Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_110205831.1 DNK54_RS04735 acetylornithine transaminase
Query= BRENDA::Q0K2K2 (423 letters) >NCBI__GCF_003194585.1:WP_110205831.1 Length = 396 Score = 226 bits (577), Expect = 7e-64 Identities = 156/408 (38%), Positives = 210/408 (51%), Gaps = 47/408 (11%) Query: 13 TLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLE 72 T TPR V + E AT+WD +G Y D GIAV GH HP +++A+ QL Sbjct: 18 TFGTPRLV-------LAKGEGATVWDADGNEYLDLLGGIAVNLLGHAHPALIEAVTQQLG 70 Query: 73 RFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKIARAHTGRPGV 132 H + V LAER+ AL+ G + L +G EA E A KI R TGR V Sbjct: 71 TLGHVS-NFFTSGPQVELAERLLALLGQDG--RVFLSNSGTEANEAAFKITR-RTGRTHV 126 Query: 133 IAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQALEGLF 192 +A G FHGRT+ +ALT K A Y+ F P P D+ P+ A ALE Sbjct: 127 VATEGGFHGRTMGALALTSKAA-YRDPFAPLPGDVTFVPYGDAA----------ALEAAV 175 Query: 193 KTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKM 252 TD + AA+++EP+QGE G P+D++ +R + +HG ++ DE+QTG GRTG+ Sbjct: 176 -TD----QTAAVVLEPIQGEAGVNVPPSDYLARVREITSRHGALMWLDEIQTGVGRTGRW 230 Query: 253 FAMSH-----HDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVA 307 FA H V PDLIT+AK L GG+P+ A A D PG G T+ GNP+A A Sbjct: 231 FAHQHPGLAPEPVTPDLITLAKGLGGGLPIGATIALGAAGDLLQPGQHGTTFGGNPVATA 290 Query: 308 AAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCDPATGQ 367 AA AV+ V EEE L R+ +LG++LR L P ++EVRGLG ++ + Sbjct: 291 AALAVLRVAEEESLLARAEALGERLRAGLAD-----PRVSEVRGLGLLIGLDL------- 338 Query: 368 PSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALA 415 + E + V AL AG ++ + IR PL + AQ D LA Sbjct: 339 -AQERSAEVAAAALGAGFIINNPTPHR--IRLAPPLVLTDAQADRFLA 383 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: 445 Number of extensions: 19 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: 423 Length of database: 396 Length adjustment: 31 Effective length of query: 392 Effective length of database: 365 Effective search space: 143080 Effective search space used: 143080 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 24 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