Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate HSERO_RS22025 HSERO_RS22025 aromatic amino acid aminotransferase
Query= BRENDA::P04693 (397 letters) >FitnessBrowser__HerbieS:HSERO_RS22025 Length = 396 Score = 454 bits (1169), Expect = e-132 Identities = 220/397 (55%), Positives = 283/397 (71%), Gaps = 3/397 (0%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 MF + YAGDPIL+LME+F+ D RS+KVNLSIG+Y + G++P L +V A A + AQ Sbjct: 1 MFSHLPPYAGDPILSLMEQFQRDERSNKVNLSIGIYTDGKGVVPVLPSVRTAAAAV-AQA 59 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 +YLPMEG YR A+A LLFGAD P + +A +QTLGGSGALKVGAD + R+FP Sbjct: 60 DAPYVYLPMEGHGAYRQAVAKLLFGADLPA--PEHLAIVQTLGGSGALKVGADLIARFFP 117 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180 + +W+ DPTW+NH+ IF GAGF+ YP+YD T G+ F +LA + +LP ++VLLHP Sbjct: 118 QPTIWLPDPTWDNHIGIFEGAGFKTERYPYYDAQTKGLNFEGMLAKIDSLPRGAVVLLHP 177 Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240 CCHNPTG D T QW+ ++E+++ R L+PF D+AYQGF ++ED + +R +P Sbjct: 178 CCHNPTGVDPTRAQWEQIVEVVEKRGLLPFFDLAYQGFAESLDEDIWPVREAVRRQIPFF 237 Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300 +SNSFSKIFSLY ER+G LSV C A A VLGQLK TVRRNYSSPP GA +VA VL Sbjct: 238 LSNSFSKIFSLYSERIGALSVFCPQAGQAANVLGQLKLTVRRNYSSPPRNGALLVAHVLG 297 Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360 D+ L A W EVEEMR R+ MR +L L + +P+++F +LL Q GMF YTGLS+AQVD Sbjct: 298 DDKLAAQWRGEVEEMRVRVRDMRVKLASQLKSAVPDQDFSFLLRQNGMFGYTGLSSAQVD 357 Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397 RLREEFGVY + +GR+CVAGLN +NV RVA+ A V+ Sbjct: 358 RLREEFGVYAVGTGRICVAGLNDSNVARVAETMAEVL 394 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: 446 Number of extensions: 10 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: 396 Length adjustment: 31 Effective length of query: 366 Effective length of database: 365 Effective search space: 133590 Effective search space used: 133590 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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