Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate AZOBR_RS24065 AZOBR_RS24065 aspartate aminotransferase
Query= SwissProt::A3PMF8 (400 letters) >FitnessBrowser__azobra:AZOBR_RS24065 Length = 392 Score = 233 bits (595), Expect = 6e-66 Identities = 138/373 (36%), Positives = 197/373 (52%), Gaps = 16/373 (4%) Query: 30 GRDVIGLGAGEPDFDTPDNIKAAAKRAIDAGRTKYTAVDGIPELKRAICEKFERENGLKY 89 G DVI L G+PDFDTP ++ AA A+ AG T YT + G PEL+ A+ R GL Sbjct: 31 GEDVIVLSVGDPDFDTPAPVRDAAIAALHAGDTHYTPIPGRPELRAALARDVARRTGLPV 90 Query: 90 TPAQVTVGTGGKQILYNALVATLNPGDEVIIPAPYWVSYPDMVLLAGGTPVSVAAGMETG 149 P V V G + L+NA + + GDEV++P P +++Y V +G T V VA T Sbjct: 91 EPENVIVCAGAQNGLFNATLCLVEAGDEVLVPEPMYLTYEACVRASGATLVPVAPDAAT- 149 Query: 150 FKLTPEQLEAAITPRTKWFIFNSPSNPTGAAYTRAELAALCEVLMRHPQVWIMSDDMYEH 209 +L P L AA+TPRT+ +P+NPTG + EL A+ ++ RH +W+++D++Y Sbjct: 150 LRLDPAALAAAVTPRTRAIFLATPANPTGIVMSAEELEAVADLARRH-DLWVVADEVYAS 208 Query: 210 LVFDDFDFTTPAQIEPGLYDRTLTCNGVSKAYCMTGWRIGYAAGPVELIRAMGTIQSQST 269 L FD PG+ +RT+T N +SK++ MTGWR G+ P L+ MGT+ Sbjct: 209 LTFDRPHIGIATL--PGMAERTVTINSLSKSHAMTGWRAGWVVAPAPLVAHMGTLALCML 266 Query: 270 SNPCSIAQYAALEALSGPQEFLATNREAFQRRRDLVVSMLNEAKGVTCPNPEGAFYVYPD 329 Q AAL A+ E +A RE ++RRRD+ + L G+ C PE ++ D Sbjct: 267 YGLPGFVQQAALVAVEQGDEAVAAMREGYRRRRDIALEALGSVPGLRCLKPEAGMFMLVD 326 Query: 330 ISGCIGKTSAGGAKITDDEAFASALLEETGVAVVFGAAFG--LSPNFRISYATADEVLRE 387 + G T FA L ETGV+V+ AFG + R+S+A ++ L E Sbjct: 327 VRGTGLPTM----------EFAWRLFRETGVSVLDAGAFGPAAAGCVRLSFAVSEAELAE 376 Query: 388 ACARIQAFCAGLS 400 AC RI AF GL+ Sbjct: 377 ACRRIAAFVTGLA 389 Lambda K H 0.318 0.134 0.399 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: 456 Number of extensions: 34 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: 400 Length of database: 392 Length adjustment: 31 Effective length of query: 369 Effective length of database: 361 Effective search space: 133209 Effective search space used: 133209 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 09 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