Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate 8500217 DvMF_0975 phosphoglycerate kinase (RefSeq)
Query= BRENDA::P36204 (654 letters) >FitnessBrowser__Miya:8500217 Length = 393 Score = 328 bits (842), Expect = 2e-94 Identities = 182/399 (45%), Positives = 258/399 (64%), Gaps = 12/399 (3%) Query: 1 MEKMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHL 60 M + + D+DLKGKRV++R D NVP+KDG V D RIRAALP+I+ AL+ GA+V+L+SHL Sbjct: 1 MAVLKMTDLDLKGKRVLLREDLNVPLKDGKVTSDKRIRAALPSIEMALKAGARVLLVSHL 60 Query: 61 GRP-KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRF 119 GRP +GE P FSLAPVA+ LS LG +V V + D + E+ EG+ +L EN RF Sbjct: 61 GRPTEGEFDPAFSLAPVAEHLSRALGFQVPLVRDYI-DGI-----EVAEGQCVLCENVRF 114 Query: 120 HPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFL 178 GE K+D L + A+L DI V DAFG AHRA AS +F + AG L+ E+ L Sbjct: 115 LKGEKKDDEALGRKLAALCDIFVMDAFGAAHRAQASTHAAVRFAKVACAGPLLAAELDAL 174 Query: 179 SKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRV 238 S+ P KP V ++GG+KVS K+ ++ L +K DR+++GG + F+KA G EVG S Sbjct: 175 SRALDAPAKPMVGIIGGSKVSTKLTLLDTLSKKVDRLIVGGGIANNFIKAAGHEVGRSLY 234 Query: 239 EEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGP 298 E + +D A L+ A+ G EI +PVD V+ + V ++ + P+ M LDIGP Sbjct: 235 EPELVDEAARLMAAARAAGGEIPVPVDVVVGPEFADSAPATVRKVSEVKPDE-MILDIGP 293 Query: 299 ETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAA 358 ET +L++ L A T+VWNGP+G FE++ F +GTK + +A+A + A ++ GGGD+ A Sbjct: 294 ETAKLYRDILMQAGTIVWNGPVGAFEVEQFGQGTKALCMAVA---DSPAFSLAGGGDTVA 350 Query: 359 AVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIADK 397 A+ K+G+ D+ S++STGGGA LEFLEGK LP +A + ++ Sbjct: 351 AIEKYGVVDRISYMSTGGGAFLEFLEGKTLPAVAVLEER 389 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: 633 Number of extensions: 38 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 Apr 09 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