Align aromatic-amino-acid transaminase TyrB; EC 2.6.1.57 (characterized)
to candidate 5209529 Shew_1999 aromatic amino acid aminotransferase (RefSeq)
Query= CharProtDB::CH_004054 (397 letters) >FitnessBrowser__PV4:5209529 Length = 397 Score = 352 bits (904), Expect = e-102 Identities = 177/397 (44%), Positives = 255/397 (64%), Gaps = 1/397 (0%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 +F +V DPIL L + FK DPR+DKVNL +G+Y +E G P L++V AE +L + Sbjct: 2 IFNQVVLAPADPILGLTDAFKADPRADKVNLGVGIYKDESGQTPILKSVKLAEQKL-LET 60 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 + YL ++G+ Y A+ LLFG DH V+ ++R T Q GG+G+L++ A+F+ R Sbjct: 61 ETSKSYLGIDGVIAYNQAVQGLLFGTDHAVMSEKRAVTAQAPGGTGSLRMAAEFVVRNTA 120 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180 VWVS+ TW NH IF AG V Y +YD A++ + F+ +L +L+ + ++LLH Sbjct: 121 SRTVWVSNLTWANHNNIFQSAGLTVKQYGYYDAASHDIDFDAMLTSLEQANSGDLLLLHG 180 Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240 CCHNPTG DL QW+ + ++ + LIP D AYQGFGAG+EEDA +R +AS L Sbjct: 181 CCHNPTGIDLNICQWEVIAQLCVDKGLIPLFDFAYQGFGAGVEEDAQGLRLVASKVPELL 240 Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300 V+NSFSK F LY ER+G ++++ ED E A R Q+K+T+R +YS+PP GA +VA +L Sbjct: 241 VANSFSKNFGLYNERIGAVTLVAEDEETAKRAFSQIKSTIRSSYSNPPAHGALIVATILG 300 Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360 D L+ W E+ +MR RI MR VK LS + E++F ++ Q GMFS++GL+ QV Sbjct: 301 DAELRKLWEEELTQMRERIAEMRVLFVKTLSEQGVEQDFSFISAQNGMFSFSGLNKDQVA 360 Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397 RL+EEFGVY++ SGR+ VAG+ AN+ + +A A V+ Sbjct: 361 RLKEEFGVYIVGSGRISVAGMTRANMDTICRAIAQVL 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: 409 Number of extensions: 12 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