GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Pseudomonas putida KT2440

Align Aromatic-amino-acid aminotransferase (EC 2.6.1.57) (characterized)
to candidate PP_1972 PP_1972 aromatic-amino-acid aminotransferase

Query= reanno::Cup4G11:RR42_RS33490
         (400 letters)



>FitnessBrowser__Putida:PP_1972
          Length = 398

 Score =  406 bits (1044), Expect = e-118
 Identities = 206/396 (52%), Positives = 266/396 (67%)

Query: 1   MFEHIDAYPGDPILSLNESFQLDPRTDKVNLSIGIYFDDEGRLPVMQAVREAEAALMADM 60
           +F  ++  P DPIL LNE+F  DPRTDKVNL +G+Y ++EGR+P+++AV EAE    A  
Sbjct: 3   LFSAVELAPRDPILGLNEAFNADPRTDKVNLGVGVYCNEEGRIPLLRAVIEAETQRAAQH 62

Query: 61  GPRPYLPMAGFAAYRDAVQALVFGQPCQARAEGRIATVQTLGGSGALRVGADFLKRYFPD 120
             R YLP+ G A Y  AVQ L+FG      A GR+ TVQ +GG+GAL++GADFLKR  P+
Sbjct: 63  ASRGYLPIDGIATYDQAVQKLLFGAESPLLAAGRVVTVQAVGGTGALKIGADFLKRLSPN 122

Query: 121 AQVWISDPSWENHRVIFERTGFTVNTYPYYDDATGGLKFDAMLDALRLIPKRSIVLLHAC 180
           A V ISDPSWENHR +FE  GF V TY YYD  T  +    ML+ L  +P  SIV+LHAC
Sbjct: 123 AVVAISDPSWENHRALFESAGFPVQTYRYYDAPTNDVNRAGMLEDLNALPSGSIVVLHAC 182

Query: 181 CHNPTGVDLNHDQWRQLITLLKQHELLPFVDMAYQGFGAGLDDDAFAVRELVAQGVPCLV 240
           CHNPTGVDLN D W+ ++ ++K    +PF+DMAYQGFG G+ +DAFAVR     G+   V
Sbjct: 183 CHNPTGVDLNLDDWKNVLEVVKAKGHVPFLDMAYQGFGDGIAEDAFAVRLFAESGLEFFV 242

Query: 241 ANSFSKNFSLYGERCGGLSVVCDSAEETGRVLGQLTGAVRANYSNPPTHGARVVARVLTT 300
           ++SFSK+FSLYGER G LS+V  S +E+ RVL Q+   +R  YSNPPTHGA +VA VL +
Sbjct: 243 SSSFSKSFSLYGERVGALSIVTASKDESTRVLSQVKRVIRTTYSNPPTHGATIVATVLNS 302

Query: 301 PALRTIWERELAGKCERIAKMRAAIHKGLAAHVSGEALSRYLTQRGMFTYTGLTADQVDR 360
             LR +WE ELA   ERI  MR  +   LA + +    S    Q GMF+Y+GLT +QV R
Sbjct: 303 AELRQMWETELAEMRERIHGMRKQMVSLLAEYGANRDFSFVGRQVGMFSYSGLTVEQVTR 362

Query: 361 LRTEHGVYLLRSGRMCVAGLNERNVTQVAQAIASVL 396
           L+ + G+Y L +GR+ VA LN+ N+  V +AI  VL
Sbjct: 363 LKNDFGIYALDTGRIAVAALNQSNIHVVTKAIVEVL 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: 422
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: 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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