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_027721528.1 H589_RS0107920 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P58350 (410 letters) >NCBI__GCF_000425265.1:WP_027721528.1 Length = 386 Score = 177 bits (450), Expect = 4e-49 Identities = 115/383 (30%), Positives = 188/383 (49%), Gaps = 26/383 (6%) Query: 26 ILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKYTALDGTPELKK 85 ++ + +A M+REG+ +I + GEPDFDTP+ +K+A +A+ +GET YT G PEL++ Sbjct: 16 VMDVLEKAQQMEREGRSIIHMEIGEPDFDTPDCIKKACCEAMDKGETHYTHSLGIPELRE 75 Query: 86 AIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPYWTSYSDIVHIC 145 AI + + + + D + + G + LD GD VI+ P + YS+ + Sbjct: 76 AISKYHKDRYNVDVDPDRVIITQGTSPAMLLLFTFILDKGDNVIVSDPCYACYSNFISFA 135 Query: 146 EGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADYRPLLEVLLR 205 + I GF+ E ++ AI +T+ +L+NSPSNP+G S + E+ Sbjct: 136 GAEANRITTFEEDGFQYRPEAIKKAINTKTKAILINSPSNPTGTLLSP---ERMKEIAGM 192 Query: 206 HPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRT---LTVNGVSKAYAMTGWRIGYAG 262 P W++ D++Y +VY + E + T +NG SK +AMTGWR+GY Sbjct: 193 GP--WIISDEIYHGLVY--------GEKEHSILEYTDHAFVLNGFSKLFAMTGWRLGYII 242 Query: 263 GPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDLVVNGLNAI 322 P + ++ + + +S++Q A VAAL D + ++ RR ++ L + Sbjct: 243 SPEKYVRPLQKLCQNFFISANSMAQRAGVAALTESWDDVNRIKNTYDERRKYMLKRLREM 302 Query: 323 DGLDCRV-PEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGSAF--G 379 G D +V P GAFY + K S ++ D +LE A + V PG F G Sbjct: 303 -GFDIKVEPTGAFYVLVNMKHLAAKFDGSSLKLAFD------ILEQAGIGVTPGIDFGDG 355 Query: 380 LSPFFRISYATSEAELKEALERI 402 + R+SYA S L E ++R+ Sbjct: 356 AEGYIRLSYANSIENLAEGMDRL 378 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: 379 Number of extensions: 21 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: 410 Length of database: 386 Length adjustment: 31 Effective length of query: 379 Effective length of database: 355 Effective search space: 134545 Effective search space used: 134545 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