Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_011782211.1 MVAN_RS25480 putative succinyldiaminopimelate transaminase DapC
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000015305.1:WP_011782211.1 Length = 391 Score = 131 bits (329), Expect = 4e-35 Identities = 107/360 (29%), Positives = 162/360 (45%), Gaps = 14/360 (3%) Query: 34 VNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGITVEPDA 93 VNL G P P + AA A+ Y LGI LR AIA +RR+G +PD Sbjct: 27 VNLGQGFPDEDGPPAMLKAAENAIAEGVNQYPPGLGIAPLRQAIADQRRRRYGSEYDPDT 86 Query: 94 -VVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEIPCGPQTR-FQ 151 V++T G++ A L + V + P Y Y +++ GC +P R F Sbjct: 87 EVLVTVGATEAIAAAILGLVEPDSEVLLIEPFYDSYSPVIAMAGCHRRAVPMVRDGRGFA 146 Query: 152 PTAQMLAE-IDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVRLISDEVYHGLVY 210 + L + P R +++ SP NPTG+V +EL A+A ++D+ +I+DEVY LV+ Sbjct: 147 IDVEGLRRAVTPKTRALILNSPHNPTGSVASDDELRAVAELAISADLLVITDEVYEHLVF 206 Query: 211 QGAPQTSCAWQ--TSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDCLTGNFTICPP 268 G A + + ++S K + +TGW++GW P+ L V + Sbjct: 207 DGRRHRPLADYPGMAGRTITISSAGKMFNVTGWKIGWACGPSDLIAGVRAAKQYLSYVGG 266 Query: 269 VLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTDGAFYVYADVSD 328 Q A A E A D AS+ R L L IG + + + G +++ D Sbjct: 267 APFQPAVAHALATE-DAWVDALCASFQSRRDRLGSALSDIGFE-VHESFGTYFLCVDPRP 324 Query: 329 F-TSDSLAFCSKLLADTGVAIAPGIDF-DTARGGS-----FVRISFAGPSGDIEEALRRI 381 +DS AFC++L GVA P F D A G + VR +F ++EA+RR+ Sbjct: 325 LGFTDSAAFCAELPERVGVAAIPMSAFCDPAAGHAEEWKHLVRFAFCKREDTLDEAIRRL 384 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: 417 Number of extensions: 24 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: 391 Length adjustment: 30 Effective length of query: 358 Effective length of database: 361 Effective search space: 129238 Effective search space used: 129238 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