Alignments for a candidate for arcC in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcC in Burkholderia phytofirmans PsJN

Align Carbamate kinase; EC 2.7.2.2 (characterized, see rationale)
to candidate BPHYT_RS27690 BPHYT_RS27690 carbamate kinase

Query= uniprot:P13982
         (310 letters)



>FitnessBrowser__BFirm:BPHYT_RS27690
          Length = 302

 Score =  358 bits (919), Expect = e-104
 Identities = 181/301 (60%), Positives = 223/301 (74%), Gaps = 1/301 (0%)

Query: 1   MRIVVALGGNALLRRGEPMTADNQRENVRIAAEQIAKVAPGNELVIAHGNGPQVGLLALQ 60
           MRI++ALGGNALLRRGEPMT  NQ  N+R AA QI ++A GN+LV+AHGNGPQVGLLALQ
Sbjct: 1   MRILIALGGNALLRRGEPMTMANQIANIRRAASQIGQLADGNQLVVAHGNGPQVGLLALQ 60

Query: 61  GAAYDKV-SPYPLDVLGAETEGMIGYMIEQEMGNLLPFEVPFATILTQVEVDGKDPAFQN 119
            AA     +  PLDVL AE+EGMIGY++EQE+ N+LP +   AT+LT+VEVD  DPAF++
Sbjct: 61  AAASGPAGAASPLDVLDAESEGMIGYLLEQELANVLPVQRQVATLLTRVEVDADDPAFEH 120

Query: 120 PTKPIGPVYSREEAERLAAEKGWSIAPDGDKFRRVVPSPRPKRIFEIRPVKWLLEKGTIV 179
           PTKPIGPVY++ +A+ LA   GW+IA DG  FRRVV SPRP+RI  +RP++WLL+   +V
Sbjct: 121 PTKPIGPVYTKAQAQDLARRNGWTIAEDGAGFRRVVASPRPRRIVALRPIEWLLDHDVVV 180

Query: 180 ICAGGGGIPTMYDEAGKKLSGVEAVIDKDLCSSLLAQELVADILIIATDVDAAYVDWGKP 239
           + AGGGGIP      G+   GVEAVIDKD CS+LLA EL AD+L+IATDVDA Y DW  P
Sbjct: 181 VAAGGGGIPVKVAPDGQTRVGVEAVIDKDRCSALLAAELAADLLLIATDVDAVYADWRTP 240

Query: 240 TQKAIAQAHPDELERLGFAAGSMGPKVQAAIEFARATGKDAVIGSLADIVAITEGKAGTR 299
            ++ +      EL  + FAAGSM PKV+AA +F   TGK AVIGSL  I A+  G AGTR
Sbjct: 241 RERVLHDVPVAELRSMSFAAGSMAPKVEAACDFVAHTGKPAVIGSLEHIAAMANGTAGTR 300

Query: 300 V 300
           +
Sbjct: 301 I 301


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: 336
Number of extensions: 18
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: 310
Length of database: 302
Length adjustment: 27
Effective length of query: 283
Effective length of database: 275
Effective search space:    77825
Effective search space used:    77825
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 BPHYT_RS27690 BPHYT_RS27690 (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.27987.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   3.9e-120  386.5   0.2   4.3e-120  386.4   0.2    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS27690  BPHYT_RS27690 carbamate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS27690  BPHYT_RS27690 carbamate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  386.4   0.2  4.3e-120  4.3e-120       2     308 ..       2     302 .]       1     302 [] 0.98

  Alignments for each domain:
  == domain 1  score: 386.4 bits;  conditional E-value: 4.3e-120
                                TIGR00746   2 kvvvaLGGnallqrgekasaeeqrknvekaakqlvklakrgyelvithGngPqvGalllqneaads.vpa 70 
                                              ++ +aLGGnall+rge +++ +q+ n+++aa+q+ +la  g++lv++hGngPqvG l+lq +a+    +a
  lcl|FitnessBrowser__BFirm:BPHYT_RS27690   2 RILIALGGNALLRRGEPMTMANQIANIRRAASQIGQLAD-GNQLVVAHGNGPQVGLLALQAAASGPaGAA 70 
                                              899***********************************9.*********************999886899 PP

                                TIGR00746  71 kPldvlgaesqgliGYllqqalkeelakeglekkvatvltqvivdekDeaFqnPtkpigpfydeeeakrl 140
                                               Pldvl aes+g+iGYll+q+l ++l+   ++++vat+lt+v+vd++D+aF++Ptkpigp+y++++a+ l
  lcl|FitnessBrowser__BFirm:BPHYT_RS27690  71 SPLDVLDAESEGMIGYLLEQELANVLP---VQRQVATLLTRVEVDADDPAFEHPTKPIGPVYTKAQAQDL 137
                                              ***************************...9*************************************** PP

                                TIGR00746 141 aaekgailkedagrgwRrvvpsPkPkeiveaeviktLvekgvivissgGGGvPvv..kdgkelkGveavi 208
                                              a+ +g++++e +g+g+Rrvv+sP+P++iv  + i++L++++v+v+++gGGG+Pv+   dg++  Gveavi
  lcl|FitnessBrowser__BFirm:BPHYT_RS27690 138 ARRNGWTIAE-DGAGFRRVVASPRPRRIVALRPIEWLLDHDVVVVAAGGGGIPVKvaPDGQTRVGVEAVI 206
                                              **********.9*****************************************86226899999****** PP

                                TIGR00746 209 DkDlasekLaeevnaDilviltdvdavyvnygkpdekkleevkveeleelakdgefaaGsmgPkveaaie 278
                                              DkD++s++La e+ aD l+i+tdvdavy ++ +p e+ l++v v+el+++     faaGsm+Pkveaa +
  lcl|FitnessBrowser__BFirm:BPHYT_RS27690 207 DKDRCSALLAAELAADLLLIATDVDAVYADWRTPRERVLHDVPVAELRSMS----FAAGSMAPKVEAACD 272
                                              ***************************************************....*************** PP

                                TIGR00746 279 fvesrgkkaiitslekivealegkaGtvvv 308
                                              fv  +gk a+i+sle+i ++ +g aGt+++
  lcl|FitnessBrowser__BFirm:BPHYT_RS27690 273 FVAHTGKPAVIGSLEHIAAMANGTAGTRII 302
                                              ***************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (302 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.48
//
[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