Align Acetylornithine aminotransferase 2; ACOAT 2; EC 2.6.1.11 (uncharacterized)
to candidate Echvi_0150 Echvi_0150 glutamate-1-semialdehyde-2,1-aminomutase
Query= curated2:Q7WDN7 (396 letters) >FitnessBrowser__Cola:Echvi_0150 Length = 429 Score = 140 bits (352), Expect = 9e-38 Identities = 95/289 (32%), Positives = 146/289 (50%), Gaps = 25/289 (8%) Query: 20 LVFVRGQGSWLEDHAGKRYLDFVQGWAVNTLGHCAPEMKRALAEQADKLMN-PSPAFYNL 78 L + +G++L D RY++ + W LGH PE+ A+ + + + +P + Sbjct: 36 LFIKKAEGAYLFDEDDNRYIELINSWGPMILGHNHPEINEAIVKAVENGTSFGAPTAKEI 95 Query: 79 PSIELAQRLTSASCFDRVFFANSGAEANEGAIKLARKWGRVNRNGAYKIITMNHGFHGRT 138 EL ++ + ++V NSG EA A++LAR + G K + +HG Sbjct: 96 DIAELICKMVPS--VEKVRMVNSGTEATMSAVRLARGY-----TGRDKFLKFEGNYHGHG 148 Query: 139 LATMSASGKPGWDTMFAPQVEGFPK--------AEINDLDSVRALIDA---QTVAVMLEP 187 + + A+G G TM AP G K A NDL++V+ +++A + A++LEP Sbjct: 149 DSFLIAAGS-GAMTMGAPNSPGVTKGTAKDTLLAPYNDLNAVKEVLEANRDEVAAIILEP 207 Query: 188 VQGEAGVIPATREFMQGLRKLADEHGILFIVDEVQTGMGRTGSLFAYQQFDVIPDIMTLA 247 V G G++ F+QGLRKL DE GI+ I DEV TG R A + F V PD+ T+ Sbjct: 208 VPGNMGLVLPNEGFLQGLRKLCDEEGIVLIFDEVMTGF-RLAQGGAQEVFGVTPDLTTMG 266 Query: 248 KGIGGGIPLAALLAREEVCVFAHG----DQGGTYNGNPLCAAVGVAVFD 292 K IGGG+P+ A ++E+ F Q GT +GNP+ A G A+ D Sbjct: 267 KIIGGGMPVGAYGGKKEIMDFVSPVGPVYQAGTLSGNPIAMAAGFAMLD 315 Lambda K H 0.321 0.137 0.403 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: 391 Number of extensions: 25 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: 396 Length of database: 429 Length adjustment: 31 Effective length of query: 365 Effective length of database: 398 Effective search space: 145270 Effective search space used: 145270 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