Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate Ac3H11_1332 Acetylornithine aminotransferase (EC 2.6.1.11)
Query= BRENDA::Q0K2K2 (423 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1332 Length = 398 Score = 204 bits (519), Expect = 4e-57 Identities = 133/396 (33%), Positives = 194/396 (48%), Gaps = 36/396 (9%) Query: 29 DRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFTHTA-YQIVPYQGY 87 +R + +WDV G+ Y D GIAV GH H +++ A+ Q+ + HT+ Y VP Q Sbjct: 24 ERGQGCRVWDVNGKEYIDGLGGIAVNTLGHNHGKLVPALQDQIAKLIHTSNYYHVPLQEK 83 Query: 88 VTLAERINALVPIQGLNKTALFTTGAEAVENAIKIARAH-----TGRPGVIAFSGAFHGR 142 + LV + G+ +G EA E A+KIAR +P ++ + AFHGR Sbjct: 84 LA-----TKLVELSGMQNVFFCNSGLEANEAALKIARKFGVDKGIAKPEIVVYEKAFHGR 138 Query: 143 TLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQALEGLFKTDIDPARVA 202 ++ M+ TG + GFGP P E QA EG V Sbjct: 139 SIATMSATGNPKIHN-GFGPLVEGFVRVPMNDI------EAIKQATEG-------NPNVV 184 Query: 203 AIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMSHHDVEP 262 A+ E +QGEGG ++++ LR +CD+ G +++ DEVQ G GRTGK FA + P Sbjct: 185 AVFFETIQGEGGINGMRIEYLQQLRKLCDERGWLMMIDEVQCGMGRTGKWFAHQWAGIVP 244 Query: 263 DLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVAAAHAVIDVIEEEKLC 322 D++ +AK L G+P+ AV + PG G T+ GNPLA+ A I ++EE+ L Sbjct: 245 DVMPLAKGLGSGVPIGAVVAGPKAANVLQPGNHGTTFGGNPLAMRAGVETIRIMEEDGLL 304 Query: 323 ERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCDPATGQPSAEHAKRVQTRALE 382 +A +G LR L + P + E+RG G M+ E P + RA E Sbjct: 305 HNAAQVGDHLRAALQRELGSLPGVKEIRGQGLMLGIELNKPCGA---------LIGRAAE 355 Query: 383 AGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLT 418 AGL+L T +VIR + PL + A+ DA +A+LT Sbjct: 356 AGLLLSV--TADSVIRLVPPLILTTAEADAIVAILT 389 Lambda K H 0.321 0.136 0.400 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: 400 Number of extensions: 23 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: 423 Length of database: 398 Length adjustment: 31 Effective length of query: 392 Effective length of database: 367 Effective search space: 143864 Effective search space used: 143864 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 Sep 17 2021. The underlying query database was built on Sep 17 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