Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78 (characterized)
to candidate BPHYT_RS00155 BPHYT_RS00155 aminotransferase
Query= SwissProt::Q8KDS8 (400 letters) >FitnessBrowser__BFirm:BPHYT_RS00155 Length = 384 Score = 165 bits (417), Expect = 2e-45 Identities = 111/363 (30%), Positives = 189/363 (52%), Gaps = 16/363 (4%) Query: 38 DVVSLSAGEPDFPTPENVCEAGIEAIRKGFTRYTANSGIPELKKAIIRKLQRDNGLEY-A 96 D ++LS G P+F + + +A+R G +Y +GI L++A+ K+ G+ Y Sbjct: 30 DALNLSQGAPNFAPDAKLIDGVAQAMRAGHNQYAPMAGIAALREALADKVATLYGVRYDP 89 Query: 97 EDEIIVSNGGKQALANTFLALCDEGDEVIVPAPYWVSFPEMARLAEATPVIVETSIETGY 156 E+ V + L +T AL GDEVI P + S+ + RL ATPV ++ S++ + Sbjct: 90 ASEVTVIASASEGLYSTISALVHPGDEVIYFEPSFDSYGPIVRLQGATPVPIKLSLDD-F 148 Query: 157 KMTPEQLAAAITPKTRILVLNSPSNPSGAVYNEAEVRALMQVIEGKEIFVLSDEMYDMIC 216 ++ +++AAAITPKTR+++ N+P NP+ V++EA+V L V +I +L+DE+Y+ + Sbjct: 149 RVNWDEVAAAITPKTRMIITNTPHNPTATVFSEADVERLKAVTRNTDIVILADEVYEHVV 208 Query: 217 YGGVRPFSPARIPEMKPWVIVSNGTSKSYSMTGWRIGYLAAPKWIINACDKIQSQTTSNA 276 + G + S A E+ ++ + KSY +TGWR+GY AP +++ K+ +A Sbjct: 209 FDGAKHQSMACHSELAERSVIVSSFGKSYHVTGWRVGYCLAPAALMDEIRKVHQFMVFSA 268 Query: 277 NSIAQKAAVAALDGDQSIVEQRRAEFEKRRDFMFRELNTISGIECTLPEGAFYIFPSIKG 336 ++ Q A V AL +S + A ++K+RD + L S E EG+F++ +G Sbjct: 269 DTPMQYAFVDALANRESYL-GLSAFYQKKRDLLAEALRD-SRFELLPSEGSFFMLARFRG 326 Query: 337 LLGKTFGGKVMKDSTDVAEYLLTEHYVATVPGDAF---GAPENL-RLSYAASIEELAEAV 392 ++ +D L+ + VAT+P AF G L RLS++ L E Sbjct: 327 FSDES--------DSDFVLRLIRDARVATIPLSAFYTDGTDSGLIRLSFSKDDATLIEGA 378 Query: 393 NRI 395 R+ Sbjct: 379 RRL 381 Lambda K H 0.316 0.132 0.376 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: 316 Number of extensions: 17 Number of successful extensions: 3 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: 384 Length adjustment: 31 Effective length of query: 369 Effective length of database: 353 Effective search space: 130257 Effective search space used: 130257 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 (21.6 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