Align aromatic-amino-acid aminotransferase (EC 2.6.1.1) (characterized)
to candidate WP_029001498.1 H537_RS0134355 amino acid aminotransferase
Query= metacyc::PHETRANTHAUERA-MONOMER (404 letters) >NCBI__GCF_000430725.1:WP_029001498.1 Length = 397 Score = 528 bits (1360), Expect = e-154 Identities = 254/396 (64%), Positives = 309/396 (78%) Query: 1 MFEHVDAYPGDPILSLVETFHHDPRPRKVNLGIGLYYDEEGRIPLLGSVEKAEAALAANP 60 MF+H++ Y GDPIL L E F DPRP KVNL IG+Y+D+ GRIP+L SV +AEA L Sbjct: 1 MFQHLEPYAGDPILGLNEQFQTDPRPHKVNLSIGIYFDDAGRIPVLESVRRAEAQLLEQS 60 Query: 61 GPRPYLPMEGAADYRAAVQKLLFGPDSAALRAGRIATIQTIGGSGALKVGADLLKRYFPA 120 P+ YLP+EG+A RA VQKLLFG A+ +GRIAT+QT+G SG LKVGAD LKR+FP Sbjct: 61 APKSYLPIEGSAACRAEVQKLLFGAGHEAVTSGRIATLQTVGSSGGLKVGADFLKRWFPG 120 Query: 121 SEVWVSDPTWDNHRSIFEGAGIEVHDYPYYDAASGGVRFDEMIETLQSLPAQSIVLLHPC 180 VWVSDPTWDNHR++FEGAG+ V+ YPYYDAA+GG++FD M L+ +PA S+VLLH C Sbjct: 121 IGVWVSDPTWDNHRAMFEGAGLTVNTYPYYDAATGGLKFDAMCAALRQVPAGSVVLLHAC 180 Query: 181 CHNPTGVDLSTAQWQEVIAVVASRGLIPFLDIAYQGFGDNLDDDAYAARAMADAGVSFFV 240 CHNPTGVDL+ QW ++I ++ L+P+LD+AYQG+GD +++DA+A RA+ADAG+ FFV Sbjct: 181 CHNPTGVDLTREQWLQLIPILKEGKLLPYLDLAYQGYGDGIEEDAFAIRALADAGLRFFV 240 Query: 241 SNSFSKNLSFYGERCGGLSVVCQDADEAERVLGQLKFTVRRNYSSPPVHGGRVAAAVMND 300 +NSFSK++S YGER G LSVVC DA EA+ VLGQ+K TVRRNYSSPP+H G V A V+ D Sbjct: 241 ANSFSKSMSLYGERAGALSVVCADAAEADLVLGQMKATVRRNYSSPPIHAGLVVARVLGD 300 Query: 301 AGLHEEWVGEVRGMRERIKAMREKLHEVLSSTLPGRDFSYFVKQRGMFSYTGLTPEQVDR 360 A L W EV MRERI MR LH VL++ LPGR+F YF+ QRGMFSYTGL+ EQVDR Sbjct: 301 AQLRALWESEVAAMRERIAGMRRSLHGVLAAKLPGRNFDYFLTQRGMFSYTGLSAEQVDR 360 Query: 361 LREEFAVYVVQSGRMCVAGLNRGNVDYVAKAMAAVL 396 LREE AVY+V+SGRMCVAGLN GNV VA AMAAVL Sbjct: 361 LREEHAVYLVRSGRMCVAGLNTGNVQAVADAMAAVL 396 Lambda K H 0.320 0.136 0.409 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: 523 Number of extensions: 19 Number of successful extensions: 1 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: 404 Length of database: 397 Length adjustment: 31 Effective length of query: 373 Effective length of database: 366 Effective search space: 136518 Effective search space used: 136518 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 Jul 25 2024. The underlying query database was built on Jul 25 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