Alignments for a candidate for ackA in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Bacteroides thetaiotaomicron VPI-5482

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate 353219 BT3693 acetate kinase (NCBI ptt file)

Query= BRENDA::Q9WYB1
         (403 letters)



>FitnessBrowser__Btheta:353219
          Length = 399

 Score =  466 bits (1199), Expect = e-136
 Identities = 235/401 (58%), Positives = 304/401 (75%), Gaps = 3/401 (0%)

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

Query: 60  EEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVSPLA 119
              ++ ILNTL+  + G IK L EI+AVGHR+VHGGERF ESVL+++EVL+A    + LA
Sbjct: 61  TIGVEFILNTLISPEYGAIKSLDEINAVGHRMVHGGERFSESVLLNKEVLEAFAACNDLA 120

Query: 120 PLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRYGFH 179
           PLHNPANL G+ A   +LP +P V VFDTAFHQT+P  AY+YAIPYE YEKY +RRYGFH
Sbjct: 121 PLHNPANLKGVNAVSAILPNIPQVGVFDTAFHQTMPDYAYMYAIPYEMYEKYGVRRYGFH 180

Query: 180 GTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLVMGT 239
           GTSHRYVSKR  E LG      KIITCHIGNG S+AA+K GKC+DT+MG TPLEGL+MGT
Sbjct: 181 GTSHRYVSKRVCEFLGVNPVGQKIITCHIGNGGSIAAIKDGKCIDTTMGLTPLEGLMMGT 240

Query: 240 RSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDEWCK 299
           RSGD+D     FIMEKEG++   + ++LNKKSGV G+S G SSDMR++  A   G+E   
Sbjct: 241 RSGDIDAGAVTFIMEKEGLNTTGISNLLNKKSGVLGIS-GVSSDMRELLAACANGNERAI 299

Query: 300 LVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDKQKN 359
           L  ++Y YRI KYIGAYAAA+ GVD I+FT GVGEN    RE VC  +EF+G+KLD   N
Sbjct: 300 LAEKMYYYRIKKYIGAYAAALGGVDIILFTGGVGENQFECRESVCKDMEFMGIKLDNNVN 359

Query: 360 EETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIVEK 400
            + +RG+E IIST DS+VKV+V+PT+EEL+IA DT +I++K
Sbjct: 360 AK-VRGEEAIISTADSKVKVVVIPTDEELLIASDTMDILKK 399


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: 536
Number of extensions: 18
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: 399
Length adjustment: 31
Effective length of query: 372
Effective length of database: 368
Effective search space:   136896
Effective search space used:   136896
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 353219 BT3693 (acetate kinase (NCBI ptt file))
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.1230422.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                      -----------
   1.7e-162  526.7   0.7     2e-162  526.5   0.7    1.0  1  FitnessBrowser__Btheta:353219  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Btheta:353219  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  526.5   0.7    2e-162    2e-162       4     403 ..       1     396 [.       1     398 [. 0.98

  Alignments for each domain:
  == domain 1  score: 526.5 bits;  conditional E-value: 2e-162
                      TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkk.dkkil 82 
                                    +kilvln+Gsss+k++l+d++ +++v+++g +e+i l+++++k    +++k+  +++i++h+ +v+++lntl + +   +
  FitnessBrowser__Btheta:353219   1 MKILVLNCGSSSIKYKLFDMT-TKEVIAQGGIEKIGLKGSFLKLTLPNGEKKVLEKDIPEHTIGVEFILNTLISpEYGAI 79 
                                    69*******************.59999**********************************************9999*** PP

                      TIGR00016  83 kelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFDtafHqtipe 162
                                    k+l+ei+++GHR+vhGge+f+esv++++evl++ +   +lAPlHnpa+l+g++av+   +l++ ++v vFDtafHqt+p+
  FitnessBrowser__Btheta:353219  80 KSLDEINAVGHRMVHGGERFSESVLLNKEVLEAFAACNDLAPLHNPANLKGVNAVS--AILPNIPQVGVFDTAFHQTMPD 157
                                    ********************************************************..999******************* PP

                      TIGR00016 163 eaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGksidtsmGltPLeGlv 242
                                     ay+Ya+Py++y+++gvRrYGfHGtsh+yv++r+ + l+ +    ++i+cH+GnG+s++a+k+Gk+idt+mGltPLeGl+
  FitnessBrowser__Btheta:353219 158 YAYMYAIPYEMYEKYGVRRYGFHGTSHRYVSKRVCEFLGVNPVGQKIITCHIGNGGSIAAIKDGKCIDTTMGLTPLEGLM 237
                                    ****************************************9999************************************ PP

                      TIGR00016 243 mGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyi 322
                                    mGtRsGdiD +++++++e++gl +  i ++lnkksG+lgisg+ssD+R++l++ ++gne+a lA k+y +Ri+kyig+y+
  FitnessBrowser__Btheta:353219 238 MGTRSGDIDAGAVTFIMEKEGLNTTGISNLLNKKSGVLGISGVSSDMRELLAACANGNERAILAEKMYYYRIKKYIGAYA 317
                                    ******************************************************************************** PP

                      TIGR00016 323 aslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeDalr 402
                                    a+l g +D i+FtgG+Gen+ e+re v++++e++G+kld++ n    +g+e++ist +skvkv+vipt+eel+ia D++ 
  FitnessBrowser__Btheta:353219 318 AALGG-VDIILFTGGVGENQFECRESVCKDMEFMGIKLDNNVNA-KVRGEEAIISTADSKVKVVVIPTDEELLIASDTMD 395
                                    ***76.************************************99.7899****************************987 PP

                      TIGR00016 403 l 403
                                    +
  FitnessBrowser__Btheta:353219 396 I 396
                                    6 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 15.79
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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