Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_012676071.1 PERMA_RS04795 aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000021565.1:WP_012676071.1 Length = 371 Score = 238 bits (607), Expect = 2e-67 Identities = 129/375 (34%), Positives = 210/375 (56%), Gaps = 11/375 (2%) Query: 11 VPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGI 70 + PF VMD+ A++ + D V+ G+P V A A+ Y+ +LG+ Sbjct: 7 IRPFIVMDIVRKASKIK----DAVHFEIGEPDLQPSPLVWELAEKAVKDRVNYYTESLGL 62 Query: 71 PELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRN 130 P LR+ I++ Y R+G+ + P+ + +T G+SG FL+A+ + GD++A+ P YPCY+N Sbjct: 63 PLLREKISSFYYERYGVDIAPERIALTVGTSGAFLVAYSMLLNRGDKIALPDPSYPCYKN 122 Query: 131 ILSALGCEVVEIPCGPQTRFQPTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIAS 190 L + V IP G ++ +Q TA+ L E ++ V ++SP+NP G + E L + Sbjct: 123 FAYLLDIQPVFIPVGRESSYQLTAEHLREYS-DIKAVHISSPSNPVGNIYKKENLKELVE 181 Query: 191 WCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVPT 250 +CD + ISDE+YHGLVY+G T A + S NA+V+N FSKY+ M G+RLGW+++P Sbjct: 182 YCDEKGIYFISDEIYHGLVYEGKEHT--AVEFSDNAIVINGFSKYFCMPGFRLGWIILPE 239 Query: 251 VLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGI 310 L R + + N I PP +SQ AA+ AF + + N + R L L+ I Sbjct: 240 KLVRKAEIIIQNVFISPPTISQYAALGAFDHK---HLEKNKEIFRKRRDFLFRELKEIFT 296 Query: 311 DRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGP 370 + P +GAFY++A++ ++ +S F +LL VA+ PG+DF + R ++R ++ Sbjct: 297 IDVEP-EGAFYIWANIEKYSDNSFEFAKELLEKIHVAVTPGVDFGSYRTDRYIRFAYTRD 355 Query: 371 SGDIEEALRRIGSWL 385 +EE +RR+ +L Sbjct: 356 IQHMEEGVRRLKDYL 370 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: 348 Number of extensions: 18 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: 371 Length adjustment: 30 Effective length of query: 358 Effective length of database: 341 Effective search space: 122078 Effective search space used: 122078 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