GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Oscillibacter ruminantium GH1

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_040659222.1 ON16_RS02895 acetate kinase

Query= BRENDA::P0CW05
         (408 letters)



>NCBI__GCF_000307265.1:WP_040659222.1
          Length = 399

 Score =  474 bits (1221), Expect = e-138
 Identities = 234/399 (58%), Positives = 301/399 (75%), Gaps = 2/399 (0%)

Query: 1   MKVLVINAGSSSLKYQLIDMTNESALAIGLCERIGIDNSIITQKRFDGKKLEKQTD--LP 58
           MKVLVINAGSSSLKYQL+D      LA GLCERIGID     + + +GK+  K  D  +P
Sbjct: 1   MKVLVINAGSSSLKYQLMDPDTGVVLAKGLCERIGIDGKFTYKPQIEGKETLKAVDVAMP 60

Query: 59  NHKIALEEVVKALTDSEFGVIKSMDEINAVGHRVVHGGEKFNSSALINEGVEQAIKDCFE 118
            H  A++ V+ AL D + GVI SM EI+AVGHRVVHGGE FN S  I++ V  AI++C  
Sbjct: 61  THSEAIQAVLNALVDPKNGVIGSMKEIDAVGHRVVHGGEAFNKSVRIDDKVMAAIEECVP 120

Query: 119 LAPLHNPPNMMGISSCQEIMPGVPMVAVFDTAFHHTIPPYAYMYALPYELYEKYGIRKYG 178
           LAPLHNP N+ GI +C+++MP VPMVAVFDTAFH T+P  A+ YALPYE Y+   +R+YG
Sbjct: 121 LAPLHNPANITGIRACEKVMPNVPMVAVFDTAFHQTMPAKAFTYALPYEYYKNDKVRRYG 180

Query: 179 FHGTSHFYVAKRAAAMLGKPEQDVKVITCHLGNGSSITAVKGGKSIETTMGFTPLEGVAM 238
           FHGTSH YV +RAAAMLGKP  ++K+ITCHLGNGSS+TAV GGKS++T+MGFTPL G+ M
Sbjct: 181 FHGTSHKYVTERAAAMLGKPAAELKIITCHLGNGSSVTAVDGGKSVDTSMGFTPLAGLPM 240

Query: 239 GTRCGSIDPAVVPFIMEKEGLSTREIDTLMNKKSGVLGVSSLSNDFRDLDEAASKGNQKA 298
           GTR G +D  ++ F+M K  LS  E+  ++NKKSGV G+S +S+DFRDL+EAA  GNQ+A
Sbjct: 241 GTRSGDLDAGILQFLMNKYKLSIDEMLNILNKKSGVQGISEVSSDFRDLEEAAKAGNQQA 300

Query: 299 ELALEIFAYKIKKVIGEYIAVLNGVDAIVFTAGIGENSASIRKRILADLDGIGIKIDEEK 358
           +LAL+ F Y +KK+IG Y A + GVDAIVFTAG+GEN A+ R  + +DLD +G+K+D   
Sbjct: 301 QLALDTFQYGVKKLIGSYAAAMGGVDAIVFTAGVGENDAATRMAVASDLDFMGVKMDAAA 360

Query: 359 NKIRGQEIDISTPDATVRVLVIPTNEELTIARDTKEICE 397
           N +RG+E  IST D+ V+VL+IPT+EEL IA+DT  +C+
Sbjct: 361 NNVRGKETVISTADSKVKVLLIPTDEELMIAKDTAALCK 399


Lambda     K      H
   0.317    0.135    0.379 

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: 491
Number of extensions: 13
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: 408
Length of database: 399
Length adjustment: 31
Effective length of query: 377
Effective length of database: 368
Effective search space:   138736
Effective search space used:   138736
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: 50 (23.9 bits)

Align candidate WP_040659222.1 ON16_RS02895 (acetate kinase)
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

# 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/TIGR00016.hmm
# target sequence database:        /tmp/gapView.4190952.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00016  [M=405]
Accession:   TIGR00016
Description: ackA: acetate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.1e-163  527.8   0.3   9.1e-163  527.6   0.3    1.0  1  NCBI__GCF_000307265.1:WP_040659222.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000307265.1:WP_040659222.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  527.6   0.3  9.1e-163  9.1e-163       4     404 ..       1     398 [.       1     399 [] 0.97

  Alignments for each domain:
  == domain 1  score: 527.6 bits;  conditional E-value: 9.1e-163
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktv..edgekkeeeklaiedheeavkkllnt 74 
                                           +k+lv+naGssslk++l+d   +  vl++gl+eri +++++  +   e  e+ ++  +a++ h+ea++++ln+
  NCBI__GCF_000307265.1:WP_040659222.1   1 MKVLVINAGSSSLKYQLMDPD-TGVVLAKGLCERIGIDGKFTYKPqiEGKETLKAVDVAMPTHSEAIQAVLNA 72 
                                           69******************9.57889***********99887652133444566778999************ PP

                             TIGR00016  75 lkk.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllka 146
                                           l++ ++ ++ +++ei+++GHRvvhGge f++sv ++d+v+++i++ ++lAPlHnpa+++gi+a    kv++++
  NCBI__GCF_000307265.1:WP_040659222.1  73 LVDpKNGVIGSMKEIDAVGHRVVHGGEAFNKSVRIDDKVMAAIEECVPLAPLHNPANITGIRACE--KVMPNV 143
                                           **999************************************************************..99**** PP

                             TIGR00016 147 knvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGas 219
                                           + vavFDtafHqt+p +a+ YalPy++yk+ +vRrYGfHGtshkyvt+raa +l+kp+++l++i+cHlGnG+s
  NCBI__GCF_000307265.1:WP_040659222.1 144 PMVAVFDTAFHQTMPAKAFTYALPYEYYKNDKVRRYGFHGTSHKYVTERAAAMLGKPAAELKIITCHLGNGSS 216
                                           ************************************************************************* PP

                             TIGR00016 220 vsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdi 292
                                           v+av  Gks+dtsmG+tPL+Gl mGtRsGd+D +i+++l+++ +ls+de+ ++lnkksG+ gis++ssD+Rd+
  NCBI__GCF_000307265.1:WP_040659222.1 217 VTAVDGGKSVDTSMGFTPLAGLPMGTRSGDLDAGILQFLMNKYKLSIDEMLNILNKKSGVQGISEVSSDFRDL 289
                                           ************************************************************************* PP

                             TIGR00016 293 ldkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldleln 365
                                           +++ ++gn++a+lAl+++ + ++k ig+y+a++ g +DaivFt+G+Gen+a  r  v ++l+++G+k+d + n
  NCBI__GCF_000307265.1:WP_040659222.1 290 EEAAKAGNQQAQLALDTFQYGVKKLIGSYAAAMGG-VDAIVFTAGVGENDAATRMAVASDLDFMGVKMDAAAN 361
                                           *********************************76.************************************* PP

                             TIGR00016 366 naarsgkesvisteeskvkvlviptneelviaeDalrla 404
                                           n   +gke+vist +skvkvl ipt+eel+ia+D++ l+
  NCBI__GCF_000307265.1:WP_040659222.1 362 N--VRGKETVISTADSKVKVLLIPTDEELMIAKDTAALC 398
                                           *..9*******************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (399 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: 14.37
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

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:

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:

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:

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:

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