Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_011317051.1 AVA_RS00800 LL-diaminopimelate aminotransferase
Query= BRENDA::D2Z0I0 (402 letters) >NCBI__GCF_000204075.1:WP_011317051.1 Length = 407 Score = 271 bits (692), Expect = 3e-77 Identities = 139/403 (34%), Positives = 225/403 (55%), Gaps = 21/403 (5%) Query: 9 KVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHGYS 68 +++ L VFA +++ K G++++DL +G+ D+P H+I+ + + P+ HGY Sbjct: 9 RLQPLQSNVFADMDKAKALALAAGKELIDLSLGSSDLPAEAHVIEAIAKSLYDPSTHGYL 68 Query: 69 ASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPNPT 128 G R+A ++Y++++GV++DPE + IG++EG +HL LA+L PGD ++ +P Sbjct: 69 LFNGTRDFRQAAANWYEQKFGVKVDPETEVLPLIGSQEGTAHLPLALLNPGDFALLLDPG 128 Query: 129 YPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTTLC 188 YP H + G +P+ E DF VF D++ S + +VLS+PHNPT Sbjct: 129 YPSHAGGVYLASGQIYPMPLKAENDFLPVFTDIPTDVLARS----RMMVLSYPHNPTAAI 184 Query: 189 VDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTP-----------------PSILQVE 231 L FF+E V ++ I +VHDF Y D+ F+ + PSILQ + Sbjct: 185 APLSFFKEAVAFCQEHNIALVHDFPYVDMVFEDSSNWDQNLSQSPIPNHRSLVPSILQAD 244 Query: 232 GALDVAVELYSMSKGFSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALE 291 V++E +++SK ++M G+R+ + +GN +I+ L +K+ +D+ + I +I AL Sbjct: 245 PDKSVSIEFFTLSKSYNMGGFRIGYAIGNAQMIQALRQIKAAVDFNQYRGILNGAIAALT 304 Query: 292 SPYEVVEKNREIYRRRRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVGMNSLDFSLFLL 351 P VE +R+RRD + L+ +GW V PK +M++WAK+P NS++F L+ Sbjct: 305 GPQAGVEAAVSTFRQRRDAFIHALHHIGWYVPTPKATMYIWAKLPSSWSQNSIEFCTQLV 364 Query: 352 REAKVAVSPGIGFGEYGEGYVRFALVENEHRIRQAVRGIKKAL 394 ++ VA SPG GFG+ GEGYVRFALV +R AV I L Sbjct: 365 KQTGVAASPGAGFGKSGEGYVRFALVHEPSILRTAVERISNFL 407 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: 398 Number of extensions: 20 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: 407 Length adjustment: 31 Effective length of query: 371 Effective length of database: 376 Effective search space: 139496 Effective search space used: 139496 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 Jul 25 2024. The underlying query database was built on Jul 25 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