Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate WP_013683113.1 ARCVE_RS02015 aminotransferase
Query= SwissProt::P58350 (410 letters) >NCBI__GCF_000194625.1:WP_013683113.1 Length = 384 Score = 184 bits (468), Expect = 3e-51 Identities = 115/370 (31%), Positives = 204/370 (55%), Gaps = 21/370 (5%) Query: 43 VIILGAGEPDFDTPEHVKQAASDAIHRGETKYTALDGTPELKKAIREKFQRENGLAYELD 102 VI LG GEPDF P +++ A+ +G T YT+ G EL++AI E + R+ G+ + Sbjct: 33 VISLGVGEPDFAVPWRIREEIIYALEKGITSYTSNFGLKELREAIAE-YYRKFGVECSAE 91 Query: 103 EITVATGAKQILFNAMMASLDPGDEVIIPTPYWTSYSDIVHICEGKPVLIACDASSGFRL 162 + + TG + + A+ A L+ G+ V++P P + SY+ + + G+ ++A + F+L Sbjct: 92 SVLITTGVSEGVDIALRAILNEGEAVLVPEPCYVSYAPLSSLAGGE--VVAIPTTPDFKL 149 Query: 163 TAEKL-EAAITPRTRWVLLNSPSNPSGAAYSAADYRPLLEVLLRHPHVWLLVDDMYEHIV 221 + E + E A + + +++N P+NP+G +YS + + + + H + ++ D++Y + Sbjct: 150 SYELIDEYAKETKPKAIVINYPNNPTGVSYSKKELEEIADAAIEHDMI-VISDEIYAELS 208 Query: 222 YDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGWRIGYAGGPRELIKAMAVVQSQATSC 281 Y F+ ++ A L G++ R + +NG SKA+AMTG RIGYA P ++++ M + C Sbjct: 209 YT-FKHISIASLN-GMEERAIILNGFSKAFAMTGLRIGYAIAPADILEGMLKIHQYCMLC 266 Query: 282 PSSISQAASVAALNGPQDFLKERTESFQRRRDLVVNGLNAIDGLDCRVPEGAFYTFSGCA 341 +Q ++ AL +D L+E + RRR+ V + + LD ++P+GAFY F Sbjct: 267 APVTAQIGALEALRNGEDELEEMRAEYIRRRNFFVKRVGKV--LDVKMPDGAFYAFP--- 321 Query: 342 GVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGSAFGL--SPFFRISYATSEAELKEAL 399 + +G + +F LL + +VAVVPG+AFG + R +YA S +L+EA+ Sbjct: 322 ----SIESTG---LSSEEFAERLLFEKNVAVVPGNAFGECGEGYIRCAYAVSMEKLREAV 374 Query: 400 ERIAAACDRL 409 +RI + L Sbjct: 375 DRIVEFVEEL 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: 382 Number of extensions: 33 Number of successful extensions: 7 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: 384 Length adjustment: 31 Effective length of query: 379 Effective length of database: 353 Effective search space: 133787 Effective search space used: 133787 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 10 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