Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate Echvi_0124 Echvi_0124 Aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::D2Z0I0 (402 letters) >FitnessBrowser__Cola:Echvi_0124 Length = 386 Score = 216 bits (550), Expect = 9e-61 Identities = 125/379 (32%), Positives = 210/379 (55%), Gaps = 10/379 (2%) Query: 9 KVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHGYS 68 ++ + +Y F+ +L+ EG I+++G+G+PD+PP + + L + +P HGY Sbjct: 7 RLANVKEYYFSKKLREVARLKAEGHPIINMGIGSPDLPPHPSVTEALNHSSAQPTSHGYQ 66 Query: 69 ASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPNPT 128 + +GIP LR+AI FY++ Y V L P + +G+KE H+ LA L PGD V++PNP Sbjct: 67 SYQGIPALREAIASFYQKHYAVSLSPTDEILPMMGSKEAIMHISLAYLNPGDKVLIPNPG 126 Query: 129 YPIHYYAPIICGGDAISVPILPEEDF-PEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTTL 187 YP + + G A+ + E + P++ +L +L ++ K + +++PH PT Sbjct: 127 YPTYSSVTELVGAKAVYYDLKEENQWLPDI--GQLEELAQSGI---KLMWINYPHMPTGA 181 Query: 188 CVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSMSKGF 247 E + +V AK+ I +V+D Y+ + +P SIL ++GA D+A+EL S+SK F Sbjct: 182 NASREALEALVTFAKKHQILLVNDNPYSFILTQ--SPISILSIDGAKDIALELNSLSKTF 239 Query: 248 SMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRRR 307 +M GWRV + G ++ + +KS +D G+F IQ +I AL ++ IY +R Sbjct: 240 NMPGWRVGMLCGQASYLQEVLKVKSNMDSGMFLGIQEGAIAALNLDQRWFDQMDAIYHKR 299 Query: 308 RDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVGMNSLDFSLFLLREAKVAVSPGIGFGEY 367 R+ + + RVG ++ MFVWAK+ + ++L LL E + ++PG FG Sbjct: 300 REAVWKLAERVGAICERNSAGMFVWAKLATQTTPSALVDK--LLYENHIFITPGDIFGSN 357 Query: 368 GEGYVRFALVENEHRIRQA 386 G GY+RF+L E+ I++A Sbjct: 358 GHGYIRFSLCVPENLIQEA 376 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: 418 Number of extensions: 20 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: 386 Length adjustment: 31 Effective length of query: 371 Effective length of database: 355 Effective search space: 131705 Effective search space used: 131705 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 Aug 03 2021. The underlying query database was built on Aug 03 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