Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_077278775.1 B1C78_RS08600 alanine transaminase
Query= BRENDA::D2Z0I0 (402 letters) >NCBI__GCF_002000365.1:WP_077278775.1 Length = 399 Score = 476 bits (1224), Expect = e-139 Identities = 231/386 (59%), Positives = 289/386 (74%), Gaps = 5/386 (1%) Query: 7 FPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHG 66 FP++K+LP YVF +VN+LK + R GEDI+D GMGNPD P +HI+DKLCEVA R + H Sbjct: 5 FPRIKRLPPYVFNIVNDLKAKARARGEDIIDFGMGNPDQPTPKHIVDKLCEVAQRDDTHR 64 Query: 67 YSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPN 126 YS S+GIPRLR+AI +YK R+ V+LDPE AI+TIG+KEG +HL LA L PGD V+VPN Sbjct: 65 YSMSRGIPRLRRAITRWYKDRFNVDLDPETEAIVTIGSKEGLAHLALATLGPGDAVLVPN 124 Query: 127 PTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTT 186 P YPIH Y +I G D VP+ P DF L I+ S+ +PK +VLSFP NPT Sbjct: 125 PAYPIHPYGCVIAGADIRHVPLTPGVDF----FAELEKAIQDSWPRPKMLVLSFPANPTA 180 Query: 187 LCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSMSKG 246 CV+L FF++V+ +A++ GIW+VHD AYA++ FDGY PSILQV GA DVAVE YS+SK Sbjct: 181 QCVELGFFEKVIDIAREYGIWVVHDLAYAEITFDGYRAPSILQVSGAKDVAVEFYSLSKS 240 Query: 247 FSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRR 306 ++M GWRV F+ GN L+ L +KSYLDYG FTPIQVASI ALE P + V + R++Y+ Sbjct: 241 YNMPGWRVGFMCGNPKLVAALGRIKSYLDYGTFTPIQVASIAALEGPQDCVGQIRQLYQS 300 Query: 307 RRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEE-VGMNSLDFSLFLLREAKVAVSPGIGFG 365 RRDVL +GLN +GW V+KPK +MFVWA +PE+ V M SL+FS LL++AKVA SPG+GFG Sbjct: 301 RRDVLCDGLNALGWVVEKPKATMFVWAPIPEQYVHMGSLEFSKKLLKDAKVAASPGVGFG 360 Query: 366 EYGEGYVRFALVENEHRIRQAVRGIK 391 YG+ YVRF L+ENEHR RQAVRGIK Sbjct: 361 SYGDQYVRFGLIENEHRTRQAVRGIK 386 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: 554 Number of extensions: 22 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: 399 Length adjustment: 31 Effective length of query: 371 Effective length of database: 368 Effective search space: 136528 Effective search space used: 136528 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