Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_083763404.1 AMB_RS01605 aspartate aminotransferase family protein
Query= BRENDA::O30508 (406 letters) >NCBI__GCF_000009985.1:WP_083763404.1 Length = 384 Score = 338 bits (866), Expect = 2e-97 Identities = 170/383 (44%), Positives = 246/383 (64%), Gaps = 5/383 (1%) Query: 18 VPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWHV 77 +P YA A RGEG+ ++ GR +DFA G+AV +LGH HP LVKALT QA ++WH Sbjct: 1 MPTYARADLAFERGEGAYLFTADGRRYLDFAAGVAVNALGHCHPRLVKALTAQAAKVWHT 60 Query: 78 SNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAA 137 SN++ +A KLV+ +FA+ VF NSGAEA E + K+ARR+ PQ+Y II A Sbjct: 61 SNLYRVAGQESVAAKLVERSFADTVFFCNSGAEALECSIKMARRHHFAAGNPQRYRIICA 120 Query: 138 SNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDKTCAVVLEPIQG 197 +FHGRTL TV GGQ K+ +GF P +G HVPY +L AL+A+I+++T A+++EP+QG Sbjct: 121 EGAFHGRTLATVAAGGQKKHLEGFAPAVDGFDHVPYGNLNALRASITEETAAILVEPVQG 180 Query: 198 EGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSSAKSL 257 EGG++P YL R DE LL+FDEVQ+GMGR G LFA+ G+ PDI+ AK L Sbjct: 181 EGGIVPGDPDYLRRLRATADEFGLLLIFDEVQTGMGRTGTLFAHEQAGIAPDIMGVAKGL 240 Query: 258 GGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKAKHER 317 GGGFP+GA L T + A + GTHG+T+GGNPLA AVA LD++ P L+ V+A Sbjct: 241 GGGFPVGACLATTKAASGMVPGTHGSTFGGNPLAMAVAGEVLDIMAEPGFLEHVQAMAAL 300 Query: 318 FKSRLQKIGQEY-GIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQASPDVV 376 +S+++ + G+ +E+RG+GL++G + + +++ + ++ + A ++V Sbjct: 301 LRSKVEDTAARFPGVVEEVRGLGLMLGI----KPRMPNTEMVARLAEGGLLTVGAGDNIV 356 Query: 377 RFAPSLVIDDAEIDEGLERFERA 399 R P L+I+DA++DE + RA Sbjct: 357 RLLPPLIINDAQVDEAVGILARA 379 Lambda K H 0.318 0.135 0.394 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: 438 Number of extensions: 17 Number of successful extensions: 3 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: 384 Length adjustment: 31 Effective length of query: 375 Effective length of database: 353 Effective search space: 132375 Effective search space used: 132375 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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