GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Corynebacterium deserti GIMN1.010

Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate WP_053545723.1 CDES_RS11950 acetate kinase

Query= SwissProt::P77845
         (397 letters)



>NCBI__GCF_001277995.1:WP_053545723.1
          Length = 397

 Score =  744 bits (1922), Expect = 0.0
 Identities = 370/397 (93%), Positives = 387/397 (97%)

Query: 1   MALALVLNSGSSSIKFQLVNPENSAIDEPYVSGLVEQIGEPNGRIVLKIEGEKYTLETPI 60
           M+LALVLNSGSSSIKFQLVNPENSA DEP+VSGLVEQIGEP GRIVLKIEGEK+TLE PI
Sbjct: 1   MSLALVLNSGSSSIKFQLVNPENSATDEPFVSGLVEQIGEPMGRIVLKIEGEKHTLEAPI 60

Query: 61  ADHSEGLNLAFDLMDQHNCGPSQLEITAVGHRVVHGGILFSAPELITDEIVEMIRDLIPL 120
           ADHS GL LAFDLMD+HNCGP+Q++ITAVGHRVVHGGILFSAPELITDEIVEMIRDLIPL
Sbjct: 61  ADHSAGLGLAFDLMDEHNCGPTQVDITAVGHRVVHGGILFSAPELITDEIVEMIRDLIPL 120

Query: 121 APLHNPANVDGIDVARKILPDVPHVAVFDTGFFHSLPPAAALYAINKDVAAEHGIRRYGF 180
           APLHNPANVDGI+VARKILPDVPHVAVFDTGFFHSLPPAAALYAINKDVA EHGIRRYGF
Sbjct: 121 APLHNPANVDGIEVARKILPDVPHVAVFDTGFFHSLPPAAALYAINKDVALEHGIRRYGF 180

Query: 181 HGTSHEFVSKRVVEILEKPTEDINTITFHLGNGASMAAVQGGRAVDTSMGMTPLAGLVMG 240
           HGTSHEFVSKRVVE+LEKP EDINTITFHLGNGASMAA++GGRAVDTSMGMTPLAGLVMG
Sbjct: 181 HGTSHEFVSKRVVELLEKPAEDINTITFHLGNGASMAAIEGGRAVDTSMGMTPLAGLVMG 240

Query: 241 TRSGDIDPGIVFHLSRTAGMSIDEIDNLLNKKSGVKGLSGVNDFRELREMIDNNDQDAWS 300
           TRSGDIDPGIVFHLSRTAGMSIDEID LLNKKSGVKGLSGVNDFRELR+MID+NDQDAWS
Sbjct: 241 TRSGDIDPGIVFHLSRTAGMSIDEIDTLLNKKSGVKGLSGVNDFRELRQMIDDNDQDAWS 300

Query: 301 AYNIYIHQLRRYLGSYMVALGRVDTIVFTAGVGENAQFVREDALAGLEMYGIEIDPERNA 360
           AYN+YIHQLRRYLGSYM+ALGRVDTIVFTAGVGENAQFVREDAL GLEMYGIEIDPERNA
Sbjct: 301 AYNVYIHQLRRYLGSYMIALGRVDTIVFTAGVGENAQFVREDALYGLEMYGIEIDPERNA 360

Query: 361 LPNDGPRLISTDASKVKVFVIPTNEELAIARYAVKFA 397
           LPN+GPRLISTD SKVKVFVIPTNEELAIA+YAVKFA
Sbjct: 361 LPNEGPRLISTDESKVKVFVIPTNEELAIAQYAVKFA 397


Lambda     K      H
   0.318    0.137    0.395 

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: 710
Number of extensions: 15
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: 397
Length of database: 397
Length adjustment: 31
Effective length of query: 366
Effective length of database: 366
Effective search space:   133956
Effective search space used:   133956
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_053545723.1 CDES_RS11950 (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.2216694.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.2e-140  452.0   0.0   9.1e-140  451.8   0.0    1.0  1  NCBI__GCF_001277995.1:WP_053545723.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001277995.1:WP_053545723.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  451.8   0.0  9.1e-140  9.1e-140       5     403 ..       3     396 ..       1     397 [] 0.95

  Alignments for each domain:
  == domain 1  score: 451.8 bits;  conditional E-value: 9.1e-140
                             TIGR00016   5 kilvlnaGssslkfalldaen..sekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntl 75 
                                           + lvln+Gsss+kf+l++ en  +++ ++sglve+i  +  ri  + +g +k++ +  i+dh++++   ++ +
  NCBI__GCF_001277995.1:WP_053545723.1   3 LALVLNSGSSSIKFQLVNPENsaTDEPFVSGLVEQIGEPMGRIVLKIEG-EKHTLEAPIADHSAGLGLAFDLM 74 
                                           679***************9994445559*********999988866666.77888999********8777666 PP

                             TIGR00016  76 kkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkakn 148
                                             +++   ++ +i+++GHRvvhGg  f+   ++tde+++ i+d+++lAPlHnpa+++gie +   k+l+++++
  NCBI__GCF_001277995.1:WP_053545723.1  75 D-EHNCGPTQVDITAVGHRVVHGGILFSAPELITDEIVEMIRDLIPLAPLHNPANVDGIEVAR--KILPDVPH 144
                                           6.899*********************************************************9..99****** PP

                             TIGR00016 149 vavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvs 221
                                           vavFDt f + +p  a+lYa+ +++  e+g+RrYGfHGtsh++v++r+ +ll+kp++d+n i+ HlGnGas++
  NCBI__GCF_001277995.1:WP_053545723.1 145 VAVFDTGFFHSLPPAAALYAINKDVALEHGIRRYGFHGTSHEFVSKRVVELLEKPAEDINTITFHLGNGASMA 217
                                           ************************************************************************* PP

                             TIGR00016 222 avknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdild 294
                                           a++ G+++dtsmG+tPL+GlvmGtRsGdiDp+i+++l+ t g+s+dei ++lnkksG+ g+sg  +D+R++ +
  NCBI__GCF_001277995.1:WP_053545723.1 218 AIEGGRAVDTSMGMTPLAGLVMGTRSGDIDPGIVFHLSRTAGMSIDEIDTLLNKKSGVKGLSG-VNDFRELRQ 289
                                           ***************************************************************.89******* PP

                             TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367
                                            +++++++a  A++vy+h +++y+g+y+ +l g++D+ivFt+G+Gena+ vre++l +le+ G+++d+e+n  
  NCBI__GCF_001277995.1:WP_053545723.1 290 MIDDNDQDAWSAYNVYIHQLRRYLGSYMIAL-GRVDTIVFTAGVGENAQFVREDALYGLEMYGIEIDPERNAL 361
                                           *******************************.67*************************************95 PP

                             TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDalrl 403
                                             ++  ++ist+eskvkv+viptneel+ia+ a+++
  NCBI__GCF_001277995.1:WP_053545723.1 362 -PNEGPRLISTDESKVKVFVIPTNEELAIAQYAVKF 396
                                           .556679************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (397 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 25.25
//
[ok]

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

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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