Align Aromatic-amino-acid aminotransferase (EC 2.6.1.57) (characterized)
to candidate Ac3H11_4115 Aromatic-amino-acid aminotransferase (EC 2.6.1.57)
Query= reanno::Cup4G11:RR42_RS33490 (400 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4115 Length = 398 Score = 406 bits (1044), Expect = e-118 Identities = 204/396 (51%), Positives = 261/396 (65%) Query: 1 MFEHIDAYPGDPILSLNESFQLDPRTDKVNLSIGIYFDDEGRLPVMQAVREAEAALMADM 60 +F ++ P DPIL LNE F D +KVNL +G+YFDD G+LP++Q V+ AE +M+ Sbjct: 3 LFTAVEMAPRDPILGLNEQFNADTNPNKVNLGVGVYFDDNGKLPLLQCVQAAEKTMMSTP 62 Query: 61 GPRPYLPMAGFAAYRDAVQALVFGQPCQARAEGRIATVQTLGGSGALRVGADFLKRYFPD 120 R YLP+ G AY +AV++LVFG + GR+ATVQ +GG+G L++GADFLK+ P Sbjct: 63 TARGYLPIDGIVAYDNAVKSLVFGADSEPVTSGRVATVQAIGGTGGLKIGADFLKKVSPS 122 Query: 121 AQVWISDPSWENHRVIFERTGFTVNTYPYYDDATGGLKFDAMLDALRLIPKRSIVLLHAC 180 A+V ISDPSWENHR +F GF V+TY YYD G+ F+ L +L +IV+LHAC Sbjct: 123 AKVLISDPSWENHRALFTNAGFEVDTYAYYDAEKRGVNFEGFLASLNAAAPGTIVVLHAC 182 Query: 181 CHNPTGVDLNHDQWRQLITLLKQHELLPFVDMAYQGFGAGLDDDAFAVRELVAQGVPCLV 240 CHNPTG D+ QW Q+I +K L PF+DMAYQGFG G+ +D + + VA G+ V Sbjct: 183 CHNPTGYDITAAQWDQVIAAVKAKGLTPFLDMAYQGFGHGIAEDGAVIGKFVAAGLNFFV 242 Query: 241 ANSFSKNFSLYGERCGGLSVVCDSAEETGRVLGQLTGAVRANYSNPPTHGARVVARVLTT 300 + SFSK+FSLYGER GGLSV+C EE RVL QL +R NYSNPP HG VVA VL Sbjct: 243 STSFSKSFSLYGERVGGLSVLCADKEEASRVLSQLKIVIRTNYSNPPIHGGAVVAAVLNN 302 Query: 301 PALRTIWERELAGKCERIAKMRAAIHKGLAAHVSGEALSRYLTQRGMFTYTGLTADQVDR 360 P LR +WE+ELA RI MR + GL A + +S TQ GMF+Y+GL+ DQ+ R Sbjct: 303 PELRAMWEQELAEMRVRIKAMRQKLVDGLKAAGVKQDMSFITTQIGMFSYSGLSKDQMVR 362 Query: 361 LRTEHGVYLLRSGRMCVAGLNERNVTQVAQAIASVL 396 LR E GVY +GRMCVA LN +N+ V QAIA V+ Sbjct: 363 LRNEFGVYGTDTGRMCVAALNSKNIDYVCQAIAKVV 398 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: 437 Number of extensions: 16 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: 400 Length of database: 398 Length adjustment: 31 Effective length of query: 369 Effective length of database: 367 Effective search space: 135423 Effective search space used: 135423 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 17 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