GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Phyllobacterium endophyticum PEPV15

Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate WP_106716187.1 CU100_RS08590 PLP-dependent aminotransferase family protein

Query= SwissProt::H3ZPL1
         (417 letters)



>NCBI__GCF_003010935.1:WP_106716187.1
          Length = 411

 Score =  297 bits (761), Expect = 3e-85
 Identities = 170/409 (41%), Positives = 240/409 (58%), Gaps = 13/409 (3%)

Query: 17  DYEKYFSEKALGMKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEKHA 76
           D++  +S +   M+ASE+RELLKL++  D+IS AGG+P P  FP E I E    VL+++A
Sbjct: 3   DWDARYSARTGKMRASEVRELLKLLDQPDIISFAGGIPDPALFPKEAIKEAYSAVLDENA 62

Query: 77  AQALQYGTTKGFTPLRLALAEWMRERYDIPISKVDIMTTSGSQQALDLIGRVFINPGDII 136
             ALQY  ++G+ PLR  L + M     +  +  +I+ T+GSQQALD +G++FI+PGD I
Sbjct: 63  DAALQYSVSEGYKPLRQWLVQHM-AALGVACTIDNIIITTGSQQALDYLGKLFISPGDTI 121

Query: 137 VVEAPTYLAALQAFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTIPTFQ 196
           +   PTYL ALQAF  YEP + ++  +      D      Q     G +V++ Y    F 
Sbjct: 122 LTTWPTYLGALQAFNAYEPRYDRLIPEGGNTTPDAYRTNAQ---AAGGRVRLAYLTGDFS 178

Query: 197 NPAGVTMNEKRRKRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWD-------EEGR 249
           NP G T+  K R +L+ELA + D  ++ED  Y  LRY GE    + A D       +  R
Sbjct: 179 NPTGETIGRKERVKLVELAHELDIPLIEDAAYRVLRYEGENAPSMLALDIEREGHIDRTR 238

Query: 250 VIYLGTFSKILAPGFRIGWIAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGYLDK 309
           V+Y G+FSK L PG R+GW+ A    I KL + KQ+ DL + T +Q++   +V   + D 
Sbjct: 239 VLYSGSFSKSLTPGLRVGWVCAAQPVIAKLVLIKQAADLHSPTINQMVI-HHVAERHFDA 297

Query: 310 HIPKIIEFYKPRRDAMLKALEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAVAK- 368
            + K    Y+ RRD ML AL   MP+GV WT+PEGGMFVW TLP+G+D   +L ++V + 
Sbjct: 298 QVEKARGHYRQRRDHMLGALARHMPEGVTWTRPEGGMFVWMTLPDGMDGAALLARSVEQI 357

Query: 369 GVAYVPGEAFFAHRDVKNTMRLNFTYVPEEKIREGIKRLAETIKEEMKK 417
            VA+VPG AF A     NT+RLNF+    E I  G++RL   I  EM +
Sbjct: 358 RVAFVPGVAFHADGTGGNTIRLNFSLPNAEAIETGMQRLGGLIGREMDR 406


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: 444
Number of extensions: 26
Number of successful extensions: 6
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: 411
Length adjustment: 31
Effective length of query: 386
Effective length of database: 380
Effective search space:   146680
Effective search space used:   146680
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: 50 (23.9 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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