Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate 209328 DVU0392 aromatic aminotransferase
Query= SwissProt::P96847 (388 letters) >MicrobesOnline__882:209328 Length = 399 Score = 160 bits (404), Expect = 8e-44 Identities = 120/362 (33%), Positives = 173/362 (47%), Gaps = 12/362 (3%) Query: 31 GDLVNLSAGQPSAGAPEPVRAAAAAALH--LNQLGYSVALGIPELRDAIAADYQRRHGIT 88 G V+L G PS PE + A AL + Y++ G+P LR+AIAAD R G Sbjct: 30 GGCVSLGQGVPSFRTPEHIVEAVCRALRDKADAGRYTLQPGMPALREAIAADLAARKGYM 89 Query: 89 VEPDAVV-ITTGSSGGFLLAFLACFDAGDRVAMASPGYPCY-RNILSALGCEVVEIPCGP 146 V PD+ V +T G+ L+A L D GD V + SPGY + +L A G V +P Sbjct: 90 VNPDSEVGVTVGAMEALLMALLTVVDRGDEVIIPSPGYASHAEQVLMAEGVPV-HVPLRA 148 Query: 147 QTRFQPTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVRLISDEVYH 206 + A + P R V+V +P NPTGTV ++ A+ ++ LISDE Y Sbjct: 149 DDWGLDVDAIRAAVTPRTRAVIVCNPGNPTGTVYDDADVRALCELALERNIMLISDETYD 208 Query: 207 GLVYQGAPQTSCAW--QTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDCLTGNFT 264 +VY G S A + R+ +VVNSFSK YA+TGWR+G+ + + Sbjct: 209 YMVYGGGEPLSPASLPEMRRHVIVVNSFSKKYALTGWRVGYCAADAAWMGELLKVHDAAA 268 Query: 265 ICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIG--IDRLAPTDGAFYV 322 IC P +SQ AA++A T D A+ + R+L L + D + P GAFY+ Sbjct: 269 ICAPAVSQYAALAALTGPQDC-VDDMRAALSARRNLACARLDAMAPHFDYVQPR-GAFYI 326 Query: 323 YADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGDIEEALRRIG 382 A + + S +LL + V PG F G +R+SF +++EA R+ Sbjct: 327 MARYTFTDAPSDMVARRLLEEGRVITVPGASFGPT-GERHLRLSFGMEEAELDEAFDRMA 385 Query: 383 SW 384 +W Sbjct: 386 AW 387 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: 464 Number of extensions: 34 Number of successful extensions: 7 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: 399 Length adjustment: 31 Effective length of query: 357 Effective length of database: 368 Effective search space: 131376 Effective search space used: 131376 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 09 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