Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_012992099.1 THAL_RS05405 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000025605.1:WP_012992099.1 Length = 405 Score = 417 bits (1073), Expect = e-121 Identities = 210/398 (52%), Positives = 291/398 (73%), Gaps = 7/398 (1%) Query: 3 KMTIRDVDLKGKRVIMRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVILLSHLG 61 K T+RDV+L GKRV++RVDFNVP+ D G ++DDTRIRA+LPTI+Y L+ AKVIL+SHLG Sbjct: 5 KKTLRDVNLSGKRVLVRVDFNVPMDDLGNIEDDTRIRASLPTIQYLLDARAKVILMSHLG 64 Query: 62 RPKGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHP 121 RPKG P++SLAPVAKRLS + +EVK P VG EVKK VE++KEG+VLLLEN RFH Sbjct: 65 RPKGR-DPKYSLAPVAKRLSRYIAREVKLAPDCVGAEVKKLVEDMKEGDVLLLENLRFHQ 123 Query: 122 GETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFI-PSVAGFLMEKEIKFLSK 180 GE + D + AK ASL +++V DAFGT HR HAS + Q + P+V GFL+EKE+ + + Sbjct: 124 GEEQADVDFAKELASLGEVYVADAFGTCHRKHASTYLVPQILKPAVMGFLLEKEVSYFER 183 Query: 181 VTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEE 240 NP++P V ++GGAKVS K+G++ NL+++ D++ +GGAM FTF+K++G VG+S VEE Sbjct: 184 AMVNPQRPVVAIIGGAKVSSKLGILKNLLKRVDKLFVGGAMAFTFIKSMGFPVGNSLVEE 243 Query: 241 DKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPET 300 D +D A+++LE A++ V+ LPVD VI +++ +VV + IP GWMGLDIGP + Sbjct: 244 DLLDTARDILEVARKLDVKFYLPVDFVIGRELSDNTPTRVVPWQE-IPSGWMGLDIGPVS 302 Query: 301 IELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAV 360 + L ++ ++DA+T+VWNGP+GVFE+D F EGT Q A +A E A+T+ GGGD+ A+ Sbjct: 303 VSLIREVIADAQTIVWNGPLGVFELDRFKEGTYQTAKMLA---ESPALTIAGGGDTDHAI 359 Query: 361 NKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIADKK 398 ++ G+ + VSTGGGA LE LEG LP I + D++ Sbjct: 360 HRAGVYNSIDFVSTGGGAFLELLEGNTLPCIEVLDDRE 397 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: 668 Number of extensions: 29 Number of successful extensions: 6 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