Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_089322057.1 CHB58_RS00080 alanine transaminase
Query= BRENDA::D2Z0I0 (402 letters) >NCBI__GCF_900188395.1:WP_089322057.1 Length = 405 Score = 483 bits (1242), Expect = e-141 Identities = 230/395 (58%), Positives = 299/395 (75%), Gaps = 2/395 (0%) Query: 4 EWMFPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPN 63 E+ F ++ +LP YVFA+VN+LK +LRR GEDIVDLGMGNPD+P +HI+DKLCE A P Sbjct: 3 EFQFARIDRLPPYVFAVVNDLKTKLRRAGEDIVDLGMGNPDLPTPKHIVDKLCEAAQNPR 62 Query: 64 VHGYSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVI 123 H YS +KG+ +LR+A+ +YKR+Y V+LDPE I TIG+KEG +HL L ++ PGD V+ Sbjct: 63 NHRYSQTKGLYKLREALSLWYKRKYDVDLDPETEVITTIGSKEGLAHLALTLVNPGDVVM 122 Query: 124 VPNPTYPIHYYAPIICGGDAISVPILPEEDFPE-VFLRRLYDLIKTSFRKPKAVVLSFPH 182 VP P YPIH Y+ II GGD S+P+L +E F E F + K S+ +PK ++L+FPH Sbjct: 123 VPTPAYPIHPYSFIIAGGDVRSIPLLTDEGFNEDAFFESIIKAYKESWPRPKVLLLNFPH 182 Query: 183 NPTTLCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYS 242 NPTT CVD+ FF+++V AK+ + ++ D AY+++ FDGY PPSI QV+GA +VAVE YS Sbjct: 183 NPTTACVDIGFFEKIVDFAKENNLLVIQDLAYSEISFDGYVPPSIFQVKGAKEVAVEFYS 242 Query: 243 MSKGFSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNRE 302 +SK +SMAGWRV F GN+ +I L +KSYLDYG+F PIQ+A+IIAL+ VE+ R+ Sbjct: 243 LSKTYSMAGWRVGFAAGNKQVIHALYRMKSYLDYGMFQPIQIAAIIALKGDQSCVEEYRK 302 Query: 303 IYRRRRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEV-GMNSLDFSLFLLREAKVAVSPG 361 IY +RRD LV GLNR+GW V+KPK +MFVWAK+PE+ M SL+FS LL + KVAVSPG Sbjct: 303 IYEKRRDTLVNGLNRIGWRVEKPKSTMFVWAKIPEKFRSMGSLEFSKMLLLDGKVAVSPG 362 Query: 362 IGFGEYGEGYVRFALVENEHRIRQAVRGIKKALDK 396 IGFGEYG+ YVRFALVENE RI+QAVRGIK+A +K Sbjct: 363 IGFGEYGDEYVRFALVENELRIKQAVRGIKRAFEK 397 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: 545 Number of extensions: 21 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: 405 Length adjustment: 31 Effective length of query: 371 Effective length of database: 374 Effective search space: 138754 Effective search space used: 138754 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 10 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