GapMind for catabolism of small carbon sources

 

Aligments for a candidate for citrullinase in Caulobacter crescentus NA1000

Align Carbon-nitrogen hydrolase family protein; EC 3.5.-.- (characterized, see rationale)
to candidate CCNA_00212 CCNA_00212 N-carbamoylputrescine amidase

Query= uniprot:Q5NHL7_FRATT
         (286 letters)



>lcl|FitnessBrowser__Caulo:CCNA_00212 CCNA_00212
           N-carbamoylputrescine amidase
          Length = 292

 Score =  295 bits (756), Expect = 6e-85
 Identities = 144/279 (51%), Positives = 183/279 (65%), Gaps = 3/279 (1%)

Query: 4   IKVAVVQLSFNDNEAENLAKLESKIIQAAKNGAKIILTPELPSYLYFCKKQNSKYFDLAK 63
           + VA +Q S+  +   N+ K E  I +AA  GA++IL  EL    YFC  Q  ++F  A 
Sbjct: 5   LSVAAIQTSYGMDLQANIKKTEGFIREAASKGAQVILPSELFQGPYFCVAQEERWFAQAH 64

Query: 64  TIDESPIVKLYKLLAHKYNIVLPASFFERDGNACYNSIAMIDADGSIMGVYRKAHIPDGI 123
              E P+VK    LA +  +V+P S FER+G   +NS+ M DADGS+MGVYRK+HIPDG 
Sbjct: 65  PWREHPVVKAIAPLAGELGVVIPISIFEREGPHYFNSLVMADADGSLMGVYRKSHIPDGP 124

Query: 124 GYQEKYYFSPGSAGFKVWDTKYAKVGVGICWDQWFPEAARVMALKGAEILLYPTAIGSEP 183
           GY EKYYF PG  GFKVWDT++ ++GVGICWDQW+PE AR MAL GAE L YPTAIGSEP
Sbjct: 125 GYMEKYYFRPGDTGFKVWDTRFGRIGVGICWDQWYPECARAMALMGAEALFYPTAIGSEP 184

Query: 184 HLPDYDSKDHWQRVMQGHAAANMLPVLASNRYATEANDDIT---ATYYGSSFITDHTGDK 240
           H    D+   W+R MQGHA +N++PV+ +NR   E  D       T+YGSSF+ DH GD 
Sbjct: 185 HDASLDTALPWRRAMQGHAVSNVIPVIGANRIGFEPWDGYPNGGQTFYGSSFVADHRGDL 244

Query: 241 IAEADRSGDDILYATFDFAELQQQRFYWGLFRDRRPELY 279
           ++E  R+ + ++ ATFD   L   R  WG FRDRRPELY
Sbjct: 245 VSELGRADEGLVSATFDLDFLTTHRAAWGFFRDRRPELY 283


Lambda     K      H
   0.320    0.136    0.413 

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: 278
Number of extensions: 8
Number of successful extensions: 2
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: 286
Length of database: 292
Length adjustment: 26
Effective length of query: 260
Effective length of database: 266
Effective search space:    69160
Effective search space used:    69160
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: 48 (23.1 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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