Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_042204073.1 NITSA_RS01735 aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000186245.1:WP_042204073.1 Length = 365 Score = 211 bits (538), Expect = 2e-59 Identities = 129/377 (34%), Positives = 200/377 (53%), Gaps = 20/377 (5%) Query: 13 PFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPE 72 PF VMD+ + + + D ++ GQP P V+ A A+ ++ Y+ ++G+ E Sbjct: 3 PFRVMDL----VRQAQNYEDTIHFEVGQPDLLPPPGVKKALLEAVESDRYAYTESMGLFE 58 Query: 73 LRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNIL 132 LR IAA Y+ +G+ V+P ++IT G+S FL+A+L + G + +A P YPCY N Sbjct: 59 LRRKIAAHYRHDYGVEVDPACILITPGTSNAFLVAYLLTLEEGGVLGLADPSYPCYPNFA 118 Query: 133 SALGCEVVEIPCGPQTRFQPTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWC 192 + + + P + A+ LA L V ++SP+NPTGT+ E L +A++C Sbjct: 119 AMVDVQPRFFPVDRSNGYLLRAEDLA--GSRLDAVHISSPSNPTGTLYDAETLRDLATYC 176 Query: 193 DASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVL 252 + V LISDE+YHGLVY T A + S+ A+V+N FSKY+ M G R+GW++VP L Sbjct: 177 EGEGVALISDELYHGLVYGKRAHT--ALEFSQEAIVINGFSKYFCMPGLRIGWMIVPERL 234 Query: 253 RRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDR 312 R + + N I P LSQ AA+ AF + A+ ++ R L + L D Sbjct: 235 IRPAEIIAQNLFISAPTLSQYAALEAFDYDYLAQV---RETFKKRRDWLHEAL-----DP 286 Query: 313 LAPT----DGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFA 368 L P DGAFY++ D S +T DS AF +LL +A+ PG+DF + +R ++ Sbjct: 287 LLPVDAHPDGAFYLWCDASAYTEDSDAFSRELLEAIHIAVTPGVDFGKYGTQTKLRFAYT 346 Query: 369 GPSGDIEEALRRIGSWL 385 + E + R+ +L Sbjct: 347 RSIEHMAEGVERLRRYL 363 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: 351 Number of extensions: 15 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: 365 Length adjustment: 30 Effective length of query: 358 Effective length of database: 335 Effective search space: 119930 Effective search space used: 119930 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