Align Alanine--glyoxylate aminotransferase; EC 2.6.1.44 (characterized)
to candidate Synpcc7942_2160 Synpcc7942_2160 alanine-glyoxylate aminotransferase
Query= SwissProt::Q3LSM4 (393 letters) >FitnessBrowser__SynE:Synpcc7942_2160 Length = 384 Score = 335 bits (860), Expect = 1e-96 Identities = 163/368 (44%), Positives = 240/368 (65%), Gaps = 3/368 (0%) Query: 13 EPLVTPNKLLMGPGPSNAPQRVLDAMSRPILGHLHPETLKIMDDIKEGVRYLFQTNNIAT 72 +PL P +LL+GPGPSNA VL+A+SRP +GHL P+ L++M +++ +RY++QT+N T Sbjct: 17 QPLELPERLLLGPGPSNAHPAVLEAISRPPIGHLDPKFLELMTEVQGLLRYIWQTDNRLT 76 Query: 73 FCLSASGHGGMEATLCNLLEDGDVILIGHTGHWGDRSADMATRYGADVRVVKSKVGQSLS 132 +S +G MEAT+ N +E GDV+L+G G++G+R DMA RYGADVR + G S Sbjct: 77 IPVSGTGSAAMEATIANSVEPGDVVLVGVMGYFGNRLVDMAGRYGADVRTIHKPWGDVFS 136 Query: 133 LDEIRDALLIHKPSVLFLTQGDSSTGVLQGLEGVGALCHQHNCLLIVDTVASLGGAPMFM 192 L E+R AL H+P +L L ++STG Q L GVG LC + +CLL++DTV SLG P + Sbjct: 137 LAELRQALEEHRPQILALVHAETSTGAEQPLAGVGDLCREFDCLLLIDTVTSLGAVPTLL 196 Query: 193 DRWEIDAMYTGSQKVLGAPPGITPVSFSHRAVERYKRRNTKVKVYYWDMSLVGDYWGCFG 252 D W +D Y+ SQK L PPG++P + RA E+ RR KV +Y DMSL+ YW G Sbjct: 197 DEWGVDLAYSCSQKGLSCPPGVSPFTMGPRAEEKLARRKGKVANWYLDMSLLNQYW---G 253 Query: 253 RPRIYHHTISSTLLYGLREAIAMACEEGLPALIARHEDCAKRLYRGLQDAGFELYADPKD 312 R+YHHT + +G+REA+ + +EG+ + RH D A+ L+ GL+D G + ++ Sbjct: 254 SDRVYHHTAPVNMNFGIREALRLIADEGIETVWKRHRDNAEYLWAGLEDLGLTCHVPVEN 313 Query: 313 RLSTVTTIKVPQGVDWLKAAQYAMKTYLVEISGGLGPTAGQVFRIGLMGQNATTERVDRV 372 RL T+TT+++P+GVD ++ + + +E+ GGLG AG+V+RIGLMG N+ E VDR+ Sbjct: 314 RLPTLTTVRIPEGVDGKAVSRQLLDEHGIEMGGGLGELAGKVWRIGLMGYNSRRENVDRL 373 Query: 373 LQVFQEAV 380 L + + + Sbjct: 374 LSILADVL 381 Lambda K H 0.321 0.137 0.418 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: 399 Number of extensions: 17 Number of successful extensions: 2 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: 393 Length of database: 384 Length adjustment: 30 Effective length of query: 363 Effective length of database: 354 Effective search space: 128502 Effective search space used: 128502 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: 50 (23.9 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