Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate SMc02138 SMc02138 acetylornithine transaminase
Query= reanno::WCS417:GFF4238 (406 letters) >FitnessBrowser__Smeli:SMc02138 Length = 399 Score = 337 bits (863), Expect = 5e-97 Identities = 176/376 (46%), Positives = 241/376 (64%), Gaps = 5/376 (1%) Query: 30 RGEGSRVWDQAGRELIDFAGGIAVNVLGHAHPALVGALTEQAHKLWHVSNVFTNEPALRL 89 RGEG + + G +DFA G+AVN LGHAHP LV AL QA K+WH+SN++ L Sbjct: 20 RGEGVWLIAEDGTRYLDFAAGVAVNSLGHAHPHLVEALKAQADKVWHLSNLYEIAGQESL 79 Query: 90 AHKLIDATFAERVFFCNSGAEANEAAFKLARRVAFDRFGSEKYEIIAALNSFHGRTLFTV 149 A +L TFA+RVFF NSGAEA E A K ARR F + EK+ +I +FHGRTL T+ Sbjct: 80 ARRLTQVTFADRVFFTNSGAEALECAIKTARRYHFAKGHVEKFHVITFEGAFHGRTLATI 139 Query: 150 NVGGQSKYSDGFGPKITGITHVPYNDLDALKAAVSDKTCAVVLEPIQGEGGVLPAELAYL 209 GGQ KY +GFGPK G VP+ D+ A+K A++++T A+++EPIQGEGG+ A ++ Sbjct: 140 AAGGQQKYIEGFGPKAPGFYQVPFGDIGAVKNAINEETAAILVEPIQGEGGIRTASKEFM 199 Query: 210 QGARDLCDANNALLVFDEVQTGMGRSGHLFAYQHYGVTPDILTSAKSLGGGFPIAAMLTT 269 QG R+LCD LL+ DEVQ+G+GR+G LFA++ G+ PDI+ AK +GGGFP+ A L T Sbjct: 200 QGLRELCDEFGLLLILDEVQSGVGRTGKLFAHEWAGIKPDIMAVAKGIGGGFPLGACLAT 259 Query: 270 EALAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLAGVNAKHDLFKARLEQIGKQY 329 EA A +V GTHG+TYGGNPLA AV AV+DV+ L V +F+ L + ++ Sbjct: 260 EAAAAGMVAGTHGSTYGGNPLAMAVGNAVLDVVLAEGFLDQVREVALVFRQGLASLKDRF 319 Query: 330 -GIFTEVRGMGLLLGCVLSDAFKGKAKDVFNAAEKENLMILQAGPDVVRFAPSLVVEDAD 388 + E+RG GL+LG K + D+ A E L+++ AG +V+R P L+ A+ Sbjct: 320 PDVIEEIRGDGLMLGI----KAKVPSADLLKAIRAEKLLVVPAGENVLRLLPPLITTPAE 375 Query: 389 IKEGLDRFERAVKALT 404 +EGL R ERA +A++ Sbjct: 376 AREGLARLERAAEAVS 391 Lambda K H 0.320 0.137 0.400 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: 444 Number of extensions: 15 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: 399 Length adjustment: 31 Effective length of query: 375 Effective length of database: 368 Effective search space: 138000 Effective search space used: 138000 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 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