Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate BWI76_RS24630 BWI76_RS24630 putrescine aminotransferase
Query= SwissProt::Q8ZPV2 (408 letters) >FitnessBrowser__Koxy:BWI76_RS24630 Length = 468 Score = 209 bits (532), Expect = 1e-58 Identities = 142/385 (36%), Positives = 202/385 (52%), Gaps = 23/385 (5%) Query: 33 LWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWHIGNGYTNEPALRLAKKLID 92 L D QG+E+ID GG + +GH +P + A+ Q + + LAK L Sbjct: 85 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVENQLAKQPLHSQELLDPLRAMLAKTLAA 144 Query: 93 ATFAERV--FFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNAFHGRTLFTVSAGG 150 T + FF NSG E+ EAALKLA+ Y R K VA AFHG++L +SA Sbjct: 145 LTPGKLKYSFFSNSGTESVEAALKLAKAYQSPR---GKFTFVATSGAFHGKSLGALSATA 201 Query: 151 QPTYSQDFAPLPPDIRHAAYNDLNSASALID------DNTCAVIVEPVQGEGGVIPATKA 204 + T+ + F PL P RH + D+N+ L+ D+ AVI+EP+QGEGGVI Sbjct: 202 KSTFRKPFMPLLPGFRHVPFGDINAMRTLLSECKKTGDDVAAVILEPIQGEGGVILPPPG 261 Query: 205 FLQGLRELCDRHQALLIFDEVQTGVGRTGELYAYMHYGVTPDILTTAKALGGG-FPIGAM 263 +L +R+LCD ALLI DEVQTG+GRTG+++A H V PDIL AKALGGG PIGA Sbjct: 262 YLPAVRKLCDEFGALLILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGAT 321 Query: 264 LTTQDYASVM--TPGTHGTTYGGNPLATAVAGKVLDIINTPEMQNGVRQRHDAFIERLNT 321 + T++ SV+ P H TT+GGNPLA A A ++++ T + Q+ D ++ Sbjct: 322 IATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLTQNLPAQAEQKGDMLLDGFRQ 381 Query: 322 LNVRF-GMFSEIRGLGLLLGCVLQTEFAG---KAKLIAQEAAKAGVMVLIAGGDVVRFAP 377 L + + +E+RG G+L+ G +++ Q AG + +R P Sbjct: 382 LAREYPDLVNEVRGKGMLMAIEFVDNEIGYDFASEMFRQRVLVAGT---LNNARTIRVEP 438 Query: 378 ALNVSDEEIATGLD--RFALACERL 400 L ++ E+ L R ALA R+ Sbjct: 439 PLTLTLEQCEQVLKAARLALAALRV 463 Lambda K H 0.320 0.137 0.413 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: 514 Number of extensions: 25 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: 408 Length of database: 468 Length adjustment: 32 Effective length of query: 376 Effective length of database: 436 Effective search space: 163936 Effective search space used: 163936 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: 51 (24.3 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