Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate 8500663 DvMF_1411 aminotransferase class I and II (RefSeq)
Query= BRENDA::D2Z0I0 (402 letters) >FitnessBrowser__Miya:8500663 Length = 394 Score = 465 bits (1196), Expect = e-135 Identities = 229/389 (58%), Positives = 283/389 (72%), Gaps = 5/389 (1%) Query: 7 FPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHG 66 FP++ +LP YVFA VNELK QLRR+ DIVDLGMGNPDIP QHI+DKL E + + H Sbjct: 4 FPRMHRLPPYVFATVNELKMQLRRQNVDIVDLGMGNPDIPTPQHIVDKLVEASGKGVNHR 63 Query: 67 YSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPN 126 YS S+GIP LRKAICD+Y RR+GV LDP+ A+ T+GAKEG SHL LAML PGD V P+ Sbjct: 64 YSVSRGIPNLRKAICDWYMRRFGVYLDPDTEAVATMGAKEGLSHLSLAMLSPGDVVFAPD 123 Query: 127 PTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTT 186 PTYPIH YAPII G D +PI DF E L + ++ +PK + +S+PHNPT Sbjct: 124 PTYPIHTYAPIIAGADVRRIPIGRGRDFFEDLLVAT----RQTWPQPKLLFISYPHNPTC 179 Query: 187 LCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSMSKG 246 EFFQ+VV AK+ I+++HDFAYADL FDG+ PPS +Q EGA DV VE +SMSK Sbjct: 180 EIAAPEFFQKVVDFAKEHKIYVIHDFAYADLAFDGHMPPSFMQAEGAKDVGVEFFSMSKS 239 Query: 247 FSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRR 306 +SMAGWRV F VGN L+ L +KSYLDYG F PIQ+A+ +AL P E V + + YR+ Sbjct: 240 YSMAGWRVGFCVGNRDLVYALTRIKSYLDYGHFQPIQIAATVALNGPQECVTEIVDTYRK 299 Query: 307 RRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEV-GMNSLDFSLFLLREAKVAVSPGIGFG 365 RRDVL+EGL R GW V PKG+MFVWA++PEE M S++FS LL+E VAVSPG+GFG Sbjct: 300 RRDVLIEGLGRAGWVVPPPKGTMFVWAQIPEEFRAMGSVEFSKLLLKEGHVAVSPGLGFG 359 Query: 366 EYGEGYVRFALVENEHRIRQAVRGIKKAL 394 +G+ +VRFAL+ENEHR +QA++GIKK L Sbjct: 360 AHGDDHVRFALIENEHRTKQAMKGIKKVL 388 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: 544 Number of extensions: 19 Number of successful extensions: 3 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: 394 Length adjustment: 31 Effective length of query: 371 Effective length of database: 363 Effective search space: 134673 Effective search space used: 134673 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