Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_089302168.1 CHB84_RS14635 aspartate aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_900188115.1:WP_089302168.1 Length = 392 Score = 456 bits (1174), Expect = e-133 Identities = 227/381 (59%), Positives = 279/381 (73%), Gaps = 4/381 (1%) Query: 8 RAGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVA 67 R+ V PF+VM+V AA RQRTHGD+V+L AGQP++GAP+PVR AA + L LGY+ Sbjct: 13 RSDVAPFHVMEVLSAAQARQRTHGDVVSLCAGQPTSGAPKPVRDAAISLLTEGDLGYTSQ 72 Query: 68 LGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPC 127 LG+ ELR+AIA Y R+G+ V+PD VV+TTGSSGGF LAFLA FD G RVAM PGYP Sbjct: 73 LGVVELREAIAGHYAHRYGMRVDPDDVVVTTGSSGGFQLAFLAAFDHGARVAMPRPGYPA 132 Query: 128 YRNILSALGCEVVEIPCGPQTRFQPTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAA 187 YRN+LSALGCEVVE G +TRFQPT + L ++ P + G+V+ASP NPTGT++ EEL+A Sbjct: 133 YRNLLSALGCEVVEFGVGAETRFQPTTEQLDQLGP-IDGLVIASPNNPTGTILASEELSA 191 Query: 188 IASWCDASDVRLISDEVYHGLVY---QGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLG 244 IA WC V+L+SDE+YHG+ + G P S AW+ A+V+ SFSKY+ MTGWRLG Sbjct: 192 IALWCAERGVQLVSDEIYHGVSFGSSTGGPAESSAWEFGTEAIVLGSFSKYFGMTGWRLG 251 Query: 245 WLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDG 304 W+LVP LRRAVD L+GN IC P L+Q AAV+AFT E+ AE D ++ Y NR LL G Sbjct: 252 WMLVPPRLRRAVDVLSGNLAICAPALAQYAAVAAFTDESYAELDEHVLRYRANRDTLLAG 311 Query: 305 LRRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVR 364 L +GIDR+AP DGAFY YADVS+FT+DSL +C +LLADTG+AI PGIDFD GG FVR Sbjct: 312 LAELGIDRVAPADGAFYAYADVSEFTADSLGWCQRLLADTGLAITPGIDFDPVDGGGFVR 371 Query: 365 ISFAGPSGDIEEALRRIGSWL 385 S AG + DI L R+G WL Sbjct: 372 FSLAGSASDITACLERLGRWL 392 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: 566 Number of extensions: 26 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: 392 Length adjustment: 31 Effective length of query: 357 Effective length of database: 361 Effective search space: 128877 Effective search space used: 128877 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