Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate Ac3H11_3720 Uncharacterized PLP-dependent aminotransferase YfdZ
Query= BRENDA::D2Z0I0 (402 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3720 Length = 408 Score = 436 bits (1122), Expect = e-127 Identities = 215/386 (55%), Positives = 277/386 (71%), Gaps = 5/386 (1%) Query: 7 FPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHG 66 F ++ +LP YVF + ELK RR GEDI+D+ MGNPD HI+ KL EVA RP+ HG Sbjct: 10 FARIDRLPPYVFNITAELKLAARRRGEDIIDMSMGNPDGATPPHIVAKLTEVAQRPDTHG 69 Query: 67 YSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPN 126 YSASKGIPRLR+AI +YK RY V++ P+ AI+TIG+KEG +HLMLA L+ GDTV+VP+ Sbjct: 70 YSASKGIPRLRRAISHWYKDRYAVDIHPDTEAIVTIGSKEGLAHLMLATLDRGDTVLVPD 129 Query: 127 PTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTT 186 P+YPIH Y +I G D SVP+ P+ DF L I+ S+ KPK ++ FP NPT Sbjct: 130 PSYPIHIYGAVIAGADIRSVPVAPDVDF----FAELEKAIRGSYPKPKMMIFGFPSNPTA 185 Query: 187 LCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSMSKG 246 CV+L FF+ V+ LAK+ I +VHD AYAD+ +DGY PSI++V GA DVAVE +++SK Sbjct: 186 QCVELSFFERVIALAKKHDILVVHDLAYADIVYDGYRAPSIMEVPGAKDVAVEFFTLSKS 245 Query: 247 FSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRR 306 ++MAGWRV F+VGN L+ LA +KSY DYG FTP+QVA+I ALE + V+ Y+R Sbjct: 246 YNMAGWRVGFMVGNPDLVAALARIKSYHDYGTFTPLQVAAIAALEGDQQCVKDIAAQYQR 305 Query: 307 RRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEV-GMNSLDFSLFLLREAKVAVSPGIGFG 365 RRDVL +GL GW V PK SM++WA++PE + SL+F+ LL +AKV VSPGIGFG Sbjct: 306 RRDVLYKGLTEAGWAVDCPKASMYIWARIPEPYRALGSLEFARQLLDKAKVCVSPGIGFG 365 Query: 366 EYGEGYVRFALVENEHRIRQAVRGIK 391 + G+ YVRFAL+ENE RIRQAVRGI+ Sbjct: 366 DQGDEYVRFALIENEARIRQAVRGIR 391 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: 513 Number of extensions: 23 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: 408 Length adjustment: 31 Effective length of query: 371 Effective length of database: 377 Effective search space: 139867 Effective search space used: 139867 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