Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_007736227.1 C1M55_RS16390 acetylornithine transaminase
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_002893965.1:WP_007736227.1 Length = 399 Score = 228 bits (580), Expect = 3e-64 Identities = 148/422 (35%), Positives = 216/422 (51%), Gaps = 45/422 (10%) Query: 8 LLKRRQAAVPRGVGQIHPVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAV 67 L +R A++ G + V R + + + D +G++Y+DF GIAV GH HP V+ AV Sbjct: 6 LQQRWSASLMNNYG-VPRVALVRGDGAVLTDADGKQYVDFLAGIAVNILGHGHPAVVEAV 64 Query: 68 QEQLGKLSHTCFQVLAYEPYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARAAT 127 QL L H + A EP +ELAE++ + G+ + SG+EA E A K+ARA T Sbjct: 65 TTQLSTLGHVS-NLYASEPVVELAEQLLAHL-GNVTGRAFFCNSGTEANEAAFKLARA-T 121 Query: 128 GRAGVIAFTGAYHGRTMMTLGLTGKVV------PYSAGMGLMPGGIFRALAPCELHGVSE 181 GR +IA G++HGRTM L LTG+ P AG+ +P G AL Sbjct: 122 GRKKIIAAEGSFHGRTMGALALTGQPAKRAPFEPMPAGVEFVPYGDVEAL---------- 171 Query: 182 DDSIASIERIFKNDAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADE 241 A D AA+ +EP+ GEGG V + ++ R + + G LL+ DE Sbjct: 172 ------------EQAVDSDTAAVFLEPIMGEGGVVVPPEGYLVEARRITAERGALLVLDE 219 Query: 242 VQTGAGRTGTFFATEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAG 301 VQTG GRTG F+A + +GIVPD+ T AK +GGG PI + PG G T+ G Sbjct: 220 VQTGIGRTGWFYAHQAVGIVPDVITLAKGLGGGMPIGACIATGATAELFGPGKHGTTFGG 279 Query: 302 SPIACAAALAVLKVFEEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELF 361 +P+ AAALAVLK E L+ R+ ++G+ + AG+ ++ H ++ VRG G ++ + L Sbjct: 280 NPVCAAAALAVLKTIAAEDLISRADSLGKSISAGIEDL--GHPLVDYVRGSGLLLGVVLT 337 Query: 362 EGGDTHKPAAELVSKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAEC 421 E ++ + ARE G ++ + VIR P+ + D Q E +A L Sbjct: 338 E---------DVAPAVENAAREAGYLVNAAQP--GVIRLAPPLILTDEQAETFVAALPAI 386 Query: 422 FD 423 FD Sbjct: 387 FD 388 Lambda K H 0.319 0.137 0.393 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: 410 Number of extensions: 21 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: 426 Length of database: 399 Length adjustment: 31 Effective length of query: 395 Effective length of database: 368 Effective search space: 145360 Effective search space used: 145360 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 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