Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate AO356_25355 AO356_25355 aspartate aminotransferase
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25355 Length = 404 Score = 422 bits (1084), Expect = e-122 Identities = 205/393 (52%), Positives = 280/393 (71%) Query: 17 RISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKYTA 76 R++ S +I R A + +G +I L AGEPDFDTP+H+++AA +AI +G T+YT Sbjct: 11 RLARAQSSATYRIMDRVAERRAQGAKIISLCAGEPDFDTPKHIREAAIEAIGQGHTRYTQ 70 Query: 77 LDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPYWT 136 + G L++A+ KF++ENGL + V G KQ+++NA+ A+LD GD+VI+P PYW Sbjct: 71 VAGVRSLREAVAAKFRQENGLDVTWQDTLVCNGGKQVIYNALAATLDEGDQVIVPAPYWV 130 Query: 137 SYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADY 196 SY ++V +C G+ ++ CDA SGF+LT L+AAITP+TRW++LNSPSNP+GA YS + Sbjct: 131 SYPEMVQLCGGESRIVTCDADSGFKLTPAALDAAITPQTRWLILNSPSNPTGAVYSREEL 190 Query: 197 RPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGW 256 + L +VLL HPHV +L DD+YEH+++D F T AQ+EP L +RTLT+NGVSKAYAMTGW Sbjct: 191 QALADVLLAHPHVLILADDIYEHLIFDDQVFYTLAQVEPRLASRTLTMNGVSKAYAMTGW 250 Query: 257 RIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDLVV 316 RIG+A GPR L++AM +Q Q TS SSISQ A++AAL+GP+DF++E FQRRRDL+V Sbjct: 251 RIGFATGPRWLLEAMEKLQGQQTSGASSISQQAALAALDGPKDFIRESRAVFQRRRDLMV 310 Query: 317 NGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGS 376 LNA GL C P GAFY F+ CAG++G+ + G+ + TD D LL++A VAVV GS Sbjct: 311 ALLNATPGLACASPGGAFYAFASCAGLIGRTSSGGRVLHTDEDVAHALLDEADVAVVHGS 370 Query: 377 AFGLSPFFRISYATSEAELKEALERIAAACDRL 409 AFGL P+ RI+YA +A L++A E I CD L Sbjct: 371 AFGLGPYIRIAYALDDASLRQACEAIRGFCDAL 403 Lambda K H 0.318 0.134 0.393 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: 485 Number of extensions: 18 Number of successful extensions: 1 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: 410 Length of database: 404 Length adjustment: 31 Effective length of query: 379 Effective length of database: 373 Effective search space: 141367 Effective search space used: 141367 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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