Align N-succinylornithine aminotransferase (EC 2.6.1.81) (characterized)
to candidate 3609962 Dshi_3343 aminotransferase class-III (RefSeq)
Query= reanno::Btheta:353284 (373 letters) >FitnessBrowser__Dino:3609962 Length = 413 Score = 163 bits (413), Expect = 7e-45 Identities = 125/398 (31%), Positives = 197/398 (49%), Gaps = 53/398 (13%) Query: 5 DVYPLYD--INIVKGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATLGF 62 +V YD ++IV+G+G +WD G YLD Y V +GH HP V+ I+ Q L Sbjct: 15 NVPTFYDPPLHIVRGEGVWLWDAGGRRYLDCYNN--VPHVGHCHPRVVDAIARQARVL-- 70 Query: 63 YSNSVINKLQQQVAERLGKISGYEDYSL---FLINSGAEANENALKLASFYNGRTKVISF 119 N+ L + V + + +++G D L L+ +G+EA + AL++A G+T +I+ Sbjct: 71 --NTHTRYLHEGVLDYIERLTGTMDNGLDQALLVCTGSEAVDVALRMARAATGKTGLIAT 128 Query: 120 SKAFHGRTSLAVE-ATNNPTIIAPINN-NGHVTYLPLNDI-------------EAMKQEL 164 +HG T+ + +T P PI + HV +P + A + E Sbjct: 129 DNTYHGNTTAVAQLSTRRP----PIGGYSDHVRLVPAPEPGTDGAAFGAHVARAAAELET 184 Query: 165 AKGDVCAVIIEGIQGVGGIKIPTTEFMQELRKVCTETGTILILDEIQSGYGRSGK-FFAH 223 A V A+I+ I G+ F++ G +LI DE+Q G+GR G F+ + Sbjct: 185 AGHGVAALIVCPIFANEGLPCLPRGFLEPAVAALRTRGGLLISDEVQPGFGRLGDVFWGY 244 Query: 224 QYNHIQPDIITVAKGIGNGFPMAGVL----ISPMFKPVYGQLGTTFGGNHLACSAALAVM 279 Q I PD++T+ K +GNG+P+AGV+ I F+ +G T FGG+ +A +AA+AV+ Sbjct: 245 QALGIAPDVVTLGKSMGNGYPVAGVVARTEIMGAFREAFGYFNT-FGGSPVAAAAAMAVL 303 Query: 280 DVIEQDNLVENAKAVGDYLLEELK--KFPQIKEVRGRGLMIGLEFEEP------------ 325 DV+E + LVENAK VG Y LE L+ + P I VRG GL L+ + Sbjct: 304 DVLEDEGLVENAKRVGRYTLERLQALRHPAIDGVRGYGLAFALDLVDTDGAPNTALAAAV 363 Query: 326 IKELRSRLIYDEHVFTGASGTNVLRLLPPLCLSMEEAD 363 +E + R + + ++L++ PPL + E D Sbjct: 364 TEEAKRRSVLINRI---GRDMHILKIRPPLPFAPEHGD 398 Lambda K H 0.320 0.139 0.403 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: 335 Number of extensions: 20 Number of successful extensions: 7 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: 373 Length of database: 413 Length adjustment: 31 Effective length of query: 342 Effective length of database: 382 Effective search space: 130644 Effective search space used: 130644 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 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