Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate Synpcc7942_2545 Synpcc7942_2545 aspartate aminotransferase
Query= SwissProt::P96847 (388 letters) >FitnessBrowser__SynE:Synpcc7942_2545 Length = 392 Score = 171 bits (432), Expect = 4e-47 Identities = 119/366 (32%), Positives = 182/366 (49%), Gaps = 11/366 (3%) Query: 22 AAAERQRTHG-DLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAAD 80 A A+ + G D+ + SAG+P P +R AAA AL + Y A G P+LR+AIA Sbjct: 20 AQAKAMKAEGLDVCSFSAGEPDFETPLHIRNAAAQALAEGKTRYGPAAGEPDLREAIAQK 79 Query: 81 YQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALG--CE 138 + +G+ + +++T G D GD V + +P + Y ++ G Sbjct: 80 LRADNGLDYQAANILVTNGGKQSLYNLMQVLLDPGDEVIIPAPYWLSYPEMVKLAGGVPV 139 Query: 139 VVEIPCGPQTRFQPTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVR 198 +VE + QP Q+ I P R +V+ SP+NPTG V +EL AIA +A D Sbjct: 140 IVETFASDGFKLQP-QQLAGAITPRTRLLVLNSPSNPTGMVYSRQELEAIAPIIEAHDFW 198 Query: 199 LISDEVYHGLVYQGAPQTSCAWQTS---RNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRA 255 ++SDE+Y ++Y GA S + ++ N F+K Y+MTGWR+G+L P+ L A Sbjct: 199 VVSDEIYEKILYDGADHHSIGSLSPACFERTLISNGFAKAYSMTGWRVGYLAGPSELIAA 258 Query: 256 VDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAP 315 L + T +Q A++A A+ LA++ R L+L+GL +I Sbjct: 259 AASLQSHSTSNVCTFAQYGAIAALQGPQDCVAE-MLAAFTERRQLILNGLNQIAGLSCPI 317 Query: 316 TDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGDIE 375 +GAFYV+ D+S DS+ +C +LL VA PGI F R +R+S+A IE Sbjct: 318 PEGAFYVFVDISKTGLDSMTYCRQLLDQHQVAAIPGIAFGDDRS---IRLSYATDCQTIE 374 Query: 376 EALRRI 381 + L R+ Sbjct: 375 KGLERL 380 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: 402 Number of extensions: 23 Number of successful extensions: 4 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: 392 Length adjustment: 31 Effective length of query: 357 Effective length of database: 361 Effective search space: 128877 Effective search space used: 128877 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