Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_011779919.1 MVAN_RS13580 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000015305.1:WP_011779919.1 Length = 407 Score = 362 bits (930), Expect = e-104 Identities = 205/392 (52%), Positives = 261/392 (66%), Gaps = 17/392 (4%) Query: 13 GKRVIMRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPKGEPSPEF 71 G+ V++R D NVPV D G + D RI A++PT+K + GAKV++ +HLGRPKGEP P+F Sbjct: 16 GRGVLVRSDLNVPVDDDGNISDPGRIIASVPTLKALSDAGAKVVVTAHLGRPKGEPDPKF 75 Query: 72 SLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET-KNDPEL 130 SLAPVAK L E LG+ V+ VVG + E L +G++LLLEN RF P ET K+D E Sbjct: 76 SLAPVAKALGEKLGRHVQLAGDVVGTDALARAEGLTDGDILLLENIRFDPRETSKDDAER 135 Query: 131 AKFWASLADI----------HVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSK 180 K +L ++ V+D FG HR AS +A +P AG L++ EIK L++ Sbjct: 136 LKLAKALVELVGGEDGSSAAFVSDGFGVVHRKQASVYDVATLLPHYAGTLVDTEIKVLAQ 195 Query: 181 VTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEE 240 +T E+PY VVLGG+KVSDK+ VI NL KAD ++IGG M FTFL A G VGSS +EE Sbjct: 196 LTEAGERPYAVVLGGSKVSDKLAVIENLATKADSLVIGGGMCFTFLAAQGLSVGSSLLEE 255 Query: 241 DKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPET 300 ++ ++LL+ + G + LPVD V+A+K + V D IP+ MGLDIGPE+ Sbjct: 256 SMVETCRKLLD---DYGDVLHLPVDIVVAEKFAADSPAETVAA-DRIPDDKMGLDIGPES 311 Query: 301 IELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAV 360 ++ F LS+AKT+ WNGPMGVFE FA GTK VA AI T KGA +VVGGGDSAAAV Sbjct: 312 VKRFTALLSNAKTIFWNGPMGVFEFPAFAAGTKGVAEAIIGATGKGAFSVVGGGDSAAAV 371 Query: 361 NKFGL-EDKFSHVSTGGGASLEFLEGKELPGI 391 + GL ED FSH+STGGGASLE+LEGKELPGI Sbjct: 372 RQLGLPEDGFSHISTGGGASLEYLEGKELPGI 403 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: 672 Number of extensions: 38 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: 407 Length adjustment: 35 Effective length of query: 619 Effective length of database: 372 Effective search space: 230268 Effective search space used: 230268 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