Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_011840836.1 RSPH17029_RS05860 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000015985.1:WP_011840836.1 Length = 397 Score = 364 bits (935), Expect = e-105 Identities = 194/392 (49%), Positives = 259/392 (66%), Gaps = 3/392 (0%) Query: 5 TIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPK 64 T+ D+DL GK V++RVD NVP+++G V D TRI +PT++ L++G K +LL+H GRPK Sbjct: 5 TLDDMDLAGKVVLVRVDVNVPMENGEVTDATRIEKIVPTVEDILKKGGKPVLLAHFGRPK 64 Query: 65 GEPSPEFSLAPVAKRLSELL-GKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGE 123 G+ E SL V L + L G +V F VG E ++AV + EGEVLLLENTRFH GE Sbjct: 65 GKVVDEMSLRLVLPALQKALPGTKVSFAADCVGPEPEQAVAAMLEGEVLLLENTRFHAGE 124 Query: 124 TKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTY 183 KNDPELA A L ++VNDAF AHRAHAS G+A+ +PS AG LME E+K L Sbjct: 125 EKNDPELAAAMAKLGQVYVNDAFSAAHRAHASTEGLARLLPSAAGRLMEAELKALEAALG 184 Query: 184 NPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKI 243 +PE+P V V+GGAKVS K+ ++ NL+ + D ++IGG M TFL A G EVG S E D Sbjct: 185 HPERPVVAVVGGAKVSTKLDLLGNLVGRVDHLVIGGGMANTFLVAQGIEVGKSLAERDMA 244 Query: 244 DLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIEL 303 D A+E+L KAK G I LP+D V+A++ + G + V P M LD GP+T+ Sbjct: 245 DTAREILSKAKAAGCTIHLPLDVVVAREFKAGAANETVE-TSACPADAMILDAGPKTVAA 303 Query: 304 FKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKG-AITVVGGGDSAAAVNK 362 + + AKT++WNGP+G FEI+ F T AL +A LT+ G I+V GGGD+ AA+NK Sbjct: 304 LSEVFASAKTLIWNGPLGAFEIEPFDAATNAAALQVAQLTKAGQLISVAGGGDTVAALNK 363 Query: 363 FGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394 G + FS++ST GGA LE++EGKELPG+A++ Sbjct: 364 AGAAEGFSYISTAGGAFLEWMEGKELPGVAAL 395 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: 605 Number of extensions: 34 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: 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 Apr 10 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