GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Pseudomonas putida KT2440

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate PP_3544 PP_3544 Transcriptional regulator, GntR family

Query= BRENDA::A0A060PQX5
         (417 letters)



>FitnessBrowser__Putida:PP_3544
          Length = 469

 Score =  194 bits (494), Expect = 4e-54
 Identities = 116/381 (30%), Positives = 202/381 (53%), Gaps = 10/381 (2%)

Query: 34  VRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQYGTTKGFTPLRL 93
           V  +L  ++  + I+     P+PE FP++ ++            + +    + G   LR 
Sbjct: 95  VFSILDSIKDPNTIAFGSAFPSPELFPLQRLSRSLASASRSMDPRMVVTDLSPGNPQLRR 154

Query: 94  ALA-EWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAPTYLAALQAFKY 152
            +A  +M     +P+   +++IT+G+ +AL+L  +    PGD+V +EAP + A LQ  + 
Sbjct: 155 QIALRYMVGGLMLPME--ELLITNGALEALNLCLQAVTQPGDLVAIEAPAFYACLQVLER 212

Query: 153 YEPEFVQIPLDD-EGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRRKRL 211
            + + V+IP+   EGM + +L + L     E   VK V+ +  FQNP G +M E +++ +
Sbjct: 213 LKLKAVEIPVHPREGMDLGVLAQTL-----EMHPVKAVWCMTNFQNPVGASMPEAKKQAM 267

Query: 212 LELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILAPGFRIGWIAA 271
           +EL + +   ++ED+ Y EL YS +  KP KA+D +G VM+ G+F+K LAPG+RIGW+AA
Sbjct: 268 VELLARHQVPLIEDDVYAELYYSQQAPKPAKAFDTQGLVMHCGSFAKSLAPGYRIGWVAA 327

Query: 272 EPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDAMLKALEE 331
                +K+E  K    LC +  +Q     Y++ G  D H+  +    + ++  ML A+  
Sbjct: 328 -GRFAQKIERLKLMTSLCASMPAQAAIADYLQHGGYDRHLRKLRYALEGQQANMLAAIAR 386

Query: 332 FMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVKNTMRLN 391
             P   R ++P GG F+W+ LPE +D   +   A+A+G++  PG  F   R   N +RLN
Sbjct: 387 HFPAQTRVSQPSGGYFLWLELPEQMDALKLFHMALAQGISIAPGPIFSPTRRFGNCIRLN 446

Query: 392 FTYVPEEKIREGIKRLAETIK 412
           +     +   + ++ L   I+
Sbjct: 447 YGSPWHDGAEQAMETLGRIIR 467


Lambda     K      H
   0.318    0.137    0.398 

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: 440
Number of extensions: 15
Number of successful extensions: 4
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: 417
Length of database: 469
Length adjustment: 32
Effective length of query: 385
Effective length of database: 437
Effective search space:   168245
Effective search space used:   168245
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 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