Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate PfGW456L13_4910 Acetylornithine aminotransferase (EC 2.6.1.11)
Query= curated2:Q5SHH5 (395 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4910 Length = 413 Score = 261 bits (668), Expect = 2e-74 Identities = 154/402 (38%), Positives = 221/402 (54%), Gaps = 15/402 (3%) Query: 6 LEDWRALLEAEKTLDSGVYNKHDLLIV---RGQGARVWDAEGNEYIDCVGGYGVANLGHG 62 L+ R LLE + + + + + L + +G G R+WD G EY+D V G V N+GH Sbjct: 11 LQKHRPLLELDVMTAACLMSTYQPLALSFNKGLGTRLWDQAGREYLDAVAGVAVTNVGHS 70 Query: 63 NPEVVEAVKRQAETLMAMPQTLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALK 122 +P++V A+ QA L+ + + LT + ++R F NSG EANE ALK Sbjct: 71 HPKIVAAITEQAGLLLHTSNLYSIDWQQRLAQKLTQLAG--MDRAFFNNSGAEANETALK 128 Query: 123 FARAHTGRKKF-----VAAMRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEA 177 AR H K V F GRT+G+LS + P R F L +P+ D+ A Sbjct: 129 IARLHGWHKGIEQPLVVVMENAFHGRTLGTLSASDGPAVRLGFNKLPGDFVKVPFGDLGA 188 Query: 178 L---KRAVDEETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRT 234 L ++A AV++EP+QGE GV+ A P +L A RE+ + LL+LDEIQTG+GRT Sbjct: 189 LDKVQQAFGSRIVAVLMEPIQGESGVQLAPPGYLSAVRELCNRRSWLLMLDEIQTGIGRT 248 Query: 235 GKRFAFEHFGIVPDILTLAKALGGGVPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAG 294 G+ FAF+H GIVPD++TLAK LG GVP+GA + R + A G HG+TFGGNPLA G Sbjct: 249 GQWFAFQHEGIVPDVMTLAKGLGNGVPIGACLARGKAAELFTPGSHGSTFGGNPLACRVG 308 Query: 295 VAAIRYLERTRLWERAAELGPWFMEKLRA--IPSPKIREVRGMGLMVGLELKEKAAPYIA 352 + +E L E A G +E+LR +P + ++RG GLM+G+ELK+ Sbjct: 309 CTVLDIVEEQGLLENARLQGARLLERLRTELAGNPNVSQIRGQGLMIGIELKQPIRDLSL 368 Query: 353 RLEKEHRVLALQAGPTVIRFLPPLVIEKEDLERVVEAVRAVL 394 ++H +L IR LPPL +++ ++E +V V V+ Sbjct: 369 IAARDHGLLINVTRGNTIRLLPPLTLDEREVEMIVRGVGRVV 410 Lambda K H 0.319 0.137 0.402 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: 417 Number of extensions: 21 Number of successful extensions: 5 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: 395 Length of database: 413 Length adjustment: 31 Effective length of query: 364 Effective length of database: 382 Effective search space: 139048 Effective search space used: 139048 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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