Align aromatic-amino-acid transaminase TyrB; EC 2.6.1.57 (characterized)
to candidate 6937653 Sama_1805 aromatic amino acid aminotransferase (RefSeq)
Query= CharProtDB::CH_004054 (397 letters) >FitnessBrowser__SB2B:6937653 Length = 397 Score = 350 bits (897), Expect = e-101 Identities = 179/397 (45%), Positives = 251/397 (63%), Gaps = 1/397 (0%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 +F +V DPIL L + FK DPR+DKVNL +G+Y +E G P L++V +AEA L A+ Sbjct: 2 IFSQVVPAPADPILGLTDAFKADPRTDKVNLGVGIYKDEAGQTPVLKSVKQAEAILLAEE 61 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 + + YL +EG+ Y + LLFGA H V Q+R T Q GG+GAL+V A+F+ R P Sbjct: 62 NTKN-YLGIEGVTLYNKVVQELLFGATHTVTNQERAVTAQAPGGTGALRVAAEFVVRNTP 120 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180 +WVS+PTW NH IF AG Y +YD A + + F+ +L +L+ +VLLH Sbjct: 121 SRVIWVSNPTWANHQNIFETAGLTTKEYGYYDAANHDIDFDAMLRSLEAANQGDLVLLHG 180 Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240 CCHNPTG DLT +QW V E+ A+ L+P D AYQGFG G+EEDA +R +AS + Sbjct: 181 CCHNPTGIDLTLEQWQKVGELCAAKGLVPLFDFAYQGFGRGIEEDAEGLRLVASMVPELI 240 Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300 ++NSFSK F LY ER+G ++++ AE A Q+K T+R NYS+PP GA +V+ +L+ Sbjct: 241 IANSFSKNFGLYNERIGAVTLVAATAEEAKVAFSQVKRTIRANYSNPPAHGALIVSTILS 300 Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360 LKA+W E+ EMR RI MR V+ L+ ++F ++ Q GMFS++GL+ AQV+ Sbjct: 301 RPELKAAWEQELAEMRERIAEMRTLFVESLAAAGVTQDFSFISRQMGMFSFSGLNKAQVE 360 Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397 LR E GVY++ SGR+ VAG+ N+ + A AAV+ Sbjct: 361 ALRAEHGVYIVGSGRISVAGMTKTNMPVICSAIAAVL 397 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: 424 Number of extensions: 18 Number of successful extensions: 2 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 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