Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate GFF835 HP15_814 aspartate aminotransferase
Query= BRENDA::Q56232 (385 letters) >FitnessBrowser__Marino:GFF835 Length = 416 Score = 193 bits (490), Expect = 8e-54 Identities = 114/353 (32%), Positives = 192/353 (54%), Gaps = 11/353 (3%) Query: 32 DLVALTAGEPDFDTPEHVKEAARRALAQGKTKYAPPAGIPELREALAEKFRRENGLSVTP 91 D++ L+ G+PD TP+HV +A AL G+T Y AG+PEL AL + + + +T Sbjct: 58 DVIHLSIGQPDLPTPKHVIDAYIDALNAGQTGYTMDAGLPELLVALRDYYGKRYNRKLTR 117 Query: 92 EETIVTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYPEMVRFAGGVVVEVETLPEEGFV 151 + ++T G +A++ A PG + IV P ++ Y ++R GG V V+T E Sbjct: 118 DNILITSGATEAMYLAISATSAPGRQFIVTDPSFLLYAPLIRMNGGEVKFVQTRAENNHQ 177 Query: 152 PDPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALARLAVEHDFYLVSDEIYEHLLY 211 DP+ V +A+ PRT AL++N+PNNPTGAVYP+ +E + + +DE+Y+HL++ Sbjct: 178 LDPDEVIKAMGPRTYALILNNPNNPTGAVYPRSTVETILEECAYRGIQVYADEVYDHLIF 237 Query: 212 EGEHFSP---GRVAPEHTLTVNGAAKAFAMTGWRIGYACGPKEVIKAMASVSSQSTTSPD 268 + E F+ + ++ + ++ +K ++M G R+G+ + IK++ +T+ + Sbjct: 238 DDEDFASVLNCSMDLDNIMCISSFSKTYSMAGLRVGWVIASQAAIKSLRRFHMFTTSVAN 297 Query: 269 TIAQWATLEALT-NQEASRAFVEMAREAYRRRRDLLLEGLTALG-LKAVRPSGAFYVLMD 326 T +Q+A + ALT +Q+ R V++ YR RRD ++E + + +P GAF+ D Sbjct: 298 TPSQFAGVAALTGDQQCVRDMVDI----YRERRDKVVELVDQTPYMTGYKPGGAFFAFPD 353 Query: 327 TSPIAPDEVRAAERLLEAGVAVVPGTDF--AAFGHVRLSYATSEENLRKALER 377 P A L E GV +VPG F VR+S++T+ E L +A +R Sbjct: 354 LPPHVDGSDLALRMLKETGVCMVPGDAFGEGCTNAVRISFSTTCEKLEEAFDR 406 Lambda K H 0.317 0.133 0.379 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: 367 Number of extensions: 19 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: 385 Length of database: 416 Length adjustment: 31 Effective length of query: 354 Effective length of database: 385 Effective search space: 136290 Effective search space used: 136290 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 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