Align Aromatic-amino-acid aminotransferase (EC 2.6.1.57) (characterized)
to candidate WP_068168339.1 HTA01S_RS06765 aspartate/tyrosine/aromatic aminotransferase
Query= reanno::Cup4G11:RR42_RS33490 (400 letters) >NCBI__GCF_001592305.1:WP_068168339.1 Length = 402 Score = 416 bits (1069), Expect = e-121 Identities = 212/400 (53%), Positives = 266/400 (66%), Gaps = 4/400 (1%) Query: 1 MFEHIDAYPGDPILSLNESFQLDPRTDKVNLSIGIYFDDEGRLPVMQAVREAEAALMADM 60 +F ++ P DPIL LNE F D +KVNL +G+YFDD G+LP++Q V+ AE A+M Sbjct: 3 LFTAVEMAPRDPILGLNEQFAADTNPNKVNLGVGVYFDDNGKLPLLQCVQAAEKAMMDKP 62 Query: 61 GPRPYLPMAGFAAYRDAVQALVFGQPCQARAEGRIATVQTLGGSGALRVGADFLKRYFPD 120 R YLP+ G AAY AV+ LVFG GR+ATVQ +GG+G L++GADFLK+ PD Sbjct: 63 TARGYLPIDGIAAYDAAVKGLVFGADSDVVKSGRVATVQAIGGTGGLKIGADFLKKISPD 122 Query: 121 AQVWISDPSWENHRVIFERTGFTVNTYPYYDDAT----GGLKFDAMLDALRLIPKRSIVL 176 A+V ISDPSWENHR +F GFTV TYPY+D + GG+ FD ML AL +IVL Sbjct: 123 AKVLISDPSWENHRALFTNAGFTVETYPYFDQSANGGLGGINFDGMLAALNAAAPGTIVL 182 Query: 177 LHACCHNPTGVDLNHDQWRQLITLLKQHELLPFVDMAYQGFGAGLDDDAFAVRELVAQGV 236 LHACCHNPTG D+ QW Q+I +++ L F+DMAYQGFG G+ +D + + VA G+ Sbjct: 183 LHACCHNPTGYDITPAQWDQVIAVVQARNLTAFLDMAYQGFGYGIAEDGAVIGKFVAAGL 242 Query: 237 PCLVANSFSKNFSLYGERCGGLSVVCDSAEETGRVLGQLTGAVRANYSNPPTHGARVVAR 296 V+ SFSK+FSLYGER G LSVV S EET RVL QL A+R NYSNPPTHG +VA Sbjct: 243 NIFVSTSFSKSFSLYGERVGALSVVGSSKEETDRVLSQLKIAIRTNYSNPPTHGGAIVAA 302 Query: 297 VLTTPALRTIWERELAGKCERIAKMRAAIHKGLAAHVSGEALSRYLTQRGMFTYTGLTAD 356 VL P LR +WE+EL RI MR + GL A + +S TQ GMF+Y+GL+ D Sbjct: 303 VLNNPELRALWEQELGEMRVRIKAMRQKLVDGLKAAGVAKDMSFITTQIGMFSYSGLSKD 362 Query: 357 QVDRLRTEHGVYLLRSGRMCVAGLNERNVTQVAQAIASVL 396 Q+ RLR+E GVY +GRMCVA LN +N+ V QAIA V+ Sbjct: 363 QMVRLRSEFGVYGTDTGRMCVAALNSKNIDYVCQAIAKVI 402 Lambda K H 0.323 0.137 0.417 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: 443 Number of extensions: 14 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: 400 Length of database: 402 Length adjustment: 31 Effective length of query: 369 Effective length of database: 371 Effective search space: 136899 Effective search space used: 136899 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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