Alignments for a candidate for arcC in Desulfacinum infernum DSM 9756

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcC in Desulfacinum infernum DSM 9756

Align Carbamate kinase; EC 2.7.2.2; Carbamate kinase-like carbamoylphosphate synthase (uncharacterized)
to candidate WP_073037756.1 BUB04_RS05565 carbamate kinase

Query= curated2:O59023
         (314 letters)



>NCBI__GCF_900129305.1:WP_073037756.1
          Length = 314

 Score =  263 bits (673), Expect = 3e-75
 Identities = 139/310 (44%), Positives = 199/310 (64%), Gaps = 11/310 (3%)

Query: 5   VVIALGGNALQQRGQKGTYDEMMENVRKTAKQIAEIIARGYEVVITHGNGPQVGTILLHM 64
           +++ALGGNAL ++GQ+GT +E  EN+R    QIA +    + ++ITHGNGPQVG +LL  
Sbjct: 11  LLVALGGNALIRKGQEGTIEEQFENLRVPMSQIARL-CESHRILITHGNGPQVGNLLLQQ 69

Query: 65  DAGQSLHGIPAQPMDVAGAMSQGWIGYMIQQALRNELRKRGI--EKEVVTIITQTIVDKK 122
           +       +P  P+++  A +QG IGYMI+  L + L   GI  +K +V++I+  +VD K
Sbjct: 70  ECCPH---VPRLPLEILVAQTQGQIGYMIESTLDSALMDLGIVTQKHLVSLISYVVVDPK 126

Query: 123 DPAFQNPTKPVGPFYDEKTAKKLAKEKGWVVKEDAGRGWRRVVPSPDPKGHVEAETIRRL 182
           DPAF+NPTKP+GP Y E+   +L     + VK+ A +G+RRVV SP P   VE   I+RL
Sbjct: 127 DPAFRNPTKPIGPVYPEEVVPELP----FPVKKTA-KGYRRVVASPKPLHIVERREIQRL 181

Query: 183 VESGIIVIASGGGGVPVIEENGEIKGVEAVIDKDLAGEKLAEEVNADILMILTDVNGAAL 242
           +    +VI  GGGG+PV+ E     GV+AVIDKDLA  +LA EV  D+  I TDV GA +
Sbjct: 182 IAMDFVVICCGGGGIPVVREGRSFAGVDAVIDKDLASARLAREVGVDLFCIATDVPGAYV 241

Query: 243 YYGTEKETWLRNVKVEELEKYYQEGHFKAGSMGPKVLAAIRFIKNGGKRAIIAHLEKAVE 302
           +YG  ++  L  +  EE E+  +EGHF  GSMGPKV AA+ F++  GK A+I  ++    
Sbjct: 242 HYGRPEQRLLERLSAEEAERLAREGHFPQGSMGPKVEAAVEFVRATGKEAVITSIDAIEA 301

Query: 303 ALEGKTGTQV 312
           A+EG+ GT++
Sbjct: 302 AVEGRAGTRI 311


Lambda     K      H
   0.314    0.135    0.386 

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: 279
Number of extensions: 13
Number of successful extensions: 5
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: 314
Length of database: 314
Length adjustment: 27
Effective length of query: 287
Effective length of database: 287
Effective search space:    82369
Effective search space used:    82369
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: 42 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate WP_073037756.1 BUB04_RS05565 (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.9178.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.8e-115  368.9   0.0     1e-114  368.7   0.0    1.0  1  lcl|NCBI__GCF_900129305.1:WP_073037756.1  BUB04_RS05565 carbamate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900129305.1:WP_073037756.1  BUB04_RS05565 carbamate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  368.7   0.0    1e-114    1e-114       3     307 ..      11     311 ..       9     313 .. 0.97

  Alignments for each domain:
  == domain 1  score: 368.7 bits;  conditional E-value: 1e-114
                                 TIGR00746   3 vvvaLGGnallqrgekasaeeqrknvekaakqlvklakrgyelvithGngPqvGalllqneaadsvpak 71 
                                               + vaLGGnal+++g+++++eeq +n++   +q+++l + +++++ithGngPqvG+lllq+e   +vp  
  lcl|NCBI__GCF_900129305.1:WP_073037756.1  11 LLVALGGNALIRKGQEGTIEEQFENLRVPMSQIARLCE-SHRILITHGNGPQVGNLLLQQECCPHVPRL 78 
                                               579***********************************.****************************** PP

                                 TIGR00746  72 PldvlgaesqgliGYllqqalkeelakegl..ekkvatvltqvivdekDeaFqnPtkpigpfydeeeak 138
                                               Pl++l+a++qg+iGY+++  l+ +l + g+  +k+++ ++  v+vd+kD+aF+nPtkpigp+y ee   
  lcl|NCBI__GCF_900129305.1:WP_073037756.1  79 PLEILVAQTQGQIGYMIESTLDSALMDLGIvtQKHLVSLISYVVVDPKDPAFRNPTKPIGPVYPEEVVP 147
                                               **************************99863367899***************************99887 PP

                                 TIGR00746 139 rlaaekgailkedagrgwRrvvpsPkPkeiveaeviktLvekgvivissgGGGvPvvkdgkelkGveav 207
                                                   e  + +k+ +++g+Rrvv+sPkP++ive + i+ L+  + +vi++gGGG+Pvv++g+++ Gv+av
  lcl|NCBI__GCF_900129305.1:WP_073037756.1 148 ----ELPFPVKK-TAKGYRRVVASPKPLHIVERREIQRLIAMDFVVICCGGGGIPVVREGRSFAGVDAV 211
                                               ....88999999.99****************************************************** PP

                                 TIGR00746 208 iDkDlasekLaeevnaDilviltdvdavyvnygkpdekkleevkveeleelakdgefaaGsmgPkveaa 276
                                               iDkDlas++La+ev+ D + i+tdv  +yv+yg+p+++ le+++ ee+e+la++g+f +GsmgPkveaa
  lcl|NCBI__GCF_900129305.1:WP_073037756.1 212 IDKDLASARLAREVGVDLFCIATDVPGAYVHYGRPEQRLLERLSAEEAERLAREGHFPQGSMGPKVEAA 280
                                               ********************************************************************* PP

                                 TIGR00746 277 iefvesrgkkaiitslekivealegkaGtvv 307
                                               +efv+++gk+a+its++ i++a+eg aGt++
  lcl|NCBI__GCF_900129305.1:WP_073037756.1 281 VEFVRATGKEAVITSIDAIEAAVEGRAGTRI 311
                                               *****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (314 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: 00:00:00.01
# Mc/sec: 7.56
//
[ok]

This GapMind analysis is from Sep 24 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