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_24005 AO356_24005 aspartate aminotransferase
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_24005 Length = 403 Score = 377 bits (969), Expect = e-109 Identities = 193/395 (48%), Positives = 261/395 (66%), Gaps = 1/395 (0%) Query: 15 ASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKY 74 + R+ + +S +RA A++ G+ ++ L GEPDFDTP H+KQAA AI G TKY Sbjct: 6 SKRVQRVSLSANAAAKSRATALRDAGRDILDLTTGEPDFDTPAHIKQAAYAAIAAGATKY 65 Query: 75 TALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPY 134 T G L+ A++ K + EN L Y L I +A GAKQI+FNA A+LD GDEV++PTPY Sbjct: 66 TPTPGVKALRVAVQRKLRTENQLDYPLASIVIANGAKQIIFNAFAATLDDGDEVLVPTPY 125 Query: 135 WTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAA 194 W S+ D V G+PV I C G +LT +LE I RTRW++LNSP NPSGA YS A Sbjct: 126 WPSFPDSVRFNGGEPVFIECGLDQGCKLTPRQLEQHIGERTRWLILNSPGNPSGAVYSEA 185 Query: 195 DYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMT 254 + + L +VL RH HV +L+D++YEHI +DG + P L++R L V GVSK YAMT Sbjct: 186 ELQGLAQVLRRHAHVLILLDELYEHIRFDGRPSQNLLNVAPDLQSRCLLVGGVSKTYAMT 245 Query: 255 GWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDL 314 GWRIG+ GP+ L AM VVQSQ+TS SS+ QAA++AA G DFL E+ ++++RRD+ Sbjct: 246 GWRIGFGAGPQALTDAMTVVQSQSTSGASSVGQAAALAAFEGGLDFLPEQVAAYRQRRDV 305 Query: 315 VVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVP 374 +V+ L ++GL+ P G F+ F CAG+LG+ P G+R++ D D AYLL++ VA V Sbjct: 306 LVSTLRNVEGLEVLEPHGGFFVFVCCAGLLGRYRPDGQRLEHDADVVAYLLDEG-VAGVA 364 Query: 375 GSAFGLSPFFRISYATSEAELKEALERIAAACDRL 409 GSA+GLSP+FR+S AT+ + EA RIA AC +L Sbjct: 365 GSAYGLSPWFRLSIATATETVAEAGRRIAHACGQL 399 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: 495 Number of extensions: 29 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: 410 Length of database: 403 Length adjustment: 31 Effective length of query: 379 Effective length of database: 372 Effective search space: 140988 Effective search space used: 140988 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 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