GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Caulobacter crescentus NA1000

Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate CCNA_02244 CCNA_02244 aminotransferase class I family protein

Query= SwissProt::H3ZPL1
         (417 letters)



>FitnessBrowser__Caulo:CCNA_02244
          Length = 425

 Score =  290 bits (741), Expect = 7e-83
 Identities = 166/406 (40%), Positives = 238/406 (58%), Gaps = 19/406 (4%)

Query: 17  DYEKYFSEKALGMKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEKH- 75
           D+   FSE+   ++ASEIRELLKL++  D++S AGG+P P  FP + I +    +L    
Sbjct: 22  DWAGRFSERMSRVRASEIRELLKLLDQPDILSFAGGIPDPGLFPAQEIQKGYDAILADPV 81

Query: 76  -AAQALQYGTTKGFTPLRLALAEWMRERYDIPISKVDIMTTSGSQQALDLIGRVFINPGD 134
            + QALQY  ++G+ PLR  +AE M  R  +P    +IM T+GSQQALDLIG++F+  GD
Sbjct: 82  LSRQALQYSVSEGYLPLRQWIAERMT-RDGMPCGPDNIMLTAGSQQALDLIGKLFLTKGD 140

Query: 135 IIVVEAPTYLAALQAFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVK-IVYTIP 193
            ++V  PTYL ALQAF  YEP ++ +P       VD      +     G+  + + Y +P
Sbjct: 141 TVMVARPTYLGALQAFNGYEPAYLDLPETALSQGVD------EAALMAGRAPRPLGYFVP 194

Query: 194 TFQNPAGVTMNEKRRKRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWD-------E 246
            F NP GV++    R+ LL +A + D  +VED  Y ELR++GE    +   D       +
Sbjct: 195 DFANPTGVSLTLAEREALLAMADRLDMTLVEDAAYRELRFAGEATPTVLGLDITRSGGID 254

Query: 247 EGRVIYLGTFSKILAPGFRIGWIAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGY 306
             R ++LGT SK L+P  RIGW+      I KL + KQ  DL  +T +Q++A + V  GY
Sbjct: 255 NARTLFLGTLSKTLSPALRIGWVCGPKAVIEKLVLLKQGADLHVSTINQMVAHRAVTEGY 314

Query: 307 LDKHIPKIIEFYKPRRDAMLKALEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAV 366
            D+H+ ++   Y  +   ML ALE  MP GV W+ PEGGMFVW  LPEGID   +L +A+
Sbjct: 315 -DQHLHRLRGAYGAKARVMLAALERTMPKGVTWSHPEGGMFVWIDLPEGIDGAALLARAI 373

Query: 367 -AKGVAYVPGEAFFAHRDVKNTMRLNFTYVPEEKIREGIKRLAETI 411
             + VA+VPG  FFA     N +RL+++   + +I EG++RLA  I
Sbjct: 374 EEERVAFVPGAPFFAENQTPNAIRLSYSLPTDAQIEEGVQRLARLI 419


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: 457
Number of extensions: 19
Number of successful extensions: 7
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: 425
Length adjustment: 32
Effective length of query: 385
Effective length of database: 393
Effective search space:   151305
Effective search space used:   151305
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 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