Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate 207114 DVU1655 aminotransferase, classes I and II
Query= BRENDA::D2Z0I0 (402 letters) >MicrobesOnline__882:207114 Length = 388 Score = 282 bits (721), Expect = 1e-80 Identities = 145/385 (37%), Positives = 231/385 (60%), Gaps = 7/385 (1%) Query: 9 KVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHGYS 68 ++ LP Y+FA ++++K ++ G DI+ LG+G+PD+ II+ + E RP H Y Sbjct: 9 RLATLPPYLFAGIDKVKAEVAARGVDIISLGIGDPDMATPGFIIEAMKEAIARPANHQYP 68 Query: 69 ASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPNPT 128 + G+ R+ + ++Y RR+GV LDP I IG+KEG +H A + PGD V+V P Sbjct: 69 SYVGMLAFRQEVANWYDRRFGVSLDPATEVIGLIGSKEGIAHFPFAFINPGDLVLVCTPN 128 Query: 129 YPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTTLC 188 YP+++ A GG+ VP+L E D FL L + + ++++ K + +++P+NPT Sbjct: 129 YPVYHIATGFAGGEVQFVPLLEEND----FLPDLDAIPEDTWKRAKMIFVNYPNNPTAAT 184 Query: 189 VDLEFFQEVVKLAKQEGIWIVHDFAYADLGFD-GYTPPSILQVEGALDVAVELYSMSKGF 247 L F++++V + ++ + I HD AY ++ +D PPSIL V GA DVA+E +S+SK + Sbjct: 185 APLGFYEKLVDICRRFDVIIAHDTAYTEIYYDEDNRPPSILSVPGAKDVAIEFHSLSKTY 244 Query: 248 SMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRRR 307 +M GWRV VGN L+ L +K +D G+F +Q ASI+AL + + R IYR+R Sbjct: 245 NMTGWRVGMAVGNPTLVAGLGKIKENMDSGIFQAVQEASIVALRDGDDFCRELRGIYRQR 304 Query: 308 RDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVGMNSLDFSLFLLREAKVAVSPGIGFGEY 367 RD ++ L++ G + + P+ + +VWA+VP+ G S DF +L+E V V+PG GFG Sbjct: 305 RDTVINALHKAGIQCRVPQATFYVWARVPQ--GHTSADFVTRVLQETGVVVTPGNGFGTP 362 Query: 368 GEGYVRFALVENEHRIRQAVRGIKK 392 GEG+ R +L + R+ +AV I K Sbjct: 363 GEGFFRISLTVDNARLEEAVSRIAK 387 Lambda K H 0.322 0.141 0.425 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: 423 Number of extensions: 19 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: 402 Length of database: 388 Length adjustment: 31 Effective length of query: 371 Effective length of database: 357 Effective search space: 132447 Effective search space used: 132447 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 (21.9 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