Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate N515DRAFT_3307 N515DRAFT_3307 glutamate-1-semialdehyde 2,1-aminomutase
Query= BRENDA::A0A140N9B6 (406 letters) >FitnessBrowser__Dyella79:N515DRAFT_3307 Length = 426 Score = 155 bits (393), Expect = 2e-42 Identities = 115/334 (34%), Positives = 156/334 (46%), Gaps = 25/334 (7%) Query: 22 PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTNE 81 PF R +G+ LWD +GK YID+ G +GH HP +REA+ G E Sbjct: 32 PFFTARADGAYLWDVEGKRYIDYVGSWGPMIVGHNHPRVREAVERAVKDGLSFGTPCPAE 91 Query: 82 PVL-RLAKKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNAFHG 140 + +L+ + D V NSG EA +A++LAR + +S IV F+ +HG Sbjct: 92 ITMAETITRLVPSV--DMVRMVNSGTEATMSAIRLARG------ATGRSKIVKFEGCYHG 143 Query: 141 R-TLFTVSAG------GQPAYSQDFAPLPADIRHA-AYNDINSASALIDD---STCAVIV 189 F V AG G P S AD+ AYND+ +A AL + +I+ Sbjct: 144 HGDSFLVKAGSGALTFGVPT-SPGVPKAAADLTLTLAYNDLAAAEALFAEHGADIAGLII 202 Query: 190 EPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLT 249 EP+ G +P + +LQGLR LC RH ALLIFDEV TG R A HYG+TPDL T Sbjct: 203 EPVAGNMNCIPPKDGYLQGLRALCTRHGALLIFDEVMTGF-RVALGGAQAHYGITPDLST 261 Query: 250 TAKALGGGFPVGALLATEE-CARVMTVGT--HGTTYGGNPLASAVAGKVLELINTPEMLN 306 K +GGG PVGA E ++ G T GNP+A A +LELI + Sbjct: 262 FGKIIGGGMPVGAYGGRRELMEQIAPAGPIYQAGTLSGNPVAMAAGLAMLELIQEAGFYD 321 Query: 307 GVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIG 340 + R + L + G+ +G + G Sbjct: 322 RLAARTRLLADGLQAVADGEGVPFSTNRVGAMFG 355 Lambda K H 0.319 0.135 0.406 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: 442 Number of extensions: 20 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 406 Length of database: 426 Length adjustment: 31 Effective length of query: 375 Effective length of database: 395 Effective search space: 148125 Effective search space used: 148125 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 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