Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_028950186.1 Q385_RS0102690 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000619805.1:WP_028950186.1 Length = 399 Score = 414 bits (1063), Expect = e-120 Identities = 212/398 (53%), Positives = 289/398 (72%), Gaps = 8/398 (2%) Query: 4 MTIRDVDLKGKRVIMRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVILLSHLGR 62 +T++DVD+ GKRV +RVD+NVP+ + G + DD RIR +PTI Y L++ AK+IL SHLGR Sbjct: 6 LTLKDVDVSGKRVFVRVDYNVPLDEYGNIVDDVRIRETIPTINYLLDRNAKIILASHLGR 65 Query: 63 PKGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPG 122 PKG+P P++SL PVAKRL LL KEVKF+P +G ++++ + ++KE +++LLEN RFH Sbjct: 66 PKGKPDPKYSLYPVAKRLERLLNKEVKFLPDCIGKDIEEEIFKMKERDIILLENLRFHKE 125 Query: 123 ETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFI-PSVAGFLMEKEIKFLSKV 181 E NDPE AK ASL++I+V DAFGT HR HAS GI FI P V GFL+E+E+++ K Sbjct: 126 EEANDPEFAKKLASLSEIYVVDAFGTCHRKHASVYGIKDFIQPVVMGFLLERELEYFRKA 185 Query: 182 TYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEED 241 NP++P V LGG+KVS K+GVI L++K D+I IGGAM FTF+KA+G VGSS VE+D Sbjct: 186 LLNPQRPVVAFLGGSKVSSKLGVIEFLIDKVDKIFIGGAMAFTFIKAMGYNVGSSLVEDD 245 Query: 242 KIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRID-DGIPEGWMGLDIGPET 300 ++ A E++EKAK+K V+ LPVD V Q + + VV + IP+GW+GLDIG + Sbjct: 246 MLEKALEIMEKAKQKDVKFYLPVDFVCGQAVSD--QTPVVEVAWQEIPKGWLGLDIGHAS 303 Query: 301 IELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAV 360 + L K+ L DA+T+VWNGPMGVFEID F GT ++A AIA E A+++ GGGD+ A+ Sbjct: 304 VILIKEILKDAQTIVWNGPMGVFEIDKFKMGTFELAHAIA---ESPALSIAGGGDTDYAI 360 Query: 361 NKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIADKK 398 +K G+ DK ++STGGGA LE LEGK+LP + +I K+ Sbjct: 361 HKAGVVDKIGYLSTGGGAFLELLEGKQLPCLQAITKKE 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: 700 Number of extensions: 31 Number of successful extensions: 5 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: 399 Length adjustment: 34 Effective length of query: 620 Effective length of database: 365 Effective search space: 226300 Effective search space used: 226300 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 24 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