Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_011444108.1 SARO_RS02235 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000013325.1:WP_011444108.1 Length = 389 Score = 149 bits (377), Expect = 1e-40 Identities = 118/359 (32%), Positives = 169/359 (47%), Gaps = 15/359 (4%) Query: 32 DLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGITVEP 91 D+++LS G+P P V A AL Y+ +G LR A A + R G+ V P Sbjct: 32 DVISLSVGEPDFATPAHVVQATKDALDAGDTKYTAVVGTAALRSAAALHFSRDLGLEVPP 91 Query: 92 DAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEIPCGPQTRFQ 151 V+++ G A LA D GD V + SP + Y I+ G EVV++P F+ Sbjct: 92 SQVIVSAGGKQAIFHALLATLDPGDEVLIPSPWWVSYPEIVRFAGAEVVDLPTDAAGGFR 151 Query: 152 PT-AQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASD-VRLISDEVYHGLV 209 T AQ+ A I P R +++ SP NPTG P +EL A+ V ++SD++Y L Sbjct: 152 ITAAQLEAAITPATRWLLLNSPGNPTGATYPAQELRALGEVLRRHPRVLVMSDDIYAPLR 211 Query: 210 YQGAPQTSCAWQ---TSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDCLTGNFTIC 266 Y + A + + + V+ SK +AMTG+R+G P L A+ L + + Sbjct: 212 YGEGRHATLAVECPDLADRILTVSGVSKSHAMTGFRIGVAAGPAWLISAMGRLQSHSSGN 271 Query: 267 PPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRI-GIDRLAPTDGAFYVYAD 325 P +SQ AAV+AF D + R ++ + I G+ P DGAFY D Sbjct: 272 PASISQAAAVAAFEGPQDFLLDWR-ERFRARRDMVCARVNAIPGLSTPVP-DGAFYCMVD 329 Query: 326 VSDFTS---DSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGDIEEALRRI 381 + + D A C LL ++GVA+ P F G RISFA +EEALRRI Sbjct: 330 AAPLMARFGDDEALCLHLL-ESGVAVVPASAFG---GRDGFRISFAADEAKLEEALRRI 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: 424 Number of extensions: 21 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: 389 Length adjustment: 30 Effective length of query: 358 Effective length of database: 359 Effective search space: 128522 Effective search space used: 128522 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 Jul 25 2024. The underlying query database was built on Jul 25 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