GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Caulobacter crescentus NA1000

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate CCNA_03245 CCNA_03245 beta alanine-pyruvate transaminase

Query= curated2:Q5SHH5
         (395 letters)



>FitnessBrowser__Caulo:CCNA_03245
          Length = 442

 Score =  177 bits (450), Expect = 4e-49
 Identities = 127/414 (30%), Positives = 197/414 (47%), Gaps = 43/414 (10%)

Query: 24  YNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQ- 82
           + +H  ++    G      E  E +D   G    N GH  P++ EA+++QA  +   P  
Sbjct: 25  FKRHPRMLSSASGMWYRTPESREVLDATSGLWCVNAGHDRPKIREAIQKQAAEMDYAPCF 84

Query: 83  TLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARA-HTGRKK-----FVAA 136
            +  P+  +F   L  I P  L+R+F  NSG+E+ + ALK A A H  R K      +  
Sbjct: 85  NMGHPLAFQFASRLAQITPKGLDRIFFTNSGSESVDTALKIALAYHRARGKGTKTRLIGR 144

Query: 137 MRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPY---------------------NDV 175
            RG+ G   G +SV   PK R  F  L+  V+ +P+                     +D+
Sbjct: 145 ERGYHGVGFGGISVGGIPKNRMYFGSLLTGVDHLPHTHGLPGNTCAKGQPENGAHLADDL 204

Query: 176 EALKRAVDEET-AAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRT 234
           E +    D    AAVI+EPV G  GV      +L   R I  +   LLI DE+ TG GR 
Sbjct: 205 ERIVALHDASNIAAVIVEPVAGSTGVLIPPKGYLERLRAICDKHDILLIFDEVITGFGRV 264

Query: 235 GKRFAFEHFGIVPDILTLAKAL-GGGVPLGAAVMREEVARSMPKGG-------HGTTFGG 286
           G  FA E FG+ PD++ +AK L    VP GA     ++  +M  G        HG T+  
Sbjct: 265 GAPFAAERFGVTPDLICMAKGLTNAAVPCGAVAASGKIYDAMMDGADAPIELFHGYTYSA 324

Query: 287 NPLAMAAGVAAIRYLERTRLWERAAELGPWFMEKLRAIPSPK-IREVRGMGLMVGLELKE 345
           +PLA AAG+A +       L+ RAA L  ++ + + ++   + + +VR +GL+ G+EL+ 
Sbjct: 325 HPLACAAGLATLETYREDDLFARAAGLEGYWQDAMHSLADARHVVDVRNLGLVAGIELEP 384

Query: 346 KAAPYIARLEKEHRV-----LALQAGPTVIRFLPPLVIEKEDLERVVEAVRAVL 394
           +     AR  +         L ++    +I   PPL++EK+ ++R+VE +R VL
Sbjct: 385 RPGAPTARAMEVFETCFDEGLLIRVTGDIIALSPPLILEKDHIDRMVETIRRVL 438


Lambda     K      H
   0.319    0.137    0.402 

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: 439
Number of extensions: 28
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: 395
Length of database: 442
Length adjustment: 32
Effective length of query: 363
Effective length of database: 410
Effective search space:   148830
Effective search space used:   148830
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 (21.7 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