Align Aromatic-amino-acid aminotransferase (EC 2.6.1.57) (characterized)
to candidate WP_050461862.1 AKL27_RS05885 aspartate/tyrosine/aromatic aminotransferase
Query= reanno::Cup4G11:RR42_RS33490 (400 letters) >NCBI__GCF_001189915.1:WP_050461862.1 Length = 410 Score = 500 bits (1287), Expect = e-146 Identities = 244/397 (61%), Positives = 294/397 (74%), Gaps = 1/397 (0%) Query: 1 MFEHIDAYPGDPILSLNESFQLDPRTDKVNLSIGIYFDDEGRLPVMQAVREAEAALMADM 60 +F HI YPGDPILSL E+F D RTDKV+LSIG+YFD+ GRLP++ +VR+AE AL+ + Sbjct: 13 LFGHIPPYPGDPILSLMEAFSRDQRTDKVSLSIGVYFDNAGRLPMLDSVRQAETALLQQL 72 Query: 61 GPRPYLPMAGFAAYRDAVQALVFGQPCQARAEGRIATVQTLGGSGALRVGADFLKRYFPD 120 GPRPYLPM G ++R AVQ L+FG + GR AT+QTLGGSG L+VGADFL+RYFP Sbjct: 73 GPRPYLPMEGLESFRTAVQHLLFGAASEVVTSGRAATLQTLGGSGGLKVGADFLRRYFPA 132 Query: 121 AQVWISDPSWENHRVIFERTGFTVNTYPYYDDATGGLKFDAMLDALRLIPKRSIVLLHAC 180 A++W+SDP+W+NHR IFE G V+TYPYYD ATGGL FD ML L +P++SIVLLHA Sbjct: 133 AEIWVSDPTWDNHRAIFEGAGLQVHTYPYYDPATGGLLFDQMLATLHTLPRQSIVLLHAS 192 Query: 181 CHNPTGVDLNHDQWRQLITLLKQHELLPFVDMAYQGFGAGLDDDAFAVRELVAQGVPCLV 240 CHNPTGVDL+HDQWR LI +LK+ EL+PF+D+AYQGFG GLD+DAFA+ L G+ V Sbjct: 193 CHNPTGVDLSHDQWRTLIPVLKERELIPFIDIAYQGFGDGLDEDAFALHALAEAGMQFFV 252 Query: 241 ANSFSKNFSLYGERCGGLSVVCDSAEETGRVLGQLTGAVRANYSNPPTHGARVVARVLTT 300 ANSFSKNFSLYGERCGGLSVVC + VLGQL VR NYS PPTHGAR+VA +L Sbjct: 253 ANSFSKNFSLYGERCGGLSVVCADRRDAETVLGQLKATVRRNYSTPPTHGARIVASILQD 312 Query: 301 PALRTIWERELAGKCERIAKMRAAIHKGLAAHVSGEALSRY-LTQRGMFTYTGLTADQVD 359 P L W +E +RI MR ++H L G Y LTQRGMF+YTGL+A QVD Sbjct: 313 PKLFAQWVQETGAMRQRIRAMRESLHAALNEKFDGRRNFDYLLTQRGMFSYTGLSAAQVD 372 Query: 360 RLRTEHGVYLLRSGRMCVAGLNERNVTQVAQAIASVL 396 RLR EH VYL+ SGR+C++GL NV VA AIA+VL Sbjct: 373 RLREEHAVYLVGSGRLCLSGLTTGNVGHVADAIAAVL 409 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: 544 Number of extensions: 20 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: 410 Length adjustment: 31 Effective length of query: 369 Effective length of database: 379 Effective search space: 139851 Effective search space used: 139851 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