Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_035235983.1 Q366_RS02480 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000745975.1:WP_035235983.1 Length = 391 Score = 380 bits (976), Expect = e-110 Identities = 196/392 (50%), Positives = 267/392 (68%), Gaps = 6/392 (1%) Query: 5 TIRDVDLKGKRVIMRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRP 63 ++RD+D+ GK + +RVD+N+P+ D G + DD RIRA L I Y LE+ AK++L SHLGRP Sbjct: 3 SVRDIDVNGKTLFIRVDYNLPMDDQGKITDDNRIRATLDLITYLLEKNAKLVLASHLGRP 62 Query: 64 KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGE 123 KG +FSL P A RLSELL V F +GD VKK V L+ G++L+LEN RFH E Sbjct: 63 KGNRDEKFSLRPAAVRLSELLKIPVAFADDCIGDAVKKQVNALEPGQILMLENLRFHDEE 122 Query: 124 TKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFI-PSVAGFLMEKEIKFLSKVT 182 KNDP AK A L D++VNDAF +HR AS GIA + SVAGFL+EKE++ S Sbjct: 123 KKNDPGFAKALADLCDVYVNDAFAVSHRDQASVTGIATYAKTSVAGFLLEKEVRSYSDSV 182 Query: 183 YNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDK 242 +P+KP VVV+GGAKVS K+ + N++ D ++IGGAM TFL A G + S +E D Sbjct: 183 EHPKKPLVVVIGGAKVSSKLAALENMLRFVDCMIIGGAMANTFLAANGVDTKGSMIEADL 242 Query: 243 IDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIE 302 I+ A +++ AKEKG++++LP D V+A + + E + V +D IP+GW+ LDIGPE+ + Sbjct: 243 IETAADIMAHAKEKGIDLLLPTDLVVADRFDKDAESRTVSLDQ-IPDGWLALDIGPESAQ 301 Query: 303 LFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNK 362 F +++A T+VWNGPMGVFE+D FA GT+ VA AIA + A +VVGGGD+ A K Sbjct: 302 GFANAIANAGTIVWNGPMGVFEMDRFAAGTQAVADAIA---DSPAFSVVGGGDTGLAAKK 358 Query: 363 FGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394 G+ +K S++STGGGA L +EGK LPG+A++ Sbjct: 359 CGITEKISYISTGGGAFLHMMEGKVLPGVAAL 390 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: 597 Number of extensions: 28 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: 391 Length adjustment: 34 Effective length of query: 620 Effective length of database: 357 Effective search space: 221340 Effective search space used: 221340 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