GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Caulobacter crescentus NA1000

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate CCNA_03245 CCNA_03245 beta alanine-pyruvate transaminase

Query= curated2:Q8TUZ5
         (389 letters)



>FitnessBrowser__Caulo:CCNA_03245
          Length = 442

 Score =  203 bits (517), Expect = 7e-57
 Identities = 143/416 (34%), Positives = 210/416 (50%), Gaps = 47/416 (11%)

Query: 15  YSRFPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNL 74
           + R P  L    G      E  E +D  +G+     GH  P + EA+++Q   + +    
Sbjct: 25  FKRHPRMLSSASGMWYRTPESREVLDATSGLWCVNAGHDRPKIREAIQKQAAEMDYAPCF 84

Query: 75  YYNEPQA-EAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFTGC------TKFIAF 127
               P A + A  LA+  PK L+++FF NSG+ESV+ A+K+A  +         T+ I  
Sbjct: 85  NMGHPLAFQFASRLAQITPKGLDRIFFTNSGSESVDTALKIALAYHRARGKGTKTRLIGR 144

Query: 128 EGGFHGRTMGALSATWKPEFREPFEPLVPEFEHVPY---------------------GDV 166
           E G+HG   G +S    P+ R  F  L+   +H+P+                      D+
Sbjct: 145 ERGYHGVGFGGISVGGIPKNRMYFGSLLTGVDHLPHTHGLPGNTCAKGQPENGAHLADDL 204

Query: 167 NAVEKAID-DDTAAVIVEPVQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRT 225
             +    D  + AAVIVEPV G  GV IPP+G+L  LR +CD+H +LLI DEV +G GR 
Sbjct: 205 ERIVALHDASNIAAVIVEPVAGSTGVLIPPKGYLERLRAICDKHDILLIFDEVITGFGRV 264

Query: 226 GQFFAFEHEDVLPDIVCLAKGL-GGGVPVGATIAREEVAEAFEPGD-------HGSTFGG 277
           G  FA E   V PD++C+AKGL    VP GA  A  ++ +A   G        HG T+  
Sbjct: 265 GAPFAAERFGVTPDLICMAKGLTNAAVPCGAVAASGKIYDAMMDGADAPIELFHGYTYSA 324

Query: 278 NPLACAAVCAAVSTVLEENL-PEAAERKG--KLAMRILSEAEDVVEEVRGRGLMMGVEV- 333
           +PLACAA  A + T  E++L   AA  +G  + AM  L++A  VV +VR  GL+ G+E+ 
Sbjct: 325 HPLACAAGLATLETYREDDLFARAAGLEGYWQDAMHSLADARHVV-DVRNLGLVAGIELE 383

Query: 334 ----GDDERAKDVAREMLDRGALVNVTSGDVIRLVPPLVIGEDELEKALAELADAL 385
                   RA +V     D G L+ VT GD+I L PPL++ +D +++ +  +   L
Sbjct: 384 PRPGAPTARAMEVFETCFDEGLLIRVT-GDIIALSPPLILEKDHIDRMVETIRRVL 438


Lambda     K      H
   0.318    0.137    0.405 

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: 409
Number of extensions: 27
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: 389
Length of database: 442
Length adjustment: 31
Effective length of query: 358
Effective length of database: 411
Effective search space:   147138
Effective search space used:   147138
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