Alignments for a candidate for arcC in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcC in Pseudomonas putida KT2440

Align Carbamate kinase; EC 2.7.2.2 (characterized, see rationale)
to candidate PP_0999 PP_0999 carbamate kinase

Query= uniprot:P13982
         (310 letters)



>FitnessBrowser__Putida:PP_0999
          Length = 309

 Score =  493 bits (1268), Expect = e-144
 Identities = 247/310 (79%), Positives = 272/310 (87%), Gaps = 1/310 (0%)

Query: 1   MRIVVALGGNALLRRGEPMTADNQRENVRIAAEQIAKVAPGNELVIAHGNGPQVGLLALQ 60
           MRIVVALGGNALLRRGEPMTADNQR N+R A EQIAK+ PGNELVIAHGNGPQVGLL+LQ
Sbjct: 1   MRIVVALGGNALLRRGEPMTADNQRANIRTATEQIAKIHPGNELVIAHGNGPQVGLLSLQ 60

Query: 61  GAAYDKVSPYPLDVLGAETEGMIGYMIEQEMGNLLPFEVPFATILTQVEVDGKDPAFQNP 120
             +Y     YPLDVLGAETEGMIGYMIEQE+GNLL FEVPFAT+LTQVEVD  DPAF++P
Sbjct: 61  ALSYKPDEAYPLDVLGAETEGMIGYMIEQELGNLLAFEVPFATLLTQVEVDANDPAFKDP 120

Query: 121 TKPIGPVYSREEAERLAAEKGWSIAPDGDKFRRVVPSPRPKRIFEIRPVKWLLEKGTIVI 180
           TK IGPVYS+EEAERLA EKGW +  DGDK+RRVV SP+PKRIFEIRP+KWLLEK +IVI
Sbjct: 121 TKFIGPVYSKEEAERLAKEKGWVVKADGDKYRRVVASPKPKRIFEIRPIKWLLEKSSIVI 180

Query: 181 CAGGGGIPTMYDEAGKKLSGVEAVIDKDLCSSLLAQELVADILIIATDVDAAYVDWGKPT 240
           CAGGGGIPTMYDE  +KL G+EAVIDKDLCS+LLA++L AD+LIIATDVDAAY+DWGKPT
Sbjct: 181 CAGGGGIPTMYDE-NRKLKGIEAVIDKDLCSALLAEQLEADLLIIATDVDAAYIDWGKPT 239

Query: 241 QKAIAQAHPDELERLGFAAGSMGPKVQAAIEFARATGKDAVIGSLADIVAITEGKAGTRV 300
           +KAIAQAHPD LE LGFAAGSMGPKVQAA +FAR TGK AVI SL +I  I +GKAGTRV
Sbjct: 240 RKAIAQAHPDALETLGFAAGSMGPKVQAACDFARNTGKVAVISSLENIEDIVKGKAGTRV 299

Query: 301 STRKAGIEYR 310
           ST K GI YR
Sbjct: 300 STEKPGISYR 309


Lambda     K      H
   0.317    0.136    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: 381
Number of extensions: 11
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: 310
Length of database: 309
Length adjustment: 27
Effective length of query: 283
Effective length of database: 282
Effective search space:    79806
Effective search space used:    79806
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate PP_0999 PP_0999 (carbamate kinase)
to HMM TIGR00746 (arcC: carbamate kinase (EC 2.7.2.2))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00746.hmm
# target sequence database:        /tmp/gapView.11054.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00746  [M=309]
Accession:   TIGR00746
Description: arcC: carbamate kinase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     1e-133  431.1   0.1   1.2e-133  430.9   0.1    1.0  1  lcl|FitnessBrowser__Putida:PP_0999  PP_0999 carbamate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0999  PP_0999 carbamate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  430.9   0.1  1.2e-133  1.2e-133       1     308 [.       1     300 [.       1     301 [. 0.98

  Alignments for each domain:
  == domain 1  score: 430.9 bits;  conditional E-value: 1.2e-133
                           TIGR00746   1 kkvvvaLGGnallqrgekasaeeqrknvekaakqlvklakrgyelvithGngPqvGalllqneaadsvpakPldv 75 
                                         +++vvaLGGnall+rge ++a++qr n+++a++q++k++  g+elvi+hGngPqvG l lq   ++  +a+Pldv
  lcl|FitnessBrowser__Putida:PP_0999   1 MRIVVALGGNALLRRGEPMTADNQRANIRTATEQIAKIHP-GNELVIAHGNGPQVGLLSLQALSYKPDEAYPLDV 74 
                                         589*************************************.********************************** PP

                           TIGR00746  76 lgaesqgliGYllqqalkeelakeglekkvatvltqvivdekDeaFqnPtkpigpfydeeeakrlaaekgailke 150
                                         lgae++g+iGY+++q+l + la   +e ++at+ltqv+vd++D+aF++Ptk+igp+y++eea+rla+ekg+ +k 
  lcl|FitnessBrowser__Putida:PP_0999  75 LGAETEGMIGYMIEQELGNLLA---FEVPFATLLTQVEVDANDPAFKDPTKFIGPVYSKEEAERLAKEKGWVVKA 146
                                         **********************...************************************************99 PP

                           TIGR00746 151 dagrgwRrvvpsPkPkeiveaeviktLvekgvivissgGGGvPvvkdgke.lkGveaviDkDlasekLaeevnaD 224
                                          +g+++Rrvv+sPkPk+i+e++ ik+L+ek  ivi++gGGG+P+++d+++ lkG+eaviDkDl+s++Lae+++aD
  lcl|FitnessBrowser__Putida:PP_0999 147 -DGDKYRRVVASPKPKRIFEIRPIKWLLEKSSIVICAGGGGIPTMYDENRkLKGIEAVIDKDLCSALLAEQLEAD 220
                                         .9******************************************9987655************************ PP

                           TIGR00746 225 ilviltdvdavyvnygkpdekkleevkveeleelakdgefaaGsmgPkveaaiefvesrgkkaiitslekiveal 299
                                          l+i+tdvda+y+++gkp+ k++++++++ le+l     faaGsmgPkv+aa +f++++gk a+i+sle+i++++
  lcl|FitnessBrowser__Putida:PP_0999 221 LLIIATDVDAAYIDWGKPTRKAIAQAHPDALETLG----FAAGSMGPKVQAACDFARNTGKVAVISSLENIEDIV 291
                                         ***********************************....************************************ PP

                           TIGR00746 300 egkaGtvvv 308
                                         +gkaGt+v+
  lcl|FitnessBrowser__Putida:PP_0999 292 KGKAGTRVS 300
                                         *******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (309 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.22
//
[ok]

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources