AALT++G+ ++V GGGD+ AA+N+ G+ + Sbjct: 310 NCRTLVWNGPLGAFETKPFDTATMALAHTVAALTKEGSLVSVAGGGDTVAALNQAGVSSE 369 Query: 369 FSHVSTGGGASLEFLEGKELPGIASI 394 + VST GGA LE++EGK LPG+A++ Sbjct: 370 MTFVSTAGGAFLEWMEGKALPGVAAL 395 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: 577 Number of extensions: 32 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: 397 Length adjustment: 34 Effective length of query: 620 Effective length of database: 363 Effective search space: 225060 Effective search space used: 225060 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