Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate 8501474 DvMF_2204 aminotransferase class I and II (RefSeq)
Query= metacyc::MONOMER-21143 (387 letters) >FitnessBrowser__Miya:8501474 Length = 390 Score = 236 bits (602), Expect = 8e-67 Identities = 136/391 (34%), Positives = 218/391 (55%), Gaps = 8/391 (2%) Query: 1 MKLAKNLQRLGTESAFSVLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGH 60 M+++ L R+ + +V A+A +L+A+G ++ L +G+PDF TP+HV +AAK A+D+G Sbjct: 1 MRISDRLTRIKPSATLAVNAKALELKAKGVQVVSLAVGEPDFPTPEHVREAAKTAIDQGF 60 Query: 61 HGYVLSNGILECRQAVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHP 120 Y GI E RQAV + Y + E ++ GGK +Y QC PG E++ P Sbjct: 61 TRYTQVPGIPELRQAVCGYFARFYGVEAPMEATVVTNGGKQALYNLFQCLLNPGDEVLVP 120 Query: 121 TPAFPIYESMINYTGSTPVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFV 180 P + Y +++ G PV ++ K PE++ +T KTR+L+L +P+NPTG+ Sbjct: 121 APYWVSYPALVELAGGVPVFVASPAERGFKVTPEELDRAVTPKTRVLLLNSPSNPTGACY 180 Query: 181 EKSAIDVLAEGLKKHPHVAILSDEIYSRQIYDGKEMPTFFNYPDLQ-DRLIVLDGWSKAY 239 ++ D + E + ++SDEIY R +Y+ E + ++ + + + V++G +K + Sbjct: 181 SRAETDAIMEWAIAR-DLFVVSDEIYDRLVYEPAEAVSVCDWWERHPENVAVVNGLAKTF 239 Query: 240 AMTGWRMGWSVWPEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQR 299 AMTGWR+G+++ +LI + K+ S S + + +Q A +AAL GP DA+ EM F +R Sbjct: 240 AMTGWRVGYALAHPDLIKAMTKIQGQSTSNICSVAQKAALAALTGPYDAVEEMKKSFRRR 299 Query: 300 RKLIHEGLNSLPGVECSLPGGAFYAFPKVIGTGM----NGSEFAKKCMHEAGVAIVPGTA 355 R L H ++S PGV C P GAFY F + + + M +A VA+VPG A Sbjct: 300 RDLAHGIVSSWPGVICPKPDGAFYLFADMRALFTPALPDSASLCTYIMEQANVALVPGAA 359 Query: 356 FGKTCQDYVRFSYAASQDNISNALENIKKML 386 FG +RFSYA S D + AL+ + K+L Sbjct: 360 FGDDA--CLRFSYAVSDDTLMIALDKVAKVL 388 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: 398 Number of extensions: 23 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: 387 Length of database: 390 Length adjustment: 30 Effective length of query: 357 Effective length of database: 360 Effective search space: 128520 Effective search space used: 128520 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