Align Aspartate/prephenate aminotransferase; AspAT / PAT; Transaminase A; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate RR42_RS35305 RR42_RS35305 aspartate aminotransferase
Query= SwissProt::Q02635 (400 letters) >FitnessBrowser__Cup4G11:RR42_RS35305 Length = 401 Score = 469 bits (1206), Expect = e-137 Identities = 226/398 (56%), Positives = 289/398 (72%) Query: 1 MAFLADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRG 60 M L D L+R+KPS + Q+ REL+A GRDVIGL AGEPDF+TP +I++AA A+ G Sbjct: 1 MLSLTDRLNRIKPSPSSMAGQRVRELRAAGRDVIGLTAGEPDFETPAHIREAAWRAMQAG 60 Query: 61 ETKYTPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVI 120 +T+YT V G ELR A A+KFKREN LDY A++ IV TG KQ++FNA M T+ GDEV++ Sbjct: 61 KTRYTDVGGTAELRHAAAQKFKRENGLDYAASEIIVSTGAKQVIFNALMCTVQQGDEVIV 120 Query: 121 PAPYWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAA 180 PAPYWVSYP++ GG PVFV + EN FKL E+L+RAI+ +T+W + NSP+NPSGAA Sbjct: 121 PAPYWVSYPDITLFAGGVPVFVACQAENGFKLTPEELERAISARTRWLILNSPNNPSGAA 180 Query: 181 YSHEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKA 240 Y+ EL A+ +VL +HPHVWV+TDD+YEHLTY F T + P L RTLT+NGVSKA Sbjct: 181 YTRTELVAIAEVLERHPHVWVMTDDIYEHLTYDGAAFVTLAQAAPSLKARTLTINGVSKA 240 Query: 241 YAMTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQG 300 YAMTGWRIGYA P LIKAM +Q Q TSGA ++AQ AA+ AL+GPQDFI NK +FQ Sbjct: 241 YAMTGWRIGYAGAPAPLIKAMVKLQSQSTSGANAVAQAAAIAALDGPQDFIAANKAVFQA 300 Query: 301 RRDLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGV 360 RRD VV+ L Q GI C P GAFYV+ SC LIG P G VI + +D+V+ +L+++ + Sbjct: 301 RRDRVVAALGQVDGIHCQAPAGAFYVFASCEALIGARTPHGSVIRSSDDWVNWVLDSQDL 360 Query: 361 AVVHGSAFGLGPNFRISYATSEALLEEACRRIQRFCAA 398 AV+ GSA+G+ +FR+S+A S A L+E CRRI+ AA Sbjct: 361 AVLQGSAYGVDTHFRLSFAASMAQLDEGCRRIEAAAAA 398 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: 486 Number of extensions: 16 Number of successful extensions: 1 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: 401 Length adjustment: 31 Effective length of query: 369 Effective length of database: 370 Effective search space: 136530 Effective search space used: 136530 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 Sep 17 2021. The underlying query database was built on Sep 17 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