Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate N515DRAFT_0006 N515DRAFT_0006 aspartate aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >FitnessBrowser__Dyella79:N515DRAFT_0006 Length = 399 Score = 181 bits (460), Expect = 2e-50 Identities = 122/389 (31%), Positives = 188/389 (48%), Gaps = 15/389 (3%) Query: 8 QRLGTE--SAFSVLAE-AKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGHHGYV 64 QR+G SA V+AE A++L+A G+ +I +G P+F HV +AA++AL Y Sbjct: 6 QRVGRAKPSAIMVIAEKARQLKAAGRDIISFSIGVPNFLPGDHVYEAAREALKHDSGQYG 65 Query: 65 LSNGILECRQAVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHPTPAF 124 + G A R I+ L + I G K +Y + + G EI P + Sbjct: 66 SNRGAEPLLDAFLRHIEALGFSGYGRMNLSIGIGAKQVLYNLAEAMLDEGDEICFAAPYW 125 Query: 125 PIYESMINYTGSTPVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFVEKSA 184 Y + + G+ +++ K P ++ + + K ++ + NP+NPTG + Sbjct: 126 TTYHDIADIVGAKANVLHCGPEQNYKLVPAQLEAALQRKPKVFLFNNPSNPTGMVYTREE 185 Query: 185 IDVLAEGLKKHPHVAILSDEIYSRQIYDGKEMPTF-FNYPDLQDRLIVLDGWSKAYAMTG 243 I LA+ L K+P I++D+IY+ ++DG F F P+L++RL+ +D SK Y M G Sbjct: 186 IAALADVLVKYPDTWIVTDDIYNSMVFDGIGYHNFVFAQPELRERLVFVDSVSKTYGMPG 245 Query: 244 WRMGWSVWPEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQRRKLI 303 WR+G PE + V L N ++ V A +AA GP D +F +R ++ Sbjct: 246 WRVGLIAGPESVAKAVTTLNSNHITSVPEVITAAAVAAFGGPQDVPRAKCEEFAGKRDVV 305 Query: 304 HEGLNSLPGVECSLPGGAFYAFPKVI--------GTGM-NGSEFAKKCMHEAGVAIVPGT 354 E L ++PGV C P GAFYAFP + GT + N EF + GVA VPG+ Sbjct: 306 FEALTAIPGVVCPRPQGAFYAFPDISVAFGKSHQGTKISNDVEFCAALLEATGVACVPGS 365 Query: 355 AFGKTCQDYVRFSYAASQDNISNALENIK 383 AFG+ +R SY + LE I+ Sbjct: 366 AFGE--PRAMRISYTCPTAQLKPGLERIQ 392 Lambda K H 0.319 0.137 0.414 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: 413 Number of extensions: 28 Number of successful extensions: 4 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: 387 Length of database: 399 Length adjustment: 31 Effective length of query: 356 Effective length of database: 368 Effective search space: 131008 Effective search space used: 131008 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 (21.7 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