Alignments for a candidate for arcC in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcC in Marinobacter adhaerens HP15

Align Carbamate kinase; EC 2.7.2.2 (characterized, see rationale)
to candidate GFF4048 HP15_3988 bacterial carbamate kinase

Query= uniprot:P13982
         (310 letters)



>FitnessBrowser__Marino:GFF4048
          Length = 302

 Score =  346 bits (888), Expect = e-100
 Identities = 183/304 (60%), Positives = 225/304 (74%), Gaps = 3/304 (0%)

Query: 1   MRIVVALGGNALLRRGEPMTADNQRENVRIAAEQIAKVA-PGNELVIAHGNGPQVGLLAL 59
           M +V ALGGNALL+RGEP+TA+ QR NV+IAA  +A V   G+ LV+ HGNGPQVGLLAL
Sbjct: 1   MLVVAALGGNALLKRGEPLTAEVQRNNVQIAARSLAAVVRAGHNLVVTHGNGPQVGLLAL 60

Query: 60  QGAAYDKVSPYPLDVLGAETEGMIGYMIEQEMGNLLPFEVPFATILTQVEVDGKDPAFQN 119
           QGA+Y     YPLDVLGAETEGMIGYMIEQE+ N L  + P AT+LTQV VD +DPAF+ 
Sbjct: 61  QGASYKPDEAYPLDVLGAETEGMIGYMIEQELENALGHDRPVATLLTQVVVDPRDPAFEK 120

Query: 120 PTKPIGPVYSREEAERLAAEKGWSIAPDGDKFRRVVPSPRPKRIFEIRPVKWLLEKGTIV 179
           PTK +GPVY REE ER AA  GWSIAPDGDK+RRVVPSP+P  I ++R +K LL++G +V
Sbjct: 121 PTKFVGPVYDREEGERRAAAAGWSIAPDGDKWRRVVPSPKPLEIPDMRVLKLLLDQGVVV 180

Query: 180 ICAGGGGIPTMYDEAGKKLSGVEAVIDKDLCSSLLAQELVADILIIATDVDAAYVDWGKP 239
           +CAGGGGIP +  + G  + G+EAVIDKD  S+LLA++L AD L++ TDV+A Y D+G  
Sbjct: 181 VCAGGGGIPVLRRDDG-SMVGIEAVIDKDAASALLARQLGADALLLLTDVEAVYRDFGTD 239

Query: 240 TQKAIAQAHPDELERLGFAAGSMGPKVQAAIEFARATGKDAVIGSLADIVAITEGKAGTR 299
              A+++    E   L   AGSMGPK+QAA +FA+A G    IG L D VAI EG AGTR
Sbjct: 240 RSTALSELTVSEARALEMPAGSMGPKLQAACDFAQAGGISG-IGRLQDAVAILEGSAGTR 298

Query: 300 VSTR 303
           VS +
Sbjct: 299 VSAK 302


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: 324
Number of extensions: 17
Number of successful extensions: 4
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 GFF4048 HP15_3988 (bacterial 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.24141.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.4e-118  381.4   0.0   1.5e-118  381.3   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF4048  HP15_3988 bacterial carbamate ki


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF4048  HP15_3988 bacterial carbamate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  381.3   0.0  1.5e-118  1.5e-118       3     308 ..       3     300 ..       1     301 [. 0.97

  Alignments for each domain:
  == domain 1  score: 381.3 bits;  conditional E-value: 1.5e-118
                           TIGR00746   3 vvvaLGGnallqrgekasaeeqrknvekaakqlvklakrgyelvithGngPqvGalllqneaadsvpakPldvlg 77 
                                         vv aLGGnall+rge ++ae qr+nv++aa++l++++++g++lv+thGngPqvG l+lq + ++  +a+Pldvlg
  lcl|FitnessBrowser__Marino:GFF4048   3 VVAALGGNALLKRGEPLTAEVQRNNVQIAARSLAAVVRAGHNLVVTHGNGPQVGLLALQGASYKPDEAYPLDVLG 77 
                                         7999*********************************************************************** PP

                           TIGR00746  78 aesqgliGYllqqalkeelakeglekkvatvltqvivdekDeaFqnPtkpigpfydeeeakrlaaekgailkeda 152
                                         ae++g+iGY+++q+l+++l      ++vat+ltqv+vd+ D+aF++Ptk++gp+yd+ee +r aa++g++++  +
  lcl|FitnessBrowser__Marino:GFF4048  78 AETEGMIGYMIEQELENALG---HDRPVATLLTQVVVDPRDPAFEKPTKFVGPVYDREEGERRAAAAGWSIAP-D 148
                                         *****************999...99************************************************.9 PP

                           TIGR00746 153 grgwRrvvpsPkPkeiveaeviktLvekgvivissgGGGvPvvk.dgkelkGveaviDkDlasekLaeevnaDil 226
                                         g++wRrvvpsPkP+ei +++v+k L+++gv+v+++gGGG+Pv + d+ ++ G+eaviDkD as++La++++aD+l
  lcl|FitnessBrowser__Marino:GFF4048 149 GDKWRRVVPSPKPLEIPDMRVLKLLLDQGVVVVCAGGGGIPVLRrDDGSMVGIEAVIDKDAASALLARQLGADAL 223
                                         ******************************************8626667************************** PP

                           TIGR00746 227 viltdvdavyvnygkpdekkleevkveeleelakdgefaaGsmgPkveaaiefvesrgkkaiitslekivealeg 301
                                         ++ltdv+avy+++g++   +l+e++v+e+++l+    + aGsmgPk++aa +f++++g  + i++l+++v++leg
  lcl|FitnessBrowser__Marino:GFF4048 224 LLLTDVEAVYRDFGTDRSTALSELTVSEARALE----MPAGSMGPKLQAACDFAQAGGI-SGIGRLQDAVAILEG 293
                                         ********************************9....9*****************9886.679************ PP

                           TIGR00746 302 kaGtvvv 308
                                          aGt+v+
  lcl|FitnessBrowser__Marino:GFF4048 294 SAGTRVS 300
                                         *****97 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: 00:00:00.01
# Mc/sec: 9.20
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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