Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_015934127.1 MNOD_RS37310 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000022085.1:WP_015934127.1 Length = 409 Score = 182 bits (461), Expect = 2e-50 Identities = 122/382 (31%), Positives = 192/382 (50%), Gaps = 21/382 (5%) Query: 16 VMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRD 75 ++ + A+ R+R ++ L AG+P PEPV+ AAA A+ + Y++ G PEL+ Sbjct: 25 ILRITAEASARKRAGRPVIVLGAGEPDFDTPEPVKTAAARAMREGRTKYTILDGAPELKA 84 Query: 76 AIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSAL 135 A+ ++R +G+ D + TG+ AF+A D GD V + +P + Y +I++ Sbjct: 85 AVREKFRRDNGLDYALDEITCGTGAKQVLYNAFMASLDPGDEVVIPAPFWTSYADIVAIC 144 Query: 136 GCEVVEIPCGPQTRFQPTAQMLAE-IDPPLRGVVVASPANPTGTVIPPEELAAIASWCDA 194 G + +PC F+ T Q L I P R +++ SP+NPTG+ ++L +A D Sbjct: 145 GGVPIIVPCAETDGFRLTPQALERAIGPRTRWLLLNSPSNPTGSAYTADDLVGLAEVLDR 204 Query: 195 -SDVRLISDEVYHGLVYQG---APQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVPT 250 V L+SD++Y ++Y G A S A Q + VN SK YAMTGWR+G+ P Sbjct: 205 HPHVWLMSDDMYEHILYDGRRFATPASAAPQLRLRTLTVNGVSKAYAMTGWRIGYGAGPK 264 Query: 251 VLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRI-G 309 L +A+ + T CP +SQ AA+ A + + +D +A + R L+++ L + G Sbjct: 265 ALIQAMATVQSQSTSCPSSISQAAALEALVGDQASISDRRVA-FQRRRDLVVEALNAMPG 323 Query: 310 IDRLAPTDGAFYVYADVSDF----------TSDSLAFCSKLLADTGVAIAPGIDFDTARG 359 + P +GAFY +A+ + D AFC LL VA+ PG F A Sbjct: 324 LSCRRP-EGAFYTFANCAGLLGRTTPDGTVLEDDRAFCRHLLESADVAVVPGSCFGLA-- 380 Query: 360 GSFVRISFAGPSGDIEEALRRI 381 F RIS+A ++ EA RI Sbjct: 381 -GFFRISYATSEAELTEACGRI 401 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: 437 Number of extensions: 29 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: 409 Length adjustment: 31 Effective length of query: 357 Effective length of database: 378 Effective search space: 134946 Effective search space used: 134946 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