GapMind for catabolism of small carbon sources

 

Alignments for a candidate for citrullinase in Pseudomonas fluorescens FW300-N1B4

Align Carbon-nitrogen hydrolase family protein; EC 3.5.-.- (characterized, see rationale)
to candidate Pf1N1B4_4326 N-carbamoylputrescine amidase (3.5.1.53)

Query= uniprot:Q5NHL7_FRATT
         (286 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4326
          Length = 302

 Score =  298 bits (763), Expect = 1e-85
 Identities = 139/286 (48%), Positives = 197/286 (68%), Gaps = 3/286 (1%)

Query: 1   MANIKVAVVQLSFNDNEAENLAKLESKIIQAAKNGAKIILTPELPSYLYFCKKQNSKYFD 60
           M  + +A  Q+    +   NL + E  + +AA  GA++IL  EL +  YFC +Q+ K+  
Sbjct: 1   MTLLTIATTQMPCTWDLQHNLDQAERLVREAAAKGAQVILLQELFATPYFCIEQSHKHLA 60

Query: 61  LAKTIDESPIVKLYKLLAHKYNIVLPASFFERDGNACYNSIAMIDADGSIMGVYRKAHIP 120
           LA+   +SP++K +  LA +  +VLP S+FE+ GNA +NS+++ DADG ++GVYRK HIP
Sbjct: 61  LAEEYRDSPVLKRFAALAKELGVVLPLSWFEKAGNAYFNSLSVADADGRLLGVYRKTHIP 120

Query: 121 DGIGYQEKYYFSPGSAGFKVWDTKYAKVGVGICWDQWFPEAARVMALKGAEILLYPTAIG 180
           + IGYQEK YFSPG  GF+VWDT + ++GVGICWDQWFPE AR +AL GAE+LL+PTAIG
Sbjct: 121 NAIGYQEKEYFSPGDTGFRVWDTAFGRIGVGICWDQWFPETARCLALMGAEVLLFPTAIG 180

Query: 181 SEPHLPDYDSKDHWQRVMQGHAAANMLPVLASNRYATE---ANDDITATYYGSSFITDHT 237
           SEP     DS+DHWQ  M+GHAAAN+LPV+A+NR   E    +  +   +YGSSFI +H 
Sbjct: 181 SEPGCAALDSRDHWQMTMRGHAAANILPVVAANRVGPEVATTDPTLQMNFYGSSFICNHK 240

Query: 238 GDKIAEADRSGDDILYATFDFAELQQQRFYWGLFRDRRPELYDEIV 283
           G  +AEADR    +L  + D   ++++R  WG++RDRRP++Y  ++
Sbjct: 241 GKLLAEADRDSTGVLVHSLDLTAMREERLSWGIYRDRRPDMYGALL 286


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: 272
Number of extensions: 5
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: 302
Length adjustment: 26
Effective length of query: 260
Effective length of database: 276
Effective search space:    71760
Effective search space used:    71760
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 (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