Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate 3607759 Dshi_1168 aminotransferase class I and II (RefSeq)
Query= SwissProt::P96847 (388 letters) >FitnessBrowser__Dino:3607759 Length = 391 Score = 330 bits (846), Expect = 4e-95 Identities = 174/377 (46%), Positives = 234/377 (62%), Gaps = 4/377 (1%) Query: 8 RAGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVA 67 R+ V PF VMDV AA + ++++ GQP AP P R A AA L + +GY+VA Sbjct: 6 RSEVDPFIVMDVMEAARRAEAAGRHIIHMEVGQPGTAAPLPARRAVAAQLDQDAMGYTVA 65 Query: 68 LGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPC 127 LG+PELR AIA Y R +G+ ++P VV+T+GSS FLLAF FDAG RV +A PGYP Sbjct: 66 LGLPELRRAIAGLYARWYGVDLDPARVVVTSGSSAAFLLAFTTYFDAGARVGVAEPGYPS 125 Query: 128 YRNILSALGCEVVEIPCGPQTRFQPTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAA 187 YR IL AL V +P P+T + TA+ LA+ D + G ++ASP NPTGT++ + L A Sbjct: 126 YRQILKALSLAPVGLPTQPETGHRMTAEALAQAD--IAGAIIASPNNPTGTMLDRDGLGA 183 Query: 188 IASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLL 247 + + C D ISDE+YHGL Y + A + S + V+NSFSKY++MTGWR+GWL+ Sbjct: 184 LIAACRDRDRVFISDEIYHGLHY--GDRAVSALEISDDVCVINSFSKYFSMTGWRIGWLV 241 Query: 248 VPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRR 307 VP R V+ L N IC P ++QIAA+ A A E + N A YA NR L++DGLR Sbjct: 242 VPEAQVRVVERLAQNMFICAPHVAQIAALGALGDAARPELEANRAVYAANRQLVIDGLRA 301 Query: 308 IGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISF 367 G+D AP DGAFYVY D +SDS + +L GVA+ PG+DFD RG +R+S+ Sbjct: 302 AGLDAFAPPDGAFYVYVDTGALSSDSRTLAADILEKAGVAVTPGLDFDPVRGHGTLRLSY 361 Query: 368 AGPSGDIEEALRRIGSW 384 A + DI E + R+ ++ Sbjct: 362 ARATEDIAEGMTRLTNY 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: 460 Number of extensions: 20 Number of successful extensions: 3 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: 391 Length adjustment: 30 Effective length of query: 358 Effective length of database: 361 Effective search space: 129238 Effective search space used: 129238 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