Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_014450272.1 LFE_RS10875 aspartate aminotransferase family protein
Query= BRENDA::O30508 (406 letters) >NCBI__GCF_000284315.1:WP_014450272.1 Length = 413 Score = 293 bits (750), Expect = 6e-84 Identities = 161/393 (40%), Positives = 247/393 (62%), Gaps = 13/393 (3%) Query: 15 RYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRI 74 R ++ NY+ + + +G+GS ++D G +DF GGIA+ LGH++P++V A+ +QAQR+ Sbjct: 23 RVLLGNYSRESLVFEKGKGSFLFDTRGDGYLDFLGGIAIHVLGHSYPSIVHAIQKQAQRV 82 Query: 75 WHVSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEI 134 H SN++ N PA+ LA LV+ TFA+RVF +NSG EA EAA KLARR+ N ++EI Sbjct: 83 THTSNLYYNIPAIELAEMLVEKTFADRVFFSNSGTEAIEAALKLARRFGNP---RGRFEI 139 Query: 135 IAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDKTCAVVLEP 194 I+ NSFHGRTL + + GQ K +GFGP EG ++ YND++ + + +D+T AVV+EP Sbjct: 140 ISMENSFHGRTLGAMTMTGQQKVREGFGPLPEGFSYARYNDMDHVISQKTDRTVAVVVEP 199 Query: 195 IQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSSA 254 +QGE GV+PA + ++ R + LL+ DE+Q+GMGR G LFA+ YG+VPDIL ++ Sbjct: 200 VQGEIGVIPATKEFMRDLRHWTHQEGILLILDEIQTGMGRTGALFAHELYGIVPDILVAS 259 Query: 255 KSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLD---GV 311 K+LGGG P+GA+LTT ++ L G+HG+T+GGNP++ A A L + + L GV Sbjct: 260 KALGGGLPLGALLTTEHLSTFLPPGSHGSTFGGNPVSCAAGLALLKSLYDEDFLPTRIGV 319 Query: 312 KAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMV--L 369 + + +K + + G EIRG G ++G ++ A+++ N + V+V Sbjct: 320 MSDY-LWKGLSELSSRHKGKILEIRGFGFMVGVRVS----SSAKEMKNQFLESHVLVNAT 374 Query: 370 QASPDVVRFAPSLVIDDAEIDEGLERFERAVAK 402 S DVVR P + + E+D+ L F+R + + Sbjct: 375 GLSDDVVRLLPPVSVGYDEMDQFLNVFDRILER 407 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: 427 Number of extensions: 18 Number of successful extensions: 4 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: 413 Length adjustment: 31 Effective length of query: 375 Effective length of database: 382 Effective search space: 143250 Effective search space used: 143250 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 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