GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Microbacterium profundi Shh49

Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate WP_033106603.1 JF52_RS0110675 acetate kinase

Query= SwissProt::P77845
         (397 letters)



>NCBI__GCF_000763375.1:WP_033106603.1
          Length = 406

 Score =  363 bits (933), Expect = e-105
 Identities = 193/403 (47%), Positives = 261/403 (64%), Gaps = 15/403 (3%)

Query: 1   MALALVLNSGSSSIKFQLVNPENSAIDEPYVSGLVEQIGEPNGRIVLKI----EGEKYTL 56
           M++ L++NSGSSS+K+ L++ +    + P   GL+E+IG+    I   +    +GE    
Sbjct: 1   MSVVLIINSGSSSLKYSLIDMDR---ESPLGEGLIERIGQDVSAISHTVRRRSDGEAAPT 57

Query: 57  --------ETPIADHSEGLNLAFDLMDQHNCGPSQLEITAVGHRVVHGGILFSAPELITD 108
                   E  IA H E   +  +  + H     +    AVGHRVVHGG  F +P L+TD
Sbjct: 58  VLDVTEKSERTIAAHDEAFAVMLEQFEAHGPALDEHAPVAVGHRVVHGGARFFSPTLVTD 117

Query: 109 EIVEMIRDLIPLAPLHNPANVDGIDVARKILPDVPHVAVFDTGFFHSLPPAAALYAINKD 168
            + + I +L  LAPLHNPAN+ GI  AR +  DVPHVAVFDT F  +L P+A  YAI+  
Sbjct: 118 AVEQSIGELEVLAPLHNPANLAGIRAARAVFQDVPHVAVFDTAFHQTLKPSAYTYAIDAA 177

Query: 169 VAAEHGIRRYGFHGTSHEFVSKRVVEILEKPTEDINTITFHLGNGASMAAVQGGRAVDTS 228
            A +H IRRYGFHGTSH++VS++  + L +    +  + FHLGNGAS+ A+ GGR+V+TS
Sbjct: 178 FAEKHRIRRYGFHGTSHKYVSEQAADFLGRDLASLRQLVFHLGNGASVTAIGGGRSVETS 237

Query: 229 MGMTPLAGLVMGTRSGDIDPGIVFHLSRTAGMSIDEIDNLLNKKSGVKGLSGVNDFRELR 288
           MG TPL GLVMGTRSGD+DP ++ H++R A  SIDEID LLN +SG+KGL+G +D R++ 
Sbjct: 238 MGFTPLEGLVMGTRSGDLDPAVLVHIARVADYSIDEIDTLLNTRSGLKGLAGHSDMRDIL 297

Query: 289 EMIDNNDQDAWSAYNIYIHQLRRYLGSYMVALGRVDTIVFTAGVGENAQFVREDALAGLE 348
             +D  ++ A  A+++YIH+LR Y G+Y+  LG VD I FTAGVGENA  VR +AL+ L 
Sbjct: 298 AGVDAGEEAATLAFDVYIHRLRAYAGAYIAQLGGVDVISFTAGVGENAARVRAEALSTLG 357

Query: 349 MYGIEIDPERNALPNDGPRLISTDASKVKVFVIPTNEELAIAR 391
             GIEID  RN   +   R ISTD+S   V V+PT+EEL IAR
Sbjct: 358 FLGIEIDRARNEARSHSIRRISTDSSSASVLVVPTDEELEIAR 400


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: 477
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: 406
Length adjustment: 31
Effective length of query: 366
Effective length of database: 375
Effective search space:   137250
Effective search space used:   137250
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_033106603.1 JF52_RS0110675 (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.981691.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.3e-135  435.5   0.0   9.9e-135  435.3   0.0    1.1  1  NCBI__GCF_000763375.1:WP_033106603.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000763375.1:WP_033106603.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.3   0.0  9.9e-135  9.9e-135       4     401 ..       2     403 ..       1     406 [] 0.93

  Alignments for each domain:
  == domain 1  score: 435.3 bits;  conditional E-value: 9.9e-135
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktv....edgek.......keeeklaiedhe 65 
                                           +++l++n+Gssslk++l+d+   e+ l +gl+eri  + + i+      +dge        +e+ +  i++h+
  NCBI__GCF_000763375.1:WP_033106603.1   2 SVVLIINSGSSSLKYSLIDMD-RESPLGEGLIERIGQDVSAISHTvrrrSDGEAaptvldvTEKSERTIAAHD 73 
                                           689*****************9.58999********999887765422212333222222224566678999** PP

                             TIGR00016  66 eavkkllntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavl 138
                                           ea + +l++++++   l+e++ + ++GHRvvhGg +f + ++vtd v ++i ++  lAPlHnpa+l gi+a+ 
  NCBI__GCF_000763375.1:WP_033106603.1  74 EAFAVMLEQFEAHGPALDEHAPV-AVGHRVVHGGARFFSPTLVTDAVEQSIGELEVLAPLHNPANLAGIRAAR 145
                                           ***********876677777766.69*********************************************** PP

                             TIGR00016 139 klkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnliv 211
                                              v +++++vavFDtafHqt++  ay Ya+   + +++ +RrYGfHGtshkyv+++aa+ l++ l++l+ +v
  NCBI__GCF_000763375.1:WP_033106603.1 146 --AVFQDVPHVAVFDTAFHQTLKPSAYTYAIDAAFAEKHRIRRYGFHGTSHKYVSEQAADFLGRDLASLRQLV 216
                                           ..888999***************************************************************** PP

                             TIGR00016 212 cHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisg 284
                                            HlGnGasv+a+  G+s++tsmG+tPLeGlvmGtRsGd+Dpa++ ++a   + s+dei ++ln +sGl g++g
  NCBI__GCF_000763375.1:WP_033106603.1 217 FHLGNGASVTAIGGGRSVETSMGFTPLEGLVMGTRSGDLDPAVLVHIARVADYSIDEIDTLLNTRSGLKGLAG 289
                                           ************************************************************************* PP

                             TIGR00016 285 lssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlG 357
                                             sD+Rdil+ +++g+e a+lA++vy+hR++ y g+yia+l g +D i Ft+G+Genaa vr+++l++l +lG
  NCBI__GCF_000763375.1:WP_033106603.1 290 -HSDMRDILAGVDAGEEAATLAFDVYIHRLRAYAGAYIAQLGG-VDVISFTAGVGENAARVRAEALSTLGFLG 360
                                           .99**************************************76.***************************** PP

                             TIGR00016 358 lkldlelnnaarsgkesvisteeskvkvlviptneelviaeDal 401
                                           +++d ++n+ ars++ + ist+ s+  vlv+pt+eel ia+ +l
  NCBI__GCF_000763375.1:WP_033106603.1 361 IEIDRARNE-ARSHSIRRISTDSSSASVLVVPTDEELEIARQTL 403
                                           *********.99999*************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (406 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: 23.35
//
[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:

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