Align succinylornithine transaminase; EC 2.6.1.81 (characterized)
to candidate Dsui_0664 Dsui_0664 glutamate-1-semialdehyde-2,1-aminomutase
Query= CharProtDB::CH_002469 (406 letters) >FitnessBrowser__PS:Dsui_0664 Length = 427 Score = 143 bits (360), Expect = 1e-38 Identities = 105/339 (30%), Positives = 159/339 (46%), Gaps = 23/339 (6%) Query: 21 APFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTN 80 AP RGEG R+WD +GK Y+D+ G LGHAH +A+ E A+ G Sbjct: 33 APRFFTRGEGPRVWDAEGKSYLDYVGSWGPLILGHAHAPTVKAVQEAAAL--GLSFGAPT 90 Query: 81 EPVLRLAKKLIDATFA-DRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNAFH 139 E + +A L D + D V +SG EA +A++LAR + + +V F+ +H Sbjct: 91 EAEIEIADLLCDILPSLDMVRLVSSGTEATMSAIRLARGH------TGRDLLVKFEGCYH 144 Query: 140 GRT---LFTVSAGGQPAYSQDFAPLPADI-RHAAYNDINSASALID------DSTCAVIV 189 G + L +G + +PAD+ +H + N+A L + AVIV Sbjct: 145 GHSDSLLVKAGSGLLTFGNPSSGGVPADVAKHTLVLEYNNAEQLAEAFAKQGSEIAAVIV 204 Query: 190 EPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLT 249 EP+ G ++ F+Q +RELC++H A+LIFDEV TG R G A +G+TPDL T Sbjct: 205 EPVAGNMNLIAPKPEFMQAMRELCSKHGAVLIFDEVMTGF-RVGPQCAQGLFGITPDLTT 263 Query: 250 TAKALGGGFPVGALLATEE-CARVMTVGT--HGTTYGGNPLASAVAGKVLELINTPEMLN 306 K +GGG PV A E ++ +G T GNP+A A L+ P + Sbjct: 264 LGKVIGGGMPVAAFGGKREIMEKIAPLGPVYQAGTLSGNPVAVAAGLVTLKATRAPGFYD 323 Query: 307 GVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNA 345 + R + L ++G+ + +G + G +A Sbjct: 324 SLAARTKQLTDGLTAAAKKHGVTFCAQSVGGMFGLYFSA 362 Lambda K H 0.319 0.136 0.407 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: 434 Number of extensions: 27 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: 406 Length of database: 427 Length adjustment: 31 Effective length of query: 375 Effective length of database: 396 Effective search space: 148500 Effective search space used: 148500 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 Aug 03 2021. The underlying query database was built on Aug 03 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