Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_005452968.1 SACCYDRAFT_RS01550 putative succinyldiaminopimelate transaminase DapC
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000244975.1:WP_005452968.1 Length = 386 Score = 123 bits (309), Expect = 8e-33 Identities = 111/364 (30%), Positives = 158/364 (43%), Gaps = 17/364 (4%) Query: 29 THGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGIT 88 T VNL G P PE + AA AL Y G PELR+AIAA ++ R+G Sbjct: 26 TRTSAVNLGQGFPDTDGPEGMLEAARNALFGGANQYPPGPGRPELREAIAA-HRARYGTE 84 Query: 89 VEPDA-VVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCE---VVEIPC 144 +PD +++T G++ + LA GD V + P Y Y ++ G V +P Sbjct: 85 YDPDGEILVTAGATEAIAASLLALTGPGDEVIVIEPYYDSYAAAVAMAGATRRVVSLVPD 144 Query: 145 GPQTRFQPTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVRLISDEV 204 G + A + A ++P R ++V SP NPTGTV+ ELA +A C D+ I+DEV Sbjct: 145 GDRFALDLDA-VRAAVNPNTRAILVNSPHNPTGTVLTRTELAGLAELCVERDLLAITDEV 203 Query: 205 YHGLVYQGAPQTSCAW--QTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDCLTGN 262 Y LV+ A A S V ++S K + TGW++GW+ P L AV Sbjct: 204 YEHLVFDDAEHLPLATFPGMSSRTVSISSAGKTFNCTGWKIGWVCAPRELTAAVRAAKQF 263 Query: 263 FTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTDGAFYV 322 T Q A A E + S R L GL G + P G ++V Sbjct: 264 LTFVSGGPLQPAVAHALRHE-LPWVESLRESLQAKRDRLCAGLADAGF-AVRPGAGTYFV 321 Query: 323 YADVSDF---TSDSLAFCSKLLADTGVAIAPGIDF--DTARGGSFVRISFAGPSGDIEEA 377 ADV ++ LA+ +L GVA P F +R +F ++EA Sbjct: 322 CADVRPLGFTNAEELAW--RLPESIGVAAVPVSVFTDHPEEWQHLLRFAFCKREEVLDEA 379 Query: 378 LRRI 381 + R+ Sbjct: 380 IERL 383 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: 363 Number of extensions: 13 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: 386 Length adjustment: 30 Effective length of query: 358 Effective length of database: 356 Effective search space: 127448 Effective search space used: 127448 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