Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate PP_3361 PP_3361 putative aminotransferase
Query= SwissProt::Q940M2 (476 letters) >FitnessBrowser__Putida:PP_3361 Length = 1015 Score = 323 bits (827), Expect = 2e-92 Identities = 193/452 (42%), Positives = 270/452 (59%), Gaps = 21/452 (4%) Query: 35 ADAPPHIPPFVHQPRPYKGPSADEVLQKRKKFLGPSLFHYYQKPLNIVEGKMQYLYDESG 94 A A IPP + + G + +++ +RK+ L P+L Y P+ V G +L D G Sbjct: 569 ASALAGIPPETYSQQ---GMTKAQIITRRKELLLPNLSISYTDPIKFVRGDGVWLIDNFG 625 Query: 95 RRYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHATTIYLHHAIGDFAEALAAKMPGNL 154 R YLD F + + GH HPD++ A+T Q+ LL + T YLH I ++AE L +P L Sbjct: 626 RAYLDCFNNVCHL--GHSHPDVVEALTRQAALL-NTNTRYLHDNIVEYAERLTGTLPKGL 682 Query: 155 KVVYFVNSGSEANELAMMMARLYTGSLEMISLRNAYHGGSSNTIGLTALNTWKYPLPQGE 214 V F SGSEAN L + MAR YTGS + I L AYHG + I L+ +KY G+ Sbjct: 683 CVASFGCSGSEANSLMLRMARNYTGSDQAIVLDWAYHGTTQELIDLSP---YKYKRKAGK 739 Query: 215 -----IHHVVNPDPYRGV----FGSDGSLYAKDVHDHIE-YGTSGKVAGF-IAETIQGVG 263 ++ V PD Y + G +A+ V + ++ +GK GF IAE+I V Sbjct: 740 GRAAHVYEAVVPDSYYAPEHWPVEAHGKRFAESVAEQLDAMRKAGKRPGFFIAESIPSVA 799 Query: 264 GAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTGSHYWGFQTQDVVPDIVTMAKGIG 323 G V L YLK VY +VR GG+C+ADEVQ GFGR GSH+W F+TQ VVPD V+M K IG Sbjct: 800 GQVFLPEHYLKEVYAMVRAEGGLCLADEVQVGFGRVGSHWWAFETQGVVPDAVSMGKPIG 859 Query: 324 NGLPLGAVVTTPEIASVLASKI-LFNTFGGNPVCSAGGLAVLNVIDKEKRQEHCAEVGSH 382 NG P+ AVVTT E+A + + FNTF GNPV A GLAVL+ I++++ +E+ VG + Sbjct: 860 NGHPMSAVVTTREVADAFNNGMEYFNTFAGNPVSCAVGLAVLDAIERDQLKENALSVGHY 919 Query: 383 LIQRLKDVQKRHDIIGDVRGRGLMVGIELVSDRKDKTPAKAETSVLFEQLRELGILVGKG 442 L++ L+ +Q++ D+IGDVRG GL +GI LV+DRK K PA A + + RE G+L+G Sbjct: 920 LLEGLRKLQQQFDVIGDVRGLGLFLGIVLVTDRKSKAPATALARKVADGARERGVLIGTE 979 Query: 443 GLHGNVFRIKPPMCFTKDDADFLVDALDYSIS 474 G H NV +++P M F++ +ADFL++ L S + Sbjct: 980 GPHDNVLKMRPSMIFSRANADFLLEVLKDSFT 1011 Lambda K H 0.320 0.138 0.412 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: 1135 Number of extensions: 66 Number of successful extensions: 5 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: 476 Length of database: 1015 Length adjustment: 39 Effective length of query: 437 Effective length of database: 976 Effective search space: 426512 Effective search space used: 426512 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 (21.8 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Apr 09 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