Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate 3608763 Dshi_2155 Phosphoglycerate kinase (RefSeq)
Query= BRENDA::P36204 (654 letters) >FitnessBrowser__Dino:3608763 Length = 393 Score = 350 bits (899), Expect = e-101 Identities = 188/391 (48%), Positives = 252/391 (64%), Gaps = 6/391 (1%) Query: 5 TIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPK 64 T+ D+ L GK V+ RVD NVPV DGVV D TRI +PT+ L +G +LL+H GRPK Sbjct: 5 TLDDMALDGKIVLTRVDINVPVADGVVTDTTRIERIVPTVTDILAKGGLPVLLAHFGRPK 64 Query: 65 GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET 124 G+ PE SL V L E LG+ V+F+ + A+E L + V+L ENTRF PGE Sbjct: 65 GKVVPEMSLRVVLPALEEALGRPVEFI----AHPDRAALEALPKCTVVLAENTRFAPGEE 120 Query: 125 KNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTYN 184 KNDPE+A A+L DI+ NDAF AHRAHAS GIA+ +PS AG LM+ E++ L + Sbjct: 121 KNDPEMAAALAALGDIYCNDAFSAAHRAHASTEGIARLLPSCAGRLMQAELEALQRALGT 180 Query: 185 PEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKID 244 P +P V V+GGAKVS K+ ++ NL+EK D ++IGG M TFL A G +VG+S E + D Sbjct: 181 PTRPVVAVVGGAKVSTKLALLGNLVEKVDDLVIGGGMANTFLAAQGIDVGASLAEHEMAD 240 Query: 245 LAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELF 304 A+E++EKA G I LP D V+A+K E G + + + + P M LD GPET+ Sbjct: 241 TAREIMEKAARAGCSIHLPKDIVVARKFEAGAPSQTLPVSE-CPRDAMILDAGPETVAAL 299 Query: 305 KQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGA-ITVVGGGDSAAAVNKF 363 K+ + A+T++WNGP+G FEI F T A A A T+ G ITV GGGD+ AA+NK Sbjct: 300 KEVFAQARTLIWNGPLGAFEIPPFDMATNAAARAAADATKAGTLITVAGGGDTVAALNKA 359 Query: 364 GLEDKFSHVSTGGGASLEFLEGKELPGIASI 394 G+ D F+++ST GGA LE++EGK LPG+A++ Sbjct: 360 GVADDFTYISTAGGAFLEWMEGKTLPGVAAL 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: 606 Number of extensions: 27 Number of successful extensions: 4 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