Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_012853282.1 TCUR_RS14575 putative succinyldiaminopimelate transaminase DapC
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000024385.1:WP_012853282.1 Length = 387 Score = 146 bits (369), Expect = 9e-40 Identities = 109/359 (30%), Positives = 162/359 (45%), Gaps = 12/359 (3%) Query: 34 VNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGITVEPDA 93 +NL G P G P + AA A+ Y G+PELR A+AA R+G+ +PD Sbjct: 30 INLGQGFPDTGGPPQMLEHAAQAIAEGDNQYPPGPGVPELRRAVAAQRAERYGLHYDPDG 89 Query: 94 -VVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGC---EVVEIPCGPQTR 149 V++T G++ G A LA GD V + P Y Y +++ G V P G + Sbjct: 90 EVLVTVGATEGIAAAILALAGPGDEVVVFEPYYDSYTAMIALAGAVRRPVTLRPAGGRFT 149 Query: 150 FQPTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVRLISDEVYHGLV 209 F P ++ + P R ++V SP NPTGTV EL IA+ C D+ ++DEVY L Sbjct: 150 FDPD-ELRGAVGPRTRLILVNSPHNPTGTVFTRAELEVIAALCREHDLIAVTDEVYEYLT 208 Query: 210 YQGAPQT--SCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDCLTGNFTICP 267 + G +C V ++S K +++TGW+ GW+ P RAV + T Sbjct: 209 FDGVEHVPLACLEGMRERTVAISSAGKTFSVTGWKTGWVTGPAPHVRAVQTVKQFLTYAA 268 Query: 268 PVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTDGAFYVYADVS 327 Q A A T + A G + R L+ GL G P G ++V AD+ Sbjct: 269 AAPWQRAVAYALTSQREWVA-GLRDALQAKRDRLIAGLEAAGFTVYRP-QGTYFVQADIR 326 Query: 328 DF-TSDSLAFCSKLLADTGVAIAPG-IDFDTARGGS-FVRISFAGPSGDIEEALRRIGS 383 +D + L GV P + +D G+ F+R +F I+EA+RR+ + Sbjct: 327 PLGFTDGMELARALPHKAGVVAVPSQVFYDHPEAGAHFLRFAFCKQDHVIDEAVRRLSA 385 Lambda K H 0.321 0.136 0.416 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: 428 Number of extensions: 28 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: 388 Length of database: 387 Length adjustment: 30 Effective length of query: 358 Effective length of database: 357 Effective search space: 127806 Effective search space used: 127806 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 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