Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_084936596.1 HA51_RS21490 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_002095475.1:WP_084936596.1 Length = 387 Score = 313 bits (801), Expect = 1e-89 Identities = 183/404 (45%), Positives = 259/404 (64%), Gaps = 23/404 (5%) Query: 1 MEKMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHL 60 M + + D+DL GKRV++R D NVPVK+G V D RIRA+LPTI+ AL+QGAKV++ SHL Sbjct: 1 MSVIKMTDLDLAGKRVLIRADLNVPVKEGKVTSDARIRASLPTIEAALKQGAKVMVTSHL 60 Query: 61 GRP-KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRF 119 GRP +GE + EFSL PV L E L + + + V E+ GE+++LEN RF Sbjct: 61 GRPTEGEYNEEFSLLPVVNYLKEKLNG----TTVTLAKDYLEGV-EVGAGELVVLENVRF 115 Query: 120 HPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFL 178 + GE K++ L+K +A+L D+ V DAFGTAHRA AS G+ +F P + AG L+ E++ L Sbjct: 116 NKGEKKDEETLSKKYAALCDVFVMDAFGTAHRAQASTHGVGKFAPIACAGPLLSAELEAL 175 Query: 179 SKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRV 238 KV NPE+P V V+GG+KVS K V+ +L++ AD +++GG + TF+ A+ VG S Sbjct: 176 GKVMSNPERPLVAVVGGSKVSTKFDVLQSLVKIADTVIVGGGIANTFV-AIDNNVGKSLY 234 Query: 239 EEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIE---PGVEKKVVRIDDGIPEGWMGLD 295 E D ++ AK+L + E G+ + P D+ + + P KKV + D +D Sbjct: 235 EPDFVEAAKKLRD---EHGIPV--PTDSRVGTEFSETAPSTVKKVSEVADNEEI----MD 285 Query: 296 IGPETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGD 355 G ET L DAKT++WNGP+GVFE +F +GT+ VA AIA + A +V GGGD Sbjct: 286 FGDETALAMAALLKDAKTILWNGPVGVFEFPNFRKGTEIVANAIA---DSDAFSVAGGGD 342 Query: 356 SAAAVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIADKKK 399 + AA++ FGLEDK S++STGGGA LEF+EGK+LP +A + ++ K Sbjct: 343 TLAAIDLFGLEDKISYISTGGGAFLEFVEGKKLPAVAMLEERAK 386 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: 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: 387 Length adjustment: 34 Effective length of query: 620 Effective length of database: 353 Effective search space: 218860 Effective search space used: 218860 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 24 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