Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate Dsui_2909 Dsui_2909 aspartate/tyrosine/aromatic aminotransferase
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__PS:Dsui_2909 Length = 395 Score = 157 bits (398), Expect = 4e-43 Identities = 123/387 (31%), Positives = 197/387 (50%), Gaps = 35/387 (9%) Query: 30 GARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETK-YTALDGTPELKKAIR 88 G A +R G+ +I + G PD TP+H+ DA RG+T Y+ G P L+KAI Sbjct: 19 GELKMAARRRGEDIIDMSMGNPDGATPKHIVDKMVDATQRGDTHGYSVSKGIPRLRKAIC 78 Query: 89 EKFQRENGLAYELD-EITVATGAKQILFNAMMASLDPGDEVIIPTPYWTSYSDIVHICEG 147 + + R + ++ D E V G+K+ L + M+A+LD GD V++P P + +HI Sbjct: 79 DWYLRRYNVEFDPDSEAVVTIGSKEGLAHLMLATLDRGDTVLVPNPSYP-----IHIYGA 133 Query: 148 KPVLIACDASSGFRLTA-----EKLEAAI---TPRTRWVLLNSPSNPSGAAYSAADYRPL 199 +IA + R+T E+L+ AI TP+ + ++L PSNP+ + + Sbjct: 134 ---IIAGANTRSVRMTDDVDFFEELQRAIRECTPKPKMMILGFPSNPTARCVELDFFERV 190 Query: 200 LEVLLRHPHVWLLVDDM-YEHIVYDGFRFVTPAQLE-PGLKNRTLTVNGVSKAYAMTGWR 257 V L H L+V D+ Y IV+DG+R P+ +E PG ++ + +SK+Y M GWR Sbjct: 191 --VALAKEHDILVVHDLAYADIVFDGYR--APSIMEVPGARDVAVEFFTMSKSYNMAGWR 246 Query: 258 IGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDLVVN 317 +GY G +EL A+A ++S + Q ASV AL+GPQD ++E ++++ RR+++ Sbjct: 247 VGYMVGNKELCAALARIKSYHDYGTFTPIQVASVIALDGPQDCVEEVRQTYELRRNVLAK 306 Query: 318 GLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGSA 377 GL+ G VP+ + Y ++ P +F LL +A VAV PG Sbjct: 307 GLHEA-GWMVEVPKASMYIWA--------KIPEPYAHLGSLEFAKKLLAEAKVAVSPGIG 357 Query: 378 FG--LSPFFRISYATSEAELKEALERI 402 FG R + +EA ++A+ I Sbjct: 358 FGDYGDDHVRFALIENEARTRQAIRGI 384 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: 367 Number of extensions: 21 Number of successful extensions: 8 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: 395 Length adjustment: 31 Effective length of query: 379 Effective length of database: 364 Effective search space: 137956 Effective search space used: 137956 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