GapMind for catabolism of small carbon sources

 

Alignments for a candidate for citrullinase in Pseudomonas putida KT2440

Align Carbon-nitrogen hydrolase family protein; EC 3.5.-.- (characterized, see rationale)
to candidate PP_0382 PP_0382 5-aminopentanamidase

Query= uniprot:Q5NHL7_FRATT
         (286 letters)



>FitnessBrowser__Putida:PP_0382
          Length = 264

 Score = 90.5 bits (223), Expect = 4e-23
 Identities = 83/261 (31%), Positives = 126/261 (48%), Gaps = 19/261 (7%)

Query: 20  NLAKLESKIIQAAKNGAKIILTPELPSYLYFCKKQNSKYFDLAKTIDESPIVKLYKLLAH 79
           NL +L  +   AA  GA++++ PE+  +L       ++   LA+  D  P       +A 
Sbjct: 18  NLQRLRHQAQLAADRGAQLLVCPEM--FLSGYNIGLAQVERLAEAAD-GPAAMTVVEIAQ 74

Query: 80  KYNIVLPASFFER-DGNACYNSIAMIDADGSIMGVYRKAHIPDGIGYQEKYYFSPGSAGF 138
            + I +   + ER D  A YNS+ +IDA G  +  YRK H+    G  ++  FSPG+  F
Sbjct: 75  AHRIAIVYGYPERGDDGAIYNSVQLIDAHGRSLSNYRKTHL---FGELDRSMFSPGADHF 131

Query: 139 KVWDTKYAKVGVGICWDQWFPEAARVMALKGAEILLYPTAIGSEPHLPDYDSKDHWQRVM 198
            V + +  KVG+ IC+D  FPE AR +AL GAE++L PTA     ++  YD     Q  +
Sbjct: 132 PVVELEGWKVGLLICYDIEFPENARRLALDGAELILVPTA-----NMTPYDFT--CQVTV 184

Query: 199 QGHAAANMLPVLASNRYATEANDDITATYYGSSFITDHTGDKIAEADRSGDDILYATFDF 258
           +  A  N   ++ +N    E  D+I   Y G S I    G  +A A R    +L A  + 
Sbjct: 185 RARAQENQCYLVYANYCGAE--DEI--EYCGQSSIIGPDGSLLAMAGRDECQLL-AELEH 239

Query: 259 AELQQQRFYWGLFRDRRPELY 279
             + Q R  +    D R EL+
Sbjct: 240 ERVVQGRRAFPYLTDLRQELH 260


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: 184
Number of extensions: 13
Number of successful extensions: 3
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: 264
Length adjustment: 25
Effective length of query: 261
Effective length of database: 239
Effective search space:    62379
Effective search space used:    62379
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: 47 (22.7 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