Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_012609393.1 G491_RS0104810 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000429905.1:WP_012609393.1 Length = 437 Score = 167 bits (422), Expect = 1e-45 Identities = 146/413 (35%), Positives = 210/413 (50%), Gaps = 44/413 (10%) Query: 6 IRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPKG 65 I+D DL GK V++RVD NV VK GV+ D RI A L T+ +E+G + IL++H+GRPK Sbjct: 13 IQDADLAGKVVLVRVDHNV-VKKGVIHDPYRIDATLGTLYNIVERGGRPILMTHVGRPKD 71 Query: 66 EPSPEF------SLAPVAKRLSELLGKEVKFVPAVV-GDE--------VKKAVEELKEGE 110 + + S+ P+ + L L V GD+ + + +L E Sbjct: 72 KKTGTIKVDAGTSVQPIVEYLERKLYTTFAIPEFPVDGDQGIRQIDTSINWHIRDLNEHR 131 Query: 111 V--LLLENTRFHPGET-KNDPE--LAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPS 165 + + L NTR+ GE K D LA+ A LAD+ VNDAFG+ + AS +A+ +PS Sbjct: 132 IGGIYLPNTRWFSGEAAKGDARERLARQLAGLADVFVNDAFGS-WQPDASTFDVAEHLPS 190 Query: 166 VAGFLMEKEIKFLSKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTF 225 AGFLM+KE+ L V +PEKP+V V+ GAK KIG + + +K D +++GG + F Sbjct: 191 YAGFLMQKELINLRHVL-DPEKPFVAVVAGAKYDTKIGPLQEIYKKVDHLILGGVIYNAF 249 Query: 226 LKA-LGKEVGSSRVEEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKK--VVR 282 L A G VG V E + A+EL+ + KE G + LP V + IE VE K V Sbjct: 250 LCAKYGITVGG--VSETDVKAARELVAQDKEAGKIVELPF-LVESDTIEGRVEGKYRTVS 306 Query: 283 IDDGIPEGWMG--LDIGPETIEL--FKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALA 338 D P G LDI PE+ + Q ++ AKT+ N MG+ F EG++++ Sbjct: 307 ASDFAPGQERGYFLDIAPESFDTPQVAQAIAGAKTIFVNAVMGL--TPHFYEGSQKLDAT 364 Query: 339 IAALTEKGAITVVGGGDSAAAVNKF-------GLEDKFSHVSTGGGASLEFLE 384 I A T GA GGGD+ ++ + TGGG L+ +E Sbjct: 365 IDANT--GAQKFYGGGDTLQEFKNLSPGLYLAAMDSAQYYFFTGGGTVLKAIE 415 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: 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: 437 Length adjustment: 35 Effective length of query: 619 Effective length of database: 402 Effective search space: 248838 Effective search space used: 248838 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