Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_012283431.1 HM1_RS10910 LL-diaminopimelate aminotransferase
Query= BRENDA::D2Z0I0 (402 letters) >NCBI__GCF_000019165.1:WP_012283431.1 Length = 393 Score = 317 bits (813), Expect = 3e-91 Identities = 156/384 (40%), Positives = 243/384 (63%), Gaps = 5/384 (1%) Query: 9 KVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHGYS 68 ++ L +F+ ++ L+ ++ G D+++LG+G+PD PP+ H+ L + R + +GY+ Sbjct: 9 RMASLSSAMFSRMDALRQEVEASGVDVINLGIGSPDRPPAPHVRQTLMDALVRDDAYGYA 68 Query: 69 ASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPNPT 128 + G+ + A+ D+Y+ R+GV LDP+ + +G+++G HL LA+L+PGD ++P+P Sbjct: 69 LTDGLIEFKSAVADWYQERFGVALDPKTEVLSLMGSQDGLGHLGLALLDPGDVALIPDPG 128 Query: 129 YPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTTLC 188 YPI+ ++ G +P+ E D+ L L + + R+ K ++L++P NP Sbjct: 129 YPIYRAGVLLAEGFPYPLPLERERDY----LPDLDAVPEDILRRAKLMILNYPSNPVAAT 184 Query: 189 VDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSMSKGFS 248 +L FF VV A++ I ++HD AY++L +DGY P S LQ GA +V +E +S+SK ++ Sbjct: 185 AELNFFTGVVDFARRNNIIVLHDIAYSELAYDGYRPVSFLQAPGAKEVGIEFHSLSKSYN 244 Query: 249 MAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRRRR 308 +AG R+ VGN ++ LA+LKS +DYGVF +Q A++ AL P +VE+N Y+RRR Sbjct: 245 LAGCRLGMAVGNREVLALLANLKSNIDYGVFKAVQWAAVAALRGPQAIVEENARAYQRRR 304 Query: 309 DVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVGMNSLDFSLFLLREAKVAVSPGIGFGEYG 368 DVLV+GLNR+GW++ KPK SMFVWA VP+ +S F+ LLRE V V PG FGE G Sbjct: 305 DVLVDGLNRIGWQMDKPKASMFVWAPVPKGF-TSSFAFAEELLRETGVLVVPGNAFGERG 363 Query: 369 EGYVRFALVENEHRIRQAVRGIKK 392 EGYVR ALV E R+ +AV I + Sbjct: 364 EGYVRIALVVPEGRLEEAVERIAR 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: 452 Number of extensions: 25 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: 393 Length adjustment: 31 Effective length of query: 371 Effective length of database: 362 Effective search space: 134302 Effective search space used: 134302 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