Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate 8501474 DvMF_2204 aminotransferase class I and II (RefSeq)
Query= BRENDA::Q02635 (400 letters) >FitnessBrowser__Miya:8501474 Length = 390 Score = 329 bits (843), Expect = 1e-94 Identities = 174/391 (44%), Positives = 242/391 (61%), Gaps = 7/391 (1%) Query: 4 LADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETK 63 ++D L+R+KPSAT+AV+ KA ELKAKG V+ L GEPDF TP+++++AA AID+G T+ Sbjct: 3 ISDRLTRIKPSATLAVNAKALELKAKGVQVVSLAVGEPDFPTPEHVREAAKTAIDQGFTR 62 Query: 64 YTPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAP 123 YT V GIPELR+A+ F R ++ T+V GGKQ L+N F LNPGDEV++PAP Sbjct: 63 YTQVPGIPELRQAVCGYFARFYGVEAPMEATVVTNGGKQALYNLFQCLLNPGDEVLVPAP 122 Query: 124 YWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSH 183 YWVSYP +V L GG PVFV + E FK+ E+LDRA+TPKT+ + NSPSNP+GA YS Sbjct: 123 YWVSYPALVELAGGVPVFVASPAERGFKVTPEELDRAVTPKTRVLLLNSPSNPTGACYSR 182 Query: 184 EELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAM 243 E A+ + + ++V++D++Y+ L Y + + E +NG++K +AM Sbjct: 183 AETDAIMEWAIAR-DLFVVSDEIYDRLVYEPAEAVSVCDWWERHPENVAVVNGLAKTFAM 241 Query: 244 TGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRD 303 TGWR+GYA LIKAM IQGQ TS S+AQ AA+ AL GP D + K+ F+ RRD Sbjct: 242 TGWRVGYALAHPDLIKAMTKIQGQSTSNICSVAQKAALAALTGPYDAVEEMKKSFRRRRD 301 Query: 304 LVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVV 363 L +++ G+ CP P+GAFY++ L P + T ++E VA+V Sbjct: 302 LAHGIVSSWPGVICPKPDGAFYLFADMRALFTPALPDSASLCT------YIMEQANVALV 355 Query: 364 HGSAFGLGPNFRISYATSEALLEEACRRIQR 394 G+AFG R SYA S+ L A ++ + Sbjct: 356 PGAAFGDDACLRFSYAVSDDTLMIALDKVAK 386 Lambda K H 0.318 0.134 0.402 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: 21 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: 390 Length adjustment: 31 Effective length of query: 369 Effective length of database: 359 Effective search space: 132471 Effective search space used: 132471 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 Aug 03 2021. The underlying query database was built on Aug 03 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