Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate N515DRAFT_4291 N515DRAFT_4291 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >FitnessBrowser__Dyella79:N515DRAFT_4291 Length = 393 Score = 329 bits (844), Expect = 1e-94 Identities = 176/393 (44%), Positives = 261/393 (66%), Gaps = 12/393 (3%) Query: 4 MTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRP 63 + + D+DL+GKRV++R D NVP++DG + R+ A+LPTIK A + GA+V+++SHLGRP Sbjct: 5 LRMSDLDLRGKRVLIREDLNVPIEDGRITSTQRLDASLPTIKAARDAGARVMVISHLGRP 64 Query: 64 K-GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPG 122 K G+ E SLAPVAK L + LG V+ + +G ++ EGEV++LEN R + G Sbjct: 65 KEGQFDAESSLAPVAKWLGDKLGTPVRLIADYLGGV------DVAEGEVVVLENCRMNVG 118 Query: 123 ETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFLSKV 181 E K+D L+K +A+L DI V DAFGTAHRA AS G+ ++ P + AG L+ E+ L K Sbjct: 119 EGKDDEALSKKYAALCDIFVMDAFGTAHRAQASTHGVIKYAPVAAAGPLLSAELDALGKA 178 Query: 182 TYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEED 241 +P P + ++ G+KVS K+ ++ NL+ K D++++GG + TF+ A G VG+S E D Sbjct: 179 LEHPAHPLLAIVAGSKVSTKLTLLENLIGKVDQLIVGGGIANTFIAAAGYGVGNSLYEPD 238 Query: 242 KIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETI 301 +D AK+++ AK +G E+ +PVD V+A + V +D + +G M LDIGP+T Sbjct: 239 LLDAAKKVIADAKRRGAEVPMPVDVVVAPEFSAHAPATVKPVDQ-VKDGEMILDIGPQTA 297 Query: 302 ELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVN 361 + + ++ A TVVWNGP+GVFE D F +GT+ +A A+A+ A ++ GGGD+ AAV Sbjct: 298 KNYAALIAKAGTVVWNGPVGVFEFDAFGKGTETLARAVAS---SDAFSIAGGGDTLAAVE 354 Query: 362 KFGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394 K+G+E S++STGGGA LEFLEGKELP +A++ Sbjct: 355 KYGIEKDVSYISTGGGAFLEFLEGKELPAVAAL 387 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: 639 Number of extensions: 40 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: 393 Length adjustment: 34 Effective length of query: 620 Effective length of database: 359 Effective search space: 222580 Effective search space used: 222580 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