Align aromatic-amino-acid transaminase TyrB; EC 2.6.1.57 (characterized)
to candidate Pf1N1B4_3564 Aspartate aminotransferase (EC 2.6.1.1)
Query= CharProtDB::CH_004054 (397 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3564 Length = 397 Score = 311 bits (796), Expect = 3e-89 Identities = 168/396 (42%), Positives = 237/396 (59%), Gaps = 4/396 (1%) Query: 2 FQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARL-NAQP 60 F + GDPIL LME + +DP K +L +G+Y + G+ P +AV AE RL + QP Sbjct: 3 FDAIGRVPGDPILGLMEAYAQDPNPRKFDLGVGVYKDAQGLTPIPEAVKLAEQRLVDRQP 62 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 Y+ G + I L+ GAD ++ +QR QT GG+GAL++ ADF+ + P Sbjct: 63 --TKTYIGGHGDAAFGKVINELVLGADSALIAEQRAGATQTPGGTGALRLSADFIAQCLP 120 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180 GVW+S+PTW H IFA AG +VS YP Y + N + +LA L P +VLLH Sbjct: 121 GRGVWLSNPTWPIHETIFAAAGVKVSHYP-YVGSDNRLDVEAMLAVLNQAPKGDVVLLHA 179 Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240 CCHNPTG DL++D W V++++++R+L+P +D AYQGFG G+E+DA++ R A+ L Sbjct: 180 CCHNPTGFDLSHDDWRRVLDVVRSRDLLPLIDFAYQGFGDGLEQDAWSTRLFAAELPEVL 239 Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300 +++S SK F LY +R G L V + A+ + QL R +S+PP+ GA VVA +L Sbjct: 240 ITSSCSKNFGLYRDRTGALIVCAKTADKLVDIRSQLANIARNLWSTPPDHGAAVVATILG 299 Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360 D LK+ W EVE MR RI +R LV+ L F ++ QRGMFSYTGLS QV Sbjct: 300 DPELKSRWADEVEAMRLRIAQLRSGLVEALEPHGLRERFAHIGVQRGMFSYTGLSPEQVK 359 Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAV 396 +LRE VY+++SGR VAG++ + +A+A A V Sbjct: 360 QLREHHSVYMVSSGRANVAGIDATRLDLLAEAIANV 395 Lambda K H 0.320 0.135 0.401 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: 408 Number of extensions: 22 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: 397 Length of database: 397 Length adjustment: 31 Effective length of query: 366 Effective length of database: 366 Effective search space: 133956 Effective search space used: 133956 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 (21.8 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