Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_027489558.1 LRK54_RS06590 acetylornithine/succinylornithine family transaminase
Query= BRENDA::O30508 (406 letters) >NCBI__GCF_021560695.1:WP_027489558.1 Length = 408 Score = 387 bits (995), Expect = e-112 Identities = 201/395 (50%), Positives = 266/395 (67%), Gaps = 3/395 (0%) Query: 15 RYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRI 74 RY +P Y P + G+G+RVWD GR+ +DF GIAV +LGH P L+ AL QA ++ Sbjct: 14 RYWLPVYKPRELVLDHGKGARVWDTEGRDYVDFGAGIAVNALGHQDPDLLAALAAQAHKL 73 Query: 75 WHVSNVFTNEPALRLARKLVDAT-FAERVFLANSGAEANEAAFKLARRYAN-DVYGPQKY 132 WH SNVF EP LRLA +LV A+ FAERVFL NSGAEANEAA KL R++A P++ Sbjct: 74 WHSSNVFYTEPPLRLAEELVHASGFAERVFLCNSGAEANEAAIKLVRKWAAAQGRAPERR 133 Query: 133 EIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAIS-DKTCAVV 191 I+ + SFHGRTL TV Q KY G+ P EG ++ +ND EAL+A + AV+ Sbjct: 134 VIVTFNGSFHGRTLATVTATAQAKYQQGYEPLPEGFRYLDFNDAEALEATFAAGDVAAVM 193 Query: 192 LEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDIL 251 LEP+QGEGGVLPA +L+ R+LCD+H+ALLV DE+Q GMGR G LFA++H VVPDI+ Sbjct: 194 LEPVQGEGGVLPAAPGFLKRVRELCDQHDALLVLDEIQCGMGRTGTLFAHVHDHVVPDIV 253 Query: 252 SSAKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGV 311 + AK+LGGGFPIGAML ++A+ + G HGTT+GGNP+A+AVA AL +++P VL V Sbjct: 254 TLAKALGGGFPIGAMLAGPKVAEVMQYGAHGTTFGGNPMAAAVARVALAKLSSPAVLMNV 313 Query: 312 KAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQA 371 + + ++ L +I E +F E+RG GL+IGA L D +KGKA VL+ A +++LQA Sbjct: 314 ERQANDLRAGLARINHELQLFAEVRGRGLMIGAVLADAYKGKAGAVLDHAATRGLLLLQA 373 Query: 372 SPDVVRFAPSLVIDDAEIDEGLERFERAVAKLVRG 406 PDV+RF P L I D E+ +GL R A++ G Sbjct: 374 GPDVLRFVPPLTITDEELADGLARLHAALSDFAAG 408 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: 470 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: 408 Length adjustment: 31 Effective length of query: 375 Effective length of database: 377 Effective search space: 141375 Effective search space used: 141375 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 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