Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 200475 SO1300 glutamate-1-semialdehyde-2,1-aminomutase (NCBI ptt file)
Query= BRENDA::A0A140N9B6 (406 letters) >FitnessBrowser__MR1:200475 Length = 430 Score = 141 bits (356), Expect = 3e-38 Identities = 102/336 (30%), Positives = 163/336 (48%), Gaps = 27/336 (8%) Query: 21 APFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGN--GY 78 +P + +G+ ++D GK YID+ G LGH HP++REA+ H G G Sbjct: 32 SPLFIEKADGAYIYDADGKAYIDYVGSWGPMILGHNHPKIREAVLAAV----HNGLSFGA 87 Query: 79 TNEPVLRLAKKLIDATFA-DRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNA 137 E +++A+K+I + ++V +SG EA +A++LAR F +++ I+ F+ Sbjct: 88 PTELEVQMAEKVIAMVPSIEQVRMVSSGTEATMSAIRLARGF------TNRDKILKFEGC 141 Query: 138 FHGRT--LFTVSAGGQPAYSQDFAP-LPADI-RH---AAYNDINSASALIDD---STCAV 187 +HG L + G Q +P +P D +H A YND++S +L + + Sbjct: 142 YHGHADCLLVKAGSGALTLGQPSSPGIPEDFAKHTLTAVYNDLDSVRSLFEQYPTEISCI 201 Query: 188 IVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDL 247 I+EP+ G +P FL+GLR LC+ ALLI DEV TG R + A HYGVTPDL Sbjct: 202 IIEPVAGNMNCIPPIPGFLEGLRSLCDEFGALLIIDEVMTGF-RVSKSGAQGHYGVTPDL 260 Query: 248 LTTAKALGGGFPVGALLATEECAR-VMTVGT--HGTTYGGNPLASAVAGKVLELINTPEM 304 T K +GGG PVGA ++ + + G T GNP+A + +E + + Sbjct: 261 TTLGKVIGGGMPVGAFGGRKDVMQFIAPTGPVYQAGTLSGNPIAMSAGLAQMEALCEEGL 320 Query: 305 LNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIG 340 + + E ++G+ + +G + G Sbjct: 321 YEALSAKTKRIAEGFKAAADKHGIPMAINYVGGMFG 356 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: 422 Number of extensions: 24 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: 430 Length adjustment: 32 Effective length of query: 374 Effective length of database: 398 Effective search space: 148852 Effective search space used: 148852 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