Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate HSERO_RS17885 HSERO_RS17885 aminotransferase
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__HerbieS:HSERO_RS17885 Length = 393 Score = 187 bits (475), Expect = 5e-52 Identities = 124/395 (31%), Positives = 206/395 (52%), Gaps = 22/395 (5%) Query: 13 QPASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGET 72 Q A+R+ I ++++ +AA ++++G+ +I +G GEPDF P V +AA+ A+ G+ Sbjct: 5 QLAARLQHIAPFHVMELSKKAAVLEQQGRHLIHMGIGEPDFTAPPAVVEAATRAMTEGKM 64 Query: 73 KYTALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPT 132 +YT+ G P+L+ AI + ++ GL + I V GA L A A ++ EV++P Sbjct: 65 QYTSATGLPQLRAAISDHYRSVYGLEIAPERIVVTAGASAALLLACAALVERDSEVLMPD 124 Query: 133 PYWTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYS 192 P + V EG+ LIA F+L+A+ + TR VLL SPSNP+G + Sbjct: 125 PSYPCNRHFVAAFEGRAKLIASGPEHRFQLSAQMVREHWGSATRGVLLASPSNPTGTSIL 184 Query: 193 AADYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYA 252 + R ++ +R + +VD++Y+ + Y+G F + L + + +N SK + Sbjct: 185 PDELRAIVGE-VRQRGGFTIVDEIYQGLSYEGAPFSALS-----LGDDVVVINSFSKYFN 238 Query: 253 MTGWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQD--FLKERTESFQR 310 MTGWR+G+ P L+ + + C SSI+Q A+VA PQ +ER F+R Sbjct: 239 MTGWRLGWLVLPPALVPQVEKLAQNLLICASSIAQHAAVACFT-PQTLALYEERKAEFKR 297 Query: 311 RRDLVVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHV 370 RRD +V L ++ +P+GAFY ++ C+ + ++ D +L +A V Sbjct: 298 RRDYIVPALESLGFTVPVMPDGAFYVYADCSA----LADDADQLSLD------MLNEAGV 347 Query: 371 AVVPGSAFG---LSPFFRISYATSEAELKEALERI 402 +VPG FG + R+SYATS L+EA+ R+ Sbjct: 348 VLVPGLDFGPFTARRYIRLSYATSMENLQEAVARL 382 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: 362 Number of extensions: 20 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: 393 Length adjustment: 31 Effective length of query: 379 Effective length of database: 362 Effective search space: 137198 Effective search space used: 137198 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