Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_090271605.1 BLU11_RS00885 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= reanno::WCS417:GFF4238 (406 letters) >NCBI__GCF_900105005.1:WP_090271605.1 Length = 417 Score = 217 bits (553), Expect = 4e-61 Identities = 130/401 (32%), Positives = 210/401 (52%), Gaps = 36/401 (8%) Query: 30 RGEGSRVWDQAGRELIDFAGGIAVNVLGHAHPALVGALTEQAHKLWHVS-NVFTNEPALR 88 RGEG + G+ +DF GI V GH HP +V A EQ KL H T++P L Sbjct: 18 RGEGCWLIANDGKSYLDFTAGIGVTSTGHCHPTVVAAAREQVGKLIHAQYTTVTHQPMLD 77 Query: 89 LAHKLIDAT--FAERVFFCNSGAEANEAAFKLARRVAFDRFGSEKYEIIAALNSFHGRTL 146 LA +L+ + V F N+G+EA E A +LAR + + +I FHGRT+ Sbjct: 78 LAERLVGKMPDGIDSVAFSNAGSEAVEMALRLARHA------TRRANVIVFNGGFHGRTM 131 Query: 147 FTVNVGGQ-SKYSDGFGPKITGITHVPYN------------------DLDAL--KAAVSD 185 ++ +K + + P + G+ P+ +LD + + Sbjct: 132 GAASMTTSGTKVRNAYHPMMAGVVVAPFPHSWRYGWSEEEATRFCLAELDHILKTQTAPE 191 Query: 186 KTCAVVLEPIQGEGGVLPAELAYLQGARDLCDANNALLVFDEVQTGMGRSGHLFAYQHYG 245 T A+V+EP+QGE G P A++QG + C + LLV DE+Q G GRSG +++QH+G Sbjct: 192 DTAAMVIEPVQGEFGYYPGNSAFMQGLAERCKQHGILLVCDEIQAGFGRSGKFWSHQHFG 251 Query: 246 VTPDILTSAKSLGGGFPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTP 305 +TPDI+ +AK L GFP++AM ++ L + G+ G TYG N ++CA A A + V++ Sbjct: 252 ITPDIVITAKGLASGFPLSAMAASQTLMAKGLAGSQGGTYGANAVSCAAALATLRVMDNE 311 Query: 306 EVLAGVNAKHDLFKARLEQIGKQYGIFTEVRGMGLLLGCVLSDA----FKGKAKDVFNAA 361 ++A A+ L+ + +QY ++RG GL+LG ++ + A + A+ Sbjct: 312 NLVANAAARGQQLWDHLQILRQQYPQLADLRGKGLMLGLEIAQSPDKPLADLAASLTTAS 371 Query: 362 EKENLMILQAGPD--VVRFAPSLVVEDADIKEGLDRFERAV 400 E+E L++L+ G D ++R+ P LVV +A++ + + RF R + Sbjct: 372 EEEGLLLLRCGTDSQIIRWLPPLVVSEAEVDDAVQRFTRVL 412 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: 372 Number of extensions: 17 Number of successful extensions: 6 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: 417 Length adjustment: 31 Effective length of query: 375 Effective length of database: 386 Effective search space: 144750 Effective search space used: 144750 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 24 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