Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate GFF4212 Psest_4285 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= BRENDA::Q6LFH8 (414 letters) >FitnessBrowser__psRCH2:GFF4212 Length = 452 Score = 180 bits (456), Expect = 9e-50 Identities = 120/405 (29%), Positives = 211/405 (52%), Gaps = 41/405 (10%) Query: 31 VLKRGKGVFVYDIEDRRYYDFLSAYSSVNQGHCHPDILNAMINQAKKLTICSRAFFS--D 88 ++ + GV+++D E + D ++ VN G+ +++ A Q ++L + F + Sbjct: 34 IITKASGVYLWDSEGHKILDAMAGLWCVNLGYGREELVEAATRQMRELPYYNLFFQTAHP 93 Query: 89 SLGVCERYLTNLF--GYDKVLMMNTGAEASETAYKLCRKWGYEVKKIPENSAKIIVCN-N 145 + + ++ G + V +G+EA++T ++ R + + +K P + K+++ N Sbjct: 94 PAVALAKAIADIAPAGMNHVFFTGSGSEANDTVLRMVRHY-WAIKGQP--AKKVVIGRWN 150 Query: 146 NFSGRTLGCVSASTDKKCKNNFGPFVPNFLKV--PY------------------DDLEAL 185 + G T+ S K +P + PY D LE Sbjct: 151 GYHGSTIAGASLGGMKAMHEQSDGPIPGIEHIDQPYWFGEGGDMSPEEFGVRIADQLEQK 210 Query: 186 EKELQDPNVCAFIVEPVQGEAGVIVPSDSYFPGVASLCKKYNVLFVADEVQTGLGRTGKL 245 E+ + V AFI EP+QG GVI+P ++Y+P + + +Y++LF+ADEV G GRTG+ Sbjct: 211 ILEVGEDKVAAFIAEPIQGAGGVIIPPETYWPRIKEILARYDILFIADEVICGFGRTGEW 270 Query: 246 LCTHHYGVKPDVILLGKALSGGHYPISAILANDDVMLVLKPG---EHGSTYGGNPLAAAI 302 + +YG++PD++ + K L+ G+ P+ ++ D+V+ L G HG TY G+P+AAA+ Sbjct: 271 FGSDYYGLEPDLMPIAKGLTSGYIPMGGVIVRDEVVQTLNEGGEFYHGFTYSGHPVAAAV 330 Query: 303 CVEALKVLINEKLCENADKLGAPFLQNLKEQLKDSKVVREVRGKGLLCAIEF-KNDLV-- 359 +E +++L EK+ E AP+LQ+ ++L D +V E RG GLL A+E KN Sbjct: 331 ALENIRILREEKIVERVKTKTAPYLQSRWQELLDHPLVGEARGVGLLGALELVKNKKTRE 390 Query: 360 -----NVWDICLKF-KENGLITRSVHDKTVRLTPPLCITKEQLDE 398 V +C + NGL+ R+V D T+ ++PPL I++EQ+DE Sbjct: 391 RFADPGVGMLCREHCFRNGLVMRAVGD-TMIISPPLVISEEQIDE 434 Lambda K H 0.320 0.138 0.418 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: 478 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: 414 Length of database: 452 Length adjustment: 32 Effective length of query: 382 Effective length of database: 420 Effective search space: 160440 Effective search space used: 160440 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 (21.8 bits) S2: 51 (24.3 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