Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_073039302.1 BUB04_RS11050 acetylornithine transaminase
Query= BRENDA::A0A140N9B6 (406 letters) >NCBI__GCF_900129305.1:WP_073039302.1 Length = 397 Score = 341 bits (875), Expect = 2e-98 Identities = 175/370 (47%), Positives = 236/370 (63%), Gaps = 5/370 (1%) Query: 18 YASAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNG 77 YA P RG G RLWD +GKEY+DF GIAV LGH+HPE+ + EQA K H N Sbjct: 16 YARYPVAFERGAGCRLWDTEGKEYMDFLAGIAVCNLGHSHPEVARVVCEQARKLVHVSNL 75 Query: 78 YTNEPVLRLAKKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNA 137 + P + LA +LI+ +FAD+VFF NSGAEANEAA+KLARK++ D+YG + I+ K++ Sbjct: 76 FYTRPQVELAARLIERSFADKVFFANSGAEANEAAIKLARKYSRDKYGPGRFHIITMKDS 135 Query: 138 FHGRTLFTVSAGGQPAYSQDFAPLPADIRHAAYNDINSASALIDDSTCAVIVEPIQGEGG 197 FHGRTL T+SA GQ + F PL R YN I + + + TCAV+VEPIQGEGG Sbjct: 136 FHGRTLATLSATGQEKVHKGFDPLVEGFRFVPYNSIQAVEEAVTEKTCAVLVEPIQGEGG 195 Query: 198 VVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLTTAKALGGG 257 V P + + LRELC + LLIFDEVQTG+GRTG L+AY GVTPD++T AKALG G Sbjct: 196 VRPGDPDYFRALRELCTAKDLLLIFDEVQTGMGRTGSLFAYEQLGVTPDVMTLAKALGNG 255 Query: 258 FPVGALLATEECARVMTVGTHGTTYGGNPLASAVAGKVLELINTPEMLNGVKQRHDWFVE 317 P+GA+LATEE AR T G+H +T+GG PL +A + KVLE+I+ + L V+++ +F+ Sbjct: 256 LPIGAMLATEEAARAFTPGSHASTFGGTPLVTAASAKVLEIISKEDFLADVREKGRYFLG 315 Query: 318 RLNTINHRY-GLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAKAGVMVLIAGGNVVRFA 376 RL + ++ + RG GL++G L+ K + + G ++ V+RF Sbjct: 316 RLQDLQKKHPDKILDARGRGLMLGLELSR----PGKTVVDRCLEQGFVINCTHDTVLRFV 371 Query: 377 PALNVSEEEV 386 P L V+ EE+ Sbjct: 372 PPLIVTREEI 381 Lambda K H 0.319 0.135 0.406 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: 420 Number of extensions: 16 Number of successful extensions: 2 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: 406 Length of database: 397 Length adjustment: 31 Effective length of query: 375 Effective length of database: 366 Effective search space: 137250 Effective search space used: 137250 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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