Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate H281DRAFT_00095 H281DRAFT_00095 beta-alanine--pyruvate transaminase
Query= SwissProt::P18335 (406 letters) >FitnessBrowser__Burk376:H281DRAFT_00095 Length = 443 Score = 161 bits (408), Expect = 3e-44 Identities = 121/397 (30%), Positives = 181/397 (45%), Gaps = 39/397 (9%) Query: 32 QGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHISNVFTNEP-ALRLG 90 +G G+ +D G+ GHC +V A++ Q + P A Sbjct: 36 KGMYYTSHDGRRILDGTAGLWCVNAGHCRDEIVAAVQAQAAEMDFAPTFQMGHPKAFEAA 95 Query: 91 RKLIEATFAE--RVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRSLFT 148 K+ T + + F+NSG+EA +TA K+A Y R +T+ I +HG Sbjct: 96 TKIARHTPGDLKHIFFVNSGSEAVDTALKIALAYHRSRGEGQRTRFIGRERGYHGVGFGG 155 Query: 149 VSVGGQPKYSDGF-GPKPADIIHVPF---------------------NDLHAVKAVMDDH 186 +SVGG F G I H+P ++L + A+ D Sbjct: 156 ISVGGIAPNRKAFSGALLPSIDHLPHTLNIKEAAYSKGQPAWGAHLADELERIVALHDAS 215 Query: 187 T-CAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYG 245 T AV+VEP+ G GV +LQ LRE+CD+H LL+FDEV G GR G FA ++G Sbjct: 216 TVAAVIVEPVAGSTGVLIPPQGYLQRLREICDKHGILLIFDEVITGWGRLGAPFAAQYFG 275 Query: 246 VTPDILTSAKAL-GGGFPISAMLTTAEIASAFHPGS-------HGSTYGGNPLACAVAGA 297 VTPD+LT AK P+ A+ + +I + G+ HG TY G+P+A A A A Sbjct: 276 VTPDLLTMAKGTNNAAAPMGAVAASGQIHDSIVNGAPGGIELFHGYTYSGHPIAAAAACA 335 Query: 298 AFDIINTPEVLEGIQAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAELKPQYKG---RA 354 D+ ++ + F + K+ + V D+R +GL+ G EL P+ RA Sbjct: 336 TIDLYEREQLFDQAARMAPLFERAIHKLRGERHVI-DVRNLGLVGGVELAPRDGAPGTRA 394 Query: 355 RDFLYAGAEAGVMVLNAGPDVMRFAPSLVVEDADIDE 391 D + GV+ G D++ F+P L++E+A IDE Sbjct: 395 YDVFVRCFQKGVLTRYTG-DILAFSPPLIIEEAQIDE 430 Lambda K H 0.322 0.138 0.415 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: 494 Number of extensions: 33 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: 406 Length of database: 443 Length adjustment: 32 Effective length of query: 374 Effective length of database: 411 Effective search space: 153714 Effective search space used: 153714 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 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