Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_013450014.1 SULKU_RS13855 aspartate aminotransferase family protein
Query= BRENDA::Q0K2K2 (423 letters) >NCBI__GCF_000183725.1:WP_013450014.1 Length = 388 Score = 176 bits (446), Expect = 1e-48 Identities = 129/403 (32%), Positives = 197/403 (48%), Gaps = 45/403 (11%) Query: 29 DRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFTHTA--YQIVPYQG 86 +R +NATL D EG+ Y DFAAG+AV + GH + R+ +AI+ Q + H + Y+I P + Sbjct: 18 ERGDNATLCDSEGKEYIDFAAGVAVCSVGHGNCRLARAISDQAAKILHVSNLYRIEPQE- 76 Query: 87 YVTLAERINALVPIQGLNKTALF-TTGAEAVENAIKIARAHTGRPG------VIAFSGAF 139 E +V + G + F +G EA E AIKIAR + R G +I +F Sbjct: 77 -----ECARRIVELSGYDMRCFFGNSGTEANEGAIKIARKYGERDGSIKRYKIITLENSF 131 Query: 140 HGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQALEGLFKTDIDPA 199 HGRT+ + TG+ + + FGP+P +A ++ +E L ID Sbjct: 132 HGRTITALKATGQASKHDY-FGPYPDGFVYAA------------NVEEIESL----IDET 174 Query: 200 RVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMSHHD 259 VA +++E VQGEGG Q ++ L A+ I+LI DEVQTG R G A ++ Sbjct: 175 TVA-VMIELVQGEGGVQPLDKQKVQNLSALLKSKDILLIVDEVQTGIYRCGSFLASHYYG 233 Query: 260 VEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVAAAHAVIDVIEEE 319 + PD+IT+AK L GG+P+ V R + + G G T+ GN L+ AA+ V+D++E Sbjct: 234 ITPDVITLAKGLGGGVPIGVVMTR--LKEIFSYGDHGSTFGGNYLSTVAANEVLDILEAY 291 Query: 320 KLCERSASLGQQLREHLLAQRKHCPAMAEVR-GLGSMVAAEFCDPATGQPSAEHAKRVQT 378 L + H P + R G+G M D +E ++ Sbjct: 292 NKSGEMMEHQNYFETSLKSFALHYPDIFTERVGIGMMQGLRVID-------SEVLSKIID 344 Query: 379 RALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQAL 421 A E G++++ G N +RF+ PLTI +++ D L A+ Sbjct: 345 SAFEIGVLVIKSGR--NTLRFVPPLTISKSEMDEGFRRLNSAM 385 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: 372 Number of extensions: 23 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: 388 Length adjustment: 31 Effective length of query: 392 Effective length of database: 357 Effective search space: 139944 Effective search space used: 139944 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