GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Caulobacter crescentus NA1000

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate CCNA_02326 CCNA_02326 acetylornithine aminotransferase/succinyldiaminopimelate aminotransferase

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__Caulo:CCNA_02326
          Length = 405

 Score =  225 bits (573), Expect = 2e-63
 Identities = 139/382 (36%), Positives = 206/382 (53%), Gaps = 18/382 (4%)

Query: 76  LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAA 135
           L+ T+G+E++DC+ G     +GH +P +V  ++ Q  K    S     P +  LA  L A
Sbjct: 33  LISTEGEEYLDCVAGIATNGLGHAHPALVEVLKAQAEKLWHVSNIYRIPEQEELADALCA 92

Query: 136 LTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAFHGKSLGALSATA 192
            +   +   FF NSGTE+VE ALK A+ Y S  G   +       G+FHG++  A++A+ 
Sbjct: 93  NSFADVV--FFTNSGTEAVECALKTARKYHSANGQPERIDIYGFDGSFHGRTYAAVNASG 150

Query: 193 KSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPG 252
             ++   F P LPG+  + FG+ +A++ A+          AA+I+EP+QGEGG    P  
Sbjct: 151 NPSYVDGFGPRLPGYSQLTFGDHDAIKAAI-----ASPTTAAIIVEPVQGEGGARSIPTQ 205

Query: 253 YLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACE-HENVQPDILCLAKALGGGVMPIGA 311
            L  +R+LCDE G L+I DEVQ GMGRTGK+FA E  E  +P I+ +AKALGGG  PIGA
Sbjct: 206 CLVGLRQLCDEHGVLLIYDEVQCGMGRTGKLFAYEWAEGGEPHIMAVAKALGGG-FPIGA 264

Query: 312 TIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFR 371
            +AT E    +      H +TFGGNPLA A   A + ++         +           
Sbjct: 265 CLATTEAAKGM--TVAAHGSTFGGNPLAMAVGKAALEIIKSPETLDNVKTVSGFFTQQLN 322

Query: 372 QLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPL 431
            L   +PD++ + RGKGML+ ++ + N   +   +    +++L+AG  +N   +R+ PPL
Sbjct: 323 GLKDRFPDVIVDVRGKGMLIGVKLIPNNRDFMVLAR--DEKLLIAGGGDNC--VRLLPPL 378

Query: 432 TLTIEQCELVIKAARKALAAMR 453
            LTIE+    I    KA  A R
Sbjct: 379 NLTIEEASEAIAKLEKACEAAR 400


Lambda     K      H
   0.320    0.135    0.393 

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: 430
Number of extensions: 23
Number of successful extensions: 9
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: 459
Length of database: 405
Length adjustment: 32
Effective length of query: 427
Effective length of database: 373
Effective search space:   159271
Effective search space used:   159271
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 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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