Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate 8500823 DvMF_1564 aminotransferase class I and II (RefSeq)
Query= BRENDA::P9WPZ5 (397 letters) >FitnessBrowser__Miya:8500823 Length = 400 Score = 155 bits (392), Expect = 2e-42 Identities = 115/362 (31%), Positives = 171/362 (47%), Gaps = 25/362 (6%) Query: 5 RLRPYATTVFAEMSALATRIGA-VNLGQGFPDEDGPPKMLQAAQDAIAGG--VNQYPPGP 61 R+R + M LA ++G V+LGQG P P +++A A+ +Y P Sbjct: 16 RVRNIRISATKLMPMLAAKVGGCVSLGQGVPSFRTPDHIVEAVCRALRDDPTAGRYSLQP 75 Query: 62 GSAPLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDS 121 G LR AIAA G +DPETE+ VTVGA EA+ +L +VE G EV++ P Y S Sbjct: 76 GMPALREAIAADILARKGARFDPETEIGVTVGAMEALVMIMLTVVERGDEVIIPSPGYAS 135 Query: 122 YSPVVAMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATEL 181 ++ V MA V VPL + LD +A+R AVTPRTRA+I+ SP NPTG V ++ Sbjct: 136 HAEQVLMAEGVPVHVPL--RAADWGLDVEAVRFAVTPRTRAIIVCSPGNPTGGVYDDADV 193 Query: 182 AAIAEIAVAANLVVITDEVYEHLVFDHARHLPL---AGFDGMAERTITISSAAKMFNCTG 238 A+ ++A+ +LV+I D+ Y+++V+ P + IT++S +K + TG Sbjct: 194 RALCDLALERDLVLIVDDTYDYMVYGEQPGTPRFSPVSQPELRRHVITVNSFSKKYALTG 253 Query: 239 WKIGWACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRL 298 W++G+ A +A + + Q A AL V +R +L ARRD Sbjct: 254 WRVGYVAADAAWMAELLKVHDATAVCAPTVSQHAALAALTGPQDCVDVMRAALTARRDLT 313 Query: 299 AAGLTEIGFAVHDSYGTYFLCADPRPLGY---------DDSTEFCAALPEKVGVAAIPMS 349 L D+ +F PR Y DS + E+ V +P Sbjct: 314 CRRL--------DALAPHFAYVPPRGAFYAMARYTFTDADSMTVARRMLEEARVITVPGG 365 Query: 350 AF 351 +F Sbjct: 366 SF 367 Lambda K H 0.321 0.135 0.405 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: 457 Number of extensions: 27 Number of successful extensions: 4 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: 397 Length of database: 400 Length adjustment: 31 Effective length of query: 366 Effective length of database: 369 Effective search space: 135054 Effective search space used: 135054 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 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