Alignments for a candidate for arcC in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcC in Escherichia coli BW25113

Align Carbamate kinase; EC 2.7.2.2 (uncharacterized)
to candidate 16954 b2874 predicted amino acid kinase (NCBI)

Query= curated2:Q46171
         (314 letters)



>FitnessBrowser__Keio:16954
          Length = 310

 Score =  343 bits (880), Expect = 3e-99
 Identities = 174/311 (55%), Positives = 227/311 (72%), Gaps = 6/311 (1%)

Query: 2   KIVLALGGNALQKDSKDKSAEGQLETCRQTAISVADLIEDGHEVSIVHGNGPQVGQILAS 61
           KIVLALGGNAL  D       GQ++  + T+ ++ DLI  GHEV + HGNGPQVG I  +
Sbjct: 4   KIVLALGGNALGDD-----LAGQMKAVKITSQAIVDLIAQGHEVIVTHGNGPQVGMINQA 58

Query: 62  IELAHQVDNGNPLFPFDVVGAFSEGYIGYHLQNTIREELLKRGIEKSVDTITTQVIVDKN 121
            E A + +  +P+ P  V  A S+GYIGY LQN +REELL RGI K V T+ TQV VD N
Sbjct: 59  FEAAAKTEAHSPMLPMSVCVALSQGYIGYDLQNALREELLSRGINKPVATLVTQVEVDAN 118

Query: 122 DPGFKNPTKPIGSFYTKEEAEKLEKDKGYTMKEDAGRGYRRVVASPKPVDIVEKEAIKTM 181
           DP F NPTKPIGSF+T++EAE+L K +GYT+KEDAGRGYRRVVASPKPVDI+EKE +K +
Sbjct: 119 DPAFLNPTKPIGSFFTEQEAEQLTK-QGYTLKEDAGRGYRRVVASPKPVDIIEKETVKAL 177

Query: 182 VDSGFIVIACGGGGIPVVEDGDRLEGVPAVIDKDFAAEKLAEILDADALLILTAVDRVCV 241
           VD+G +VI  GGGGIPV+ +G+ L G  AVIDKD+A+ +LAE++DAD L+ILTAV++V +
Sbjct: 178 VDAGQVVITVGGGGIPVIREGNHLRGASAVIDKDWASARLAEMIDADMLIILTAVEKVAI 237

Query: 242 NFNKPDQKALKEINLEEVDKYIEEGQFAPGSMLPKVEACKKFVLSGDKKVAIIASLTNAK 301
           NF K +++ L  ++L + +++IEEG FA GSMLPKVEA   F  S   + A+I  L+ AK
Sbjct: 238 NFGKENEQWLDRLSLSDAERFIEEGHFAKGSMLPKVEAAASFARSRAGREALITVLSKAK 297

Query: 302 AALRGESGTKI 312
             + G++GT I
Sbjct: 298 EGIEGKTGTVI 308


Lambda     K      H
   0.314    0.135    0.377 

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: 318
Number of extensions: 14
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: 314
Length of database: 310
Length adjustment: 27
Effective length of query: 287
Effective length of database: 283
Effective search space:    81221
Effective search space used:    81221
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 16954 b2874 (predicted amino acid kinase (NCBI))
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.13990.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   7.3e-120  385.6   2.2   8.2e-120  385.4   2.2    1.0  1  lcl|FitnessBrowser__Keio:16954  b2874 predicted amino acid kinas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16954  b2874 predicted amino acid kinase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  385.4   2.2  8.2e-120  8.2e-120       1     308 [.       3     309 ..       3     310 .] 0.96

  Alignments for each domain:
  == domain 1  score: 385.4 bits;  conditional E-value: 8.2e-120
                       TIGR00746   1 kkvvvaLGGnallqrgekasaeeqrknvekaakqlvklakrgyelvithGngPqvGalllqneaads....vpakPldv 75 
                                     kk+v+aLGGnal       +   q+k+v+++++++v+l+++g+e+++thGngPqvG +    eaa++    +p  P+ v
  lcl|FitnessBrowser__Keio:16954   3 KKIVLALGGNALG-----DDLAGQMKAVKITSQAIVDLIAQGHEVIVTHGNGPQVGMINQAFEAAAKteahSPMLPMSV 76 
                                     79**********9.....67889***********************************87777766656777889**** PP

                       TIGR00746  76 lgaesqgliGYllqqalkeelakeglekkvatvltqvivdekDeaFqnPtkpigpfydeeeakrlaaekgailkedagr 154
                                     ++a sqg iGY lq+al+eel  +g++k+vat++tqv+vd++D+aF nPtkpig f++e+ea+ + +++g++lkedagr
  lcl|FitnessBrowser__Keio:16954  77 CVALSQGYIGYDLQNALREELLSRGINKPVATLVTQVEVDANDPAFLNPTKPIGSFFTEQEAE-QLTKQGYTLKEDAGR 154
                                     ***************************************************************.66789********** PP

                       TIGR00746 155 gwRrvvpsPkPkeiveaeviktLvekgvivissgGGGvPvvkdgkelkGveaviDkDlasekLaeevnaDilviltdvd 233
                                     g+Rrvv+sPkP++i+e e++k Lv+ g++vi+ gGGG+Pv+++g++l+G  aviDkD as++Lae ++aD+l+ilt+v+
  lcl|FitnessBrowser__Keio:16954 155 GYRRVVASPKPVDIIEKETVKALVDAGQVVITVGGGGIPVIREGNHLRGASAVIDKDWASARLAEMIDADMLIILTAVE 233
                                     ******************************************************************************* PP

                       TIGR00746 234 avyvnygkpdekkleevkveeleelakdgefaaGsmgPkveaaiefvesrgk.kaiitslekivealegkaGtvvv 308
                                     +v++n+gk++e++l +++++++e+++++g+fa+Gsm+Pkveaa  f++sr+  +a+it l+k++e +egk+Gtv+ 
  lcl|FitnessBrowser__Keio:16954 234 KVAINFGKENEQWLDRLSLSDAERFIEEGHFAKGSMLPKVEAAASFARSRAGrEALITVLSKAKEGIEGKTGTVIC 309
                                     ************************************************98655********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (310 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.38
//
[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