GapMind for catabolism of small carbon sources

 

Aligments for a candidate for citrullinase in Pseudomonas stutzeri RCH2

Align Carbon-nitrogen hydrolase family protein; EC 3.5.-.- (characterized, see rationale)
to candidate GFF4217 Psest_4290 N-carbamoylputrescine amidase

Query= uniprot:Q5NHL7_FRATT
         (286 letters)



>lcl|FitnessBrowser__psRCH2:GFF4217 Psest_4290 N-carbamoylputrescine
           amidase
          Length = 293

 Score =  323 bits (828), Expect = 3e-93
 Identities = 150/279 (53%), Positives = 197/279 (70%)

Query: 4   IKVAVVQLSFNDNEAENLAKLESKIIQAAKNGAKIILTPELPSYLYFCKKQNSKYFDLAK 63
           + VA  Q++ + +   N+A  +  + +AA  GA+IIL  EL    YFC+K N++Y  LA 
Sbjct: 5   VTVAATQMACSWDRQANIANADKLVREAAAKGAQIILIQELFETPYFCQKPNAEYLQLAT 64

Query: 64  TIDESPIVKLYKLLAHKYNIVLPASFFERDGNACYNSIAMIDADGSIMGVYRKAHIPDGI 123
            ++E+P ++ ++ +A +  +VLP SFFE  G A +NSIA+IDADG ++GVYRK+HIPDG 
Sbjct: 65  PVEENPAIQHFQKVAAELQVVLPISFFELAGRARFNSIAIIDADGKLLGVYRKSHIPDGP 124

Query: 124 GYQEKYYFSPGSAGFKVWDTKYAKVGVGICWDQWFPEAARVMALKGAEILLYPTAIGSEP 183
           GY EKYYF+PG  GFKVW+T+YAK+GV ICWDQWFPE AR MAL GAE+L YPTAIGSEP
Sbjct: 125 GYHEKYYFNPGDTGFKVWNTRYAKIGVAICWDQWFPETARSMALMGAELLFYPTAIGSEP 184

Query: 184 HLPDYDSKDHWQRVMQGHAAANMLPVLASNRYATEANDDITATYYGSSFITDHTGDKIAE 243
           H P+  S+DHWQRV QGHA AN++P++ASNR   E  D    T+YGSSFI D  G K+ E
Sbjct: 185 HDPNITSRDHWQRVQQGHAGANLMPLIASNRIGREEQDGYDITFYGSSFIADQFGAKVEE 244

Query: 244 ADRSGDDILYATFDFAELQQQRFYWGLFRDRRPELYDEI 282
            D + + +L   FD  +L+  R  WG+FRDRRP LY  I
Sbjct: 245 MDETSEGVLVHQFDLDQLEHIRSAWGVFRDRRPNLYGSI 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: 298
Number of extensions: 8
Number of successful extensions: 1
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: 293
Length adjustment: 26
Effective length of query: 260
Effective length of database: 267
Effective search space:    69420
Effective search space used:    69420
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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