Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate 7025958 Shewana3_3106 beta alanine--pyruvate transaminase (RefSeq)
Query= curated2:Q8TUZ5 (389 letters) >FitnessBrowser__ANA3:7025958 Length = 446 Score = 191 bits (486), Expect = 3e-53 Identities = 137/417 (32%), Positives = 212/417 (50%), Gaps = 48/417 (11%) Query: 19 PVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNLYYNE 78 P L EG D GN+ +D AG+ GH + EAV +Q+ + + + Sbjct: 32 PRLLAQAEGMYYTDINGNKVLDSTAGLWCCNAGHGRREISEAVSKQIREMDYAPSFQMGH 91 Query: 79 PQA-EAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKF------TGCTKFIAFEGGF 131 P A E A L E +P+ LNKVFF NSG+ESV+ A+K+A + T+FI E G+ Sbjct: 92 PLAFELAERLTELSPEGLNKVFFTNSGSESVDTALKMALCYHRANGQASRTRFIGRELGY 151 Query: 132 HGRTMGALSATWKPEFREPFE-PLVPEFEHVPYG-DVN-----------AVEKAI----- 173 HG G +S R+ F L+ +H+P+ D+ EKA Sbjct: 152 HGVGFGGISVGGLSNNRKAFSGQLLQGVDHLPHTLDIQNSAFSRGLPSLGAEKAEVLEQL 211 Query: 174 -----DDDTAAVIVEPVQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQF 228 ++ AAVIVEP+ G AGV +PP+G+L+ LRE+ ++G+LLI DEV + GR G Sbjct: 212 VTLHGAENIAAVIVEPMSGSAGVILPPQGYLKRLREITQKYGILLIFDEVITAFGRVGAA 271 Query: 229 FAFEHEDVLPDIVCLAKGL-GGGVPVGATIAREEVAEAFEPGD-------HGSTFGGNPL 280 FA + V+PDI+ AK + G +P+GA ++ + + G HG T+ G+P+ Sbjct: 272 FASQRWGVIPDIITTAKAINNGAIPMGAVFVQDFIHDTCMQGPTELIEFFHGYTYSGHPV 331 Query: 281 ACAAVCAAVSTVLEENLPEAA---ERKGKLAMRILSEAEDVVEEVRGRGLMMGVEV---- 333 A AA A +S E L E + ER + A+ L +V+ ++R GL+ G ++ Sbjct: 332 AAAAALATLSIYENEQLFERSFELERYFEDAVHSLKGLPNVI-DIRNTGLVAGFQLAPNS 390 Query: 334 -GDDERAKDVAREMLDRGALVNVTSGDVIRLVPPLVIGEDELEKALAELADALRASG 389 G +R V +G LV T GD+I + PPL++ + ++++ + L+DA+ A G Sbjct: 391 QGAGKRGYSVFEHCFHQGTLVRAT-GDIIAISPPLIVEKHQIDQIVNSLSDAIHAVG 446 Lambda K H 0.318 0.137 0.405 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: 410 Number of extensions: 27 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 389 Length of database: 446 Length adjustment: 31 Effective length of query: 358 Effective length of database: 415 Effective search space: 148570 Effective search space used: 148570 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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