Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate CCNA_03245 CCNA_03245 beta alanine-pyruvate transaminase
Query= curated2:Q8TUZ5 (389 letters) >FitnessBrowser__Caulo:CCNA_03245 Length = 442 Score = 203 bits (517), Expect = 7e-57 Identities = 143/416 (34%), Positives = 210/416 (50%), Gaps = 47/416 (11%) Query: 15 YSRFPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNL 74 + R P L G E E +D +G+ GH P + EA+++Q + + Sbjct: 25 FKRHPRMLSSASGMWYRTPESREVLDATSGLWCVNAGHDRPKIREAIQKQAAEMDYAPCF 84 Query: 75 YYNEPQA-EAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFTGC------TKFIAF 127 P A + A LA+ PK L+++FF NSG+ESV+ A+K+A + T+ I Sbjct: 85 NMGHPLAFQFASRLAQITPKGLDRIFFTNSGSESVDTALKIALAYHRARGKGTKTRLIGR 144 Query: 128 EGGFHGRTMGALSATWKPEFREPFEPLVPEFEHVPY---------------------GDV 166 E G+HG G +S P+ R F L+ +H+P+ D+ Sbjct: 145 ERGYHGVGFGGISVGGIPKNRMYFGSLLTGVDHLPHTHGLPGNTCAKGQPENGAHLADDL 204 Query: 167 NAVEKAID-DDTAAVIVEPVQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRT 225 + D + AAVIVEPV G GV IPP+G+L LR +CD+H +LLI DEV +G GR Sbjct: 205 ERIVALHDASNIAAVIVEPVAGSTGVLIPPKGYLERLRAICDKHDILLIFDEVITGFGRV 264 Query: 226 GQFFAFEHEDVLPDIVCLAKGL-GGGVPVGATIAREEVAEAFEPGD-------HGSTFGG 277 G FA E V PD++C+AKGL VP GA A ++ +A G HG T+ Sbjct: 265 GAPFAAERFGVTPDLICMAKGLTNAAVPCGAVAASGKIYDAMMDGADAPIELFHGYTYSA 324 Query: 278 NPLACAAVCAAVSTVLEENL-PEAAERKG--KLAMRILSEAEDVVEEVRGRGLMMGVEV- 333 +PLACAA A + T E++L AA +G + AM L++A VV +VR GL+ G+E+ Sbjct: 325 HPLACAAGLATLETYREDDLFARAAGLEGYWQDAMHSLADARHVV-DVRNLGLVAGIELE 383 Query: 334 ----GDDERAKDVAREMLDRGALVNVTSGDVIRLVPPLVIGEDELEKALAELADAL 385 RA +V D G L+ VT GD+I L PPL++ +D +++ + + L Sbjct: 384 PRPGAPTARAMEVFETCFDEGLLIRVT-GDIIALSPPLILEKDHIDRMVETIRRVL 438 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: 409 Number of extensions: 27 Number of successful extensions: 6 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: 389 Length of database: 442 Length adjustment: 31 Effective length of query: 358 Effective length of database: 411 Effective search space: 147138 Effective search space used: 147138 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