Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_028584210.1 G494_RS0108610 aspartate aminotransferase family protein
Query= BRENDA::O30508 (406 letters) >NCBI__GCF_000429965.1:WP_028584210.1 Length = 398 Score = 353 bits (907), Expect = e-102 Identities = 182/391 (46%), Positives = 249/391 (63%), Gaps = 5/391 (1%) Query: 14 DRYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQR 73 + V NY+ VRG+G R+WD+ GRE +DF GIAV SLGH HP + +A+ QA+ Sbjct: 11 EEVFVGNYSRFPATMVRGQGCRLWDEDGREYLDFLAGIAVCSLGHCHPRVTEAVVAQARS 70 Query: 74 IWHVSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYE 133 + HVSN+F P + LA L TFA+RVF+ANSGAE NEAA KLAR ++ G +YE Sbjct: 71 LVHVSNLFHTRPQIELAELLTANTFADRVFMANSGAEVNEAAIKLARIHS----GEGRYE 126 Query: 134 IIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDKTCAVVLE 193 II+ + SFHGRTL TV QPK+ GF P +G + PY D ++ I D+TCA++ E Sbjct: 127 IISLTGSFHGRTLATVAATAQPKFHQGFEPMPQGFRYAPYGDPGEVEQLIGDQTCAILCE 186 Query: 194 PIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSS 253 P+QGEGGVLP YL+ R LCD+H LL+FDE+Q+GMGR G LFAY GVVPDI++S Sbjct: 187 PLQGEGGVLPLGNEYLQALRDLCDQHGLLLIFDEIQTGMGRTGTLFAYEQTGVVPDIMTS 246 Query: 254 AKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKA 313 AK+L G P+GA+LTT EIA L GTHG+T+GGNP+A+A A A L+ + P L+GV+ Sbjct: 247 AKALANGLPLGALLTTDEIAASLVPGTHGSTFGGNPVAAAAAVAVLEEMLAPGFLEGVQQ 306 Query: 314 KHERFKSRLQKIGQEYGIF-DEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQAS 372 F +L ++ + + +RG GLL+G LT+E +++ +++ A Sbjct: 307 TGAYFSGKLNELAARFPVLASGVRGQGLLLGLILTEEGIAHGGEIVQRLFGRGMVINFAG 366 Query: 373 PDVVRFAPSLVIDDAEIDEGLERFERAVAKL 403 V+RFAP LV+ AEID+ + +A+L Sbjct: 367 NTVLRFAPPLVVSRAEIDQLIAELAEVLAEL 397 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: 457 Number of extensions: 21 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: 398 Length adjustment: 31 Effective length of query: 375 Effective length of database: 367 Effective search space: 137625 Effective search space used: 137625 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 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