Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_067075818.1 MCUHO_RS07130 glutamate-1-semialdehyde 2,1-aminomutase
Query= BRENDA::B1A0U3 (469 letters) >NCBI__GCF_001602375.1:WP_067075818.1 Length = 415 Score = 118 bits (296), Expect = 3e-31 Identities = 100/320 (31%), Positives = 149/320 (46%), Gaps = 34/320 (10%) Query: 50 PLPIVFAHAKGSSVWDPEGNKYIDFLSGYSAVNQGHCHPKILKALHDQADRLTVSSRAFY 109 P P A GS + +G ID GY + GH HP I +A+ Q ++ + Y Sbjct: 27 PYPFYVERAAGSHLATVDGADLIDCCLGYGPLILGHAHPAIREAIERQLEKGWL-----Y 81 Query: 110 NDRFPVFAEYLTALFG----YDMVLPMNTGAEGVETALKLARKWGYEKKKIPNDEALIVS 165 P+ + + DMV +++G+E A++LAR GY K+ I+ Sbjct: 82 GTPTPLELDLAGIITSDHPAVDMVRFVSSGSEATMAAIRLAR--GYTGKQD------IIK 133 Query: 166 CCGCFNGRTLGVISMSCDNEATRG-------FGPLMPGHLKVDFGDAEAIERIFKEKGDR 218 G F+G V+ + T G L +V + D EA+E + D Sbjct: 134 VEGGFHGAHDAVLVKAGSGATTLGVPDSAGVLASLTAHTRQVPYNDTEALEALLAGNDD- 192 Query: 219 VAAFILEPIQGEAGVVIPPDGYLKAVRDLCSKYNVLMIADEIQTGLARTGKMLACDWEDV 278 VAAFILEPI G G V+P DGYL VR++ + ++VL+I DE+ TG R G A + Sbjct: 193 VAAFILEPIMGNVGPVLPDDGYLADVREITAAHDVLLILDEVITGY-RIGIGGAEVLYGI 251 Query: 279 RPDVVILGKALGGGILPVSAVLADKDVMLCIKPG---QHGSTFGGNPLASAVAIAALEVI 335 +PD+ GK +GGG LP+ A +++M + P TF GNP + A AAL + Sbjct: 252 KPDLATFGKIIGGG-LPIGAFGGRREIMELVAPAGPVYQAGTFSGNPASLAAGYAALRHL 310 Query: 336 KEE----RLTERSTKLGGEL 351 E R + +T+ GE+ Sbjct: 311 HEHPEIYRRLDDATRAIGEV 330 Lambda K H 0.319 0.137 0.409 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: 472 Number of extensions: 26 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: 469 Length of database: 415 Length adjustment: 32 Effective length of query: 437 Effective length of database: 383 Effective search space: 167371 Effective search space used: 167371 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: 51 (24.3 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