GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Bacteroides clarus YIT 12056

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_009121835.1 BUB52_RS13600 acetate kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>NCBI__GCF_900129655.1:WP_009121835.1
          Length = 398

 Score =  464 bits (1195), Expect = e-135
 Identities = 234/401 (58%), Positives = 301/401 (75%), Gaps = 4/401 (0%)

Query: 1   MRVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRVGD-EKHVIERELPDH 59
           M+VLV+N GSSSIKY+L +M+ ++V+ +G  E+IG++GS L   + D EK ++E+++P+H
Sbjct: 1   MKVLVLNCGSSSIKYKLFDMDHKEVIAQGGIEKIGLKGSFLKLTLPDGEKKILEKDIPEH 60

Query: 60  EEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVSPLA 119
              ++ ILNTL+  + G IK L EI+AVGHR+VHGGE+F ESVL+ +EVL A    + LA
Sbjct: 61  TVGVEFILNTLISSEYGAIKSLDEINAVGHRMVHGGEKFSESVLLTQEVLDAFTACNDLA 120

Query: 120 PLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRYGFH 179
           PLHNPANL G+ A   +LP VP + VFDTAFHQT+P  AY+YA+PYE YEKY +RRYGFH
Sbjct: 121 PLHNPANLKGVNAVSAILPDVPQIGVFDTAFHQTMPDYAYMYAVPYELYEKYGVRRYGFH 180

Query: 180 GTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLVMGT 239
           GTSHRYVSKR  E LG + E  KIITCHIGNG SV+A+K GKC+DTSMG TPLEGL+MGT
Sbjct: 181 GTSHRYVSKRVCEFLGVQPEGKKIITCHIGNGGSVSAIKDGKCMDTSMGLTPLEGLMMGT 240

Query: 240 RSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDEWCK 299
           RSGD+D     FIM+KE +    + ++LNKKSGV G+  G SSDMRD+E A   G+    
Sbjct: 241 RSGDIDAGAVTFIMDKENLDANGVSNLLNKKSGVMGIF-GESSDMRDLENAVAAGNPRAI 299

Query: 300 LVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDKQKN 359
           L  ++Y YRI KY+GAYAAA+ GVD IVFT GVGEN    R +VC  L F+GVK+D +KN
Sbjct: 300 LAEKMYFYRIKKYVGAYAAALGGVDIIVFTGGVGENQCNCRSEVCEGLGFMGVKVDLEKN 359

Query: 360 EETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIVEK 400
           +  +RG+E +IST DS+VKV+V+PT+EELMIA DT  I+ K
Sbjct: 360 K--VRGEEAVISTDDSKVKVVVIPTDEELMIASDTMAILSK 398


Lambda     K      H
   0.318    0.138    0.391 

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: 535
Number of extensions: 23
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: 403
Length of database: 398
Length adjustment: 31
Effective length of query: 372
Effective length of database: 367
Effective search space:   136524
Effective search space used:   136524
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_009121835.1 BUB52_RS13600 (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.1270360.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.3e-162  525.1   0.2     6e-162  524.9   0.2    1.0  1  NCBI__GCF_900129655.1:WP_009121835.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900129655.1:WP_009121835.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  524.9   0.2    6e-162    6e-162       4     403 ..       1     395 [.       1     397 [. 0.98

  Alignments for each domain:
  == domain 1  score: 524.9 bits;  conditional E-value: 6e-162
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 
                                           +k+lvln+Gsss+k++l+d+   ++v+++g +e+i l+++++k    +++k+  +++i++h+ +v+++lntl 
  NCBI__GCF_900129655.1:WP_009121835.1   1 MKVLVLNCGSSSIKYKLFDMD-HKEVIAQGGIEKIGLKGSFLKLTLPDGEKKILEKDIPEHTVGVEFILNTLI 72 
                                           69******************9.58899****************99999999999******************9 PP

                             TIGR00016  77 k.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkakn 148
                                           + +   +k+l+ei+++GHR+vhGgekf+esv++t+evl++     +lAPlHnpa+l+g++av+   +l+++++
  NCBI__GCF_900129655.1:WP_009121835.1  73 SsEYGAIKSLDEINAVGHRMVHGGEKFSESVLLTQEVLDAFTACNDLAPLHNPANLKGVNAVS--AILPDVPQ 143
                                           98999**********************************************************..999***** PP

                             TIGR00016 149 vavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvs 221
                                           + vFDtafHqt+p+ ay+Ya+Py+ly+++gvRrYGfHGtsh+yv++r+ + l+ + +  ++i+cH+GnG+svs
  NCBI__GCF_900129655.1:WP_009121835.1 144 IGVFDTAFHQTMPDYAYMYAVPYELYEKYGVRRYGFHGTSHRYVSKRVCEFLGVQPEGKKIITCHIGNGGSVS 216
                                           ************************************************************************* PP

                             TIGR00016 222 avknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdild 294
                                           a+k+Gk++dtsmGltPLeGl+mGtRsGdiD +++++++++++l ++ + ++lnkksG++gi g ssD+Rd+++
  NCBI__GCF_900129655.1:WP_009121835.1 217 AIKDGKCMDTSMGLTPLEGLMMGTRSGDIDAGAVTFIMDKENLDANGVSNLLNKKSGVMGIFGESSDMRDLEN 289
                                           ************************************************************************* PP

                             TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367
                                           ++++gn +a lA k+y +Ri+ky+g+y+a+l g +D ivFtgG+Gen+ ++r +v+e+l ++G+k+dle+n+ 
  NCBI__GCF_900129655.1:WP_009121835.1 290 AVAAGNPRAILAEKMYFYRIKKYVGAYAAALGG-VDIIVFTGGVGENQCNCRSEVCEGLGFMGVKVDLEKNK- 360
                                           *******************************76.**************************************. PP

                             TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDalrl 403
                                             +g+e+vist++skvkv+vipt+eel+ia D++ +
  NCBI__GCF_900129655.1:WP_009121835.1 361 -VRGEEAVISTDDSKVKVVVIPTDEELMIASDTMAI 395
                                           .9******************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (398 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: 27.22
//
[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