Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate 353246 BT3720 putative aspartate aminotransferase (NCBI ptt file)
Query= SwissProt::P96847 (388 letters) >FitnessBrowser__Btheta:353246 Length = 383 Score = 232 bits (591), Expect = 2e-65 Identities = 138/373 (36%), Positives = 204/373 (54%), Gaps = 9/373 (2%) Query: 14 FYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPEL 73 F VMDV A E Q+ D+++L G+P P V AA AA + Y+ +LG PEL Sbjct: 14 FIVMDVLERANELQKQGVDVIHLEVGEPDFDVPACVAEAAKAAYDRHLTHYTHSLGDPEL 73 Query: 74 RDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILS 133 R IAA YQR +G+TV+PD +V+T+GSS LL + ++ V +++PGY CYRN + Sbjct: 74 RREIAAFYQREYGVTVDPDCIVVTSGSSPSILLVLMLLCNSDSEVILSNPGYACYRNFVL 133 Query: 134 ALGCEVVEIPCGPQTRFQPTAQMLAE-IDPPLRGVVVASPANPTGTVIPPEELAAIASWC 192 A + V +P + Q + + + + P G+ + SP NPTG ++ L ++AS Sbjct: 134 AAQAKPVLVPLSEENGLQYDIEAIRKCVTPHTAGIFINSPMNPTGMLLDESFLRSVAS-- 191 Query: 193 DASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVL 252 V +ISDE+YHGLVY+G + + + A V+N FSK +AMTG RLG+L+ P Sbjct: 192 --LGVPIISDEIYHGLVYEGRAHSILEY--TDKAFVLNGFSKRFAMTGLRLGYLIAPKSC 247 Query: 253 RRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDR 312 R++ L N IC ++Q A ++A +A ++ + Y R ++ LR +G + Sbjct: 248 MRSLQKLQQNLFICASSIAQQAGIAALR-QADSDVERMKQIYDERRRYMISRLREMGFEI 306 Query: 313 LAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSG 372 GAFY++AD FT+DS F +L + V I PGIDF T G +VR S+A Sbjct: 307 KVEPQGAFYIFADARKFTTDSYRFAFDVLENAHVGITPGIDFGTG-GEGYVRFSYANSLE 365 Query: 373 DIEEALRRIGSWL 385 I E L RI +L Sbjct: 366 SIREGLDRISQYL 378 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: 335 Number of extensions: 16 Number of successful extensions: 6 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: 383 Length adjustment: 30 Effective length of query: 358 Effective length of database: 353 Effective search space: 126374 Effective search space used: 126374 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