Align Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase; PhPPA-AT; EC 2.6.1.1; EC 2.6.1.78; EC 2.6.1.79 (characterized)
to candidate WP_011607118.1 FRAAL_RS26455 aminotransferase
Query= SwissProt::E9L7A5 (479 letters) >NCBI__GCF_000058485.1:WP_011607118.1 Length = 402 Score = 198 bits (503), Expect = 3e-55 Identities = 138/401 (34%), Positives = 215/401 (53%), Gaps = 27/401 (6%) Query: 78 PRVNSVKPSKTVAITDQATALVQAGVPVIRLAAGEPDFDTPAPIVEAGINAIREGHTRYT 137 PRV++ + T ++ T L A + LA G PDF P + EA AI +Y Sbjct: 11 PRVSAKAMTFTESVIRDMTRLALAH-GAVNLAQGFPDFACPPELKEAAKAAIDADVNQYA 69 Query: 138 PNAGTMELRSAISHKL-KEENGLSYTPD-QILVSNGAKQSIIQAVLAVCSPGDEVLIPAP 195 G E R+A++ K+ + G S PD +I V+ G+ +++I +LA+ PGDEV++ P Sbjct: 70 ITWGAAEFRAAVAAKVGRTYPGWSVDPDTEICVTCGSTEAMIATMLALVDPGDEVIMFEP 129 Query: 196 YWVSYPEMARLADATPVILPTSISEDFLLDPKLLESKLTEKSRLLILCSPSNPTGSVYPR 255 ++ +Y L+ A P ++ + D+ +DP L + ++++R ++L +P NPTG V R Sbjct: 130 FYENYGPDTILSGARPRLVRLH-APDWSIDPAELRAAFSDRTRAIVLNTPHNPTGKVLRR 188 Query: 256 KLLEQIAEIVARHPRLLVISDEIYEHIIY-APATHTSFASLPGMWDRTLTVNGFSKAFAM 314 LE +AE+ RH L V +DEIYEHI Y P H A++PG+ DRT+T+N SK +A+ Sbjct: 189 DELELVAELCQRHDAL-VFTDEIYEHIHYLGPGGHIPPATVPGLEDRTVTINALSKTYAV 247 Query: 315 TGWRLGYIAGPKHFIAACNKIQSQFTSGASSISQKAAVAALGL--GYAGGELVATMVKSF 372 TGWR+G+ P + +A K+ T GA++ Q VAA+GL Y G + + + Sbjct: 248 TGWRVGWTIAPPAYTSAIRKVHDFLTVGAAAPLQAGGVAAMGLPPAYYDG-----LAEQY 302 Query: 373 RERRDYLVKSFGEIEGVKISEPRGAFYLFIDLSSYYGVEVDGFGSINNSESLCRYLLDKA 432 R RRD L + + G +P GA+Y+ D + +D G + +L R L+ + Sbjct: 303 RARRDLLCAALTD-TGFTFRQPDGAYYVMCDTRA-----IDPGG---DDVALARRLVTEI 353 Query: 433 QVALVPGDAFGDDTC-----IRISYAASLSTLQAAVERIKK 468 VA VPG +F D IR + LSTLQAA +R+ + Sbjct: 354 GVATVPGSSFFADPADGRHIIRFGFPKKLSTLQAAADRLAR 394 Lambda K H 0.317 0.132 0.375 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: 399 Number of extensions: 15 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: 479 Length of database: 402 Length adjustment: 32 Effective length of query: 447 Effective length of database: 370 Effective search space: 165390 Effective search space used: 165390 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: 51 (24.3 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