Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate AZOBR_RS03885 AZOBR_RS03885 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >FitnessBrowser__azobra:AZOBR_RS03885 Length = 398 Score = 362 bits (930), Expect = e-104 Identities = 186/394 (47%), Positives = 262/394 (66%), Gaps = 2/394 (0%) Query: 5 TIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPK 64 TI D+D+ GK V++R D NVP++DG V D TRI PT+ ++GAKV++LSH GRPK Sbjct: 6 TIDDLDVNGKTVLVRADLNVPMQDGKVSDTTRIDRLAPTLTELAKKGAKVVVLSHFGRPK 65 Query: 65 GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET 124 P + SL V LS +G+ V F VGD+ K A++ ++ G ++LLENTRFH E Sbjct: 66 NGPDAKNSLRNVLDALSAAVGQTVAFGEDCVGDKAKAAIDGVQPGAIVLLENTRFHAEEE 125 Query: 125 KNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTYN 184 KNDP AK A+L D++VNDAF AHRAHAS G+AQ++P+ AG LM+ E++ L+K Sbjct: 126 KNDPAFAKQIAALGDLYVNDAFSAAHRAHASTEGVAQYLPAAAGRLMQAELEALTKALEK 185 Query: 185 PEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKID 244 PE+P V+GGAK+S K+ ++ NL++K D + +GG M TFL A G +VG+S E+D D Sbjct: 186 PERPVAAVVGGAKISTKLDLLGNLVKKVDMLALGGGMANTFLYAQGVDVGASLCEKDMAD 245 Query: 245 LAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELF 304 A+ ++E AK E++LP D ++A++ + G + V DGI M LD+GP+T+E Sbjct: 246 QARAIMETAKAANCELLLPKDFIVAKEFKAGAANRAVPA-DGIGADEMALDVGPKTVEFL 304 Query: 305 KQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALT-EKGAITVVGGGDSAAAVNKF 363 KL AKTVVWNGP+G FEI F GT VA +A T E G ++V GGGD+ +A+ Sbjct: 305 GLKLQGAKTVVWNGPLGAFEIQPFDAGTNAVAGLVAERTSEGGLLSVAGGGDTVSALAHA 364 Query: 364 GLEDKFSHVSTGGGASLEFLEGKELPGIASIADK 397 G+E+KF+++S GGA LE+LEGK+LPG+A++ K Sbjct: 365 GVEEKFTYISAAGGAFLEWLEGKDLPGVAALKKK 398 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: 624 Number of extensions: 27 Number of successful extensions: 3 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: 398 Length adjustment: 34 Effective length of query: 620 Effective length of database: 364 Effective search space: 225680 Effective search space used: 225680 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