Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate H281DRAFT_04190 H281DRAFT_04190 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >FitnessBrowser__Burk376:H281DRAFT_04190 Length = 397 Score = 330 bits (847), Expect = 6e-95 Identities = 180/389 (46%), Positives = 257/389 (66%), Gaps = 12/389 (3%) Query: 6 IRDVDLKGKRVIMRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRP- 63 I + L GKRV +R D NVP D G + +DTRIRA++P +K AL+ GA V++ SHLGRP Sbjct: 11 IAEGKLSGKRVFIRADLNVPQDDQGNITEDTRIRASVPAVKAALDAGAAVMVTSHLGRPT 70 Query: 64 KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGE 123 +G+ PE SLAPVAKR +ELLG++V V V + V A GEV+LLEN R + GE Sbjct: 71 EGDFKPEDSLAPVAKRFAELLGRDVPLVANWVENGVNVA-----PGEVVLLENCRVNKGE 125 Query: 124 TKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFLSKVT 182 K+ ELA+ A L DI+VNDAFGTAHRA A+ GIA++ P + AG L+ E++ L K Sbjct: 126 KKDSDELAQKMAKLCDIYVNDAFGTAHRAEATTHGIAKYAPIACAGPLLAAELEALGKAL 185 Query: 183 YNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDK 242 P++P V ++ G+KVS K+ ++ +L EK D++++GG + TF+ A G ++G S E D Sbjct: 186 GAPKRPLVAIVAGSKVSTKLTILKSLAEKVDQLIVGGGIANTFMLAAGLKIGKSLAEADL 245 Query: 243 IDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIE 302 ++ AK +++ AK +G + +P D V A++ P + ++ + D + + + LDIGPET + Sbjct: 246 VNEAKAIIDAAKARGASVPIPTDVVTAKEFSPTAKAEIKAVAD-VEDDDLILDIGPETAQ 304 Query: 303 LFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNK 362 +L A T+VWNGP+GVFE D F GTK +A AIA A ++ GGGD+ AA+ K Sbjct: 305 ALAAQLEKAGTIVWNGPVGVFEFDQFGNGTKTLADAIA---RSSAFSIAGGGDTLAAIAK 361 Query: 363 FGLEDKFSHVSTGGGASLEFLEGKELPGI 391 +G+ DK S++STGGGA LEFLEGK+LP + Sbjct: 362 YGIHDKVSYISTGGGAFLEFLEGKKLPAV 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: 594 Number of extensions: 29 Number of successful extensions: 7 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: 397 Length adjustment: 34 Effective length of query: 620 Effective length of database: 363 Effective search space: 225060 Effective search space used: 225060 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