GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Caldicellulosiruptor kronotskyensis 2002

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_013430189.1 CALKRO_RS06180 acetate kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>NCBI__GCF_000166775.1:WP_013430189.1
          Length = 399

 Score =  490 bits (1261), Expect = e-143
 Identities = 236/400 (59%), Positives = 315/400 (78%), Gaps = 1/400 (0%)

Query: 1   MRVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRVGDEKHVIERELPDHE 60
           M+VLV+NSGSSS+KYQ I+ + E  LCKG+ +RIG+ G+ + H+   ++ V E+E+ DH 
Sbjct: 1   MKVLVLNSGSSSLKYQFIDTDTEVALCKGVVDRIGLPGAFIRHQKNGQEIVKEQEINDHN 60

Query: 61  EALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVSPLAP 120
            A+KL+L  L  E+ G+I  + EIDA+GHRVVHGGE F ++V+V+EEV KAI E   LAP
Sbjct: 61  VAIKLVLEMLTHEEAGIIHSMDEIDAIGHRVVHGGEYFSDAVIVNEEVKKAIRECIELAP 120

Query: 121 LHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRYGFHG 180
           LHNPANLMGI+A  K +PG PNVAVFDTAFHQT+P+ AY+Y++PYE YEKYKIR+YGFHG
Sbjct: 121 LHNPANLMGIEACEKEIPGKPNVAVFDTAFHQTMPRYAYMYSLPYEVYEKYKIRKYGFHG 180

Query: 181 TSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLVMGTR 240
           TSH+YV+ +AAE L + LEELK+ITCH+GNG+SV A+KYGK VDTSMGFTPL GL MGTR
Sbjct: 181 TSHKYVAIKAAEYLRRPLEELKLITCHLGNGSSVCAIKYGKSVDTSMGFTPLAGLAMGTR 240

Query: 241 SGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDEWCKL 300
           SG +DPA+  ++MEKE +  ++M D LNKKSGV G+S G SSD RD+E+AA +G+E  +L
Sbjct: 241 SGTIDPAVILYLMEKEKMDVKQMNDFLNKKSGVLGIS-GVSSDFRDLEKAANEGNERAQL 299

Query: 301 VLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDKQKNE 360
            ++++ YR+ KYIG YAA + GVDAI+FTAG+GEN+ + R+   + LE++GV  D+++N 
Sbjct: 300 AIDMFCYRVKKYIGEYAAVLGGVDAIIFTAGIGENNALVRDKCLTDLEYMGVLYDRERNF 359

Query: 361 ETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIVEK 400
              +GK   I+ P+S+VKVL+VPTNEELMIAR+TK ++ K
Sbjct: 360 NVEKGKVFEINKPESKVKVLIVPTNEELMIARETKRLLSK 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: 517
Number of extensions: 24
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: 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 WP_013430189.1 CALKRO_RS06180 (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.2693789.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.6e-171  554.4   0.5   7.4e-171  554.2   0.5    1.0  1  NCBI__GCF_000166775.1:WP_013430189.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166775.1:WP_013430189.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  554.2   0.5  7.4e-171  7.4e-171       4     404 ..       1     397 [.       1     398 [. 0.98

  Alignments for each domain:
  == domain 1  score: 554.2 bits;  conditional E-value: 7.4e-171
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 
                                           +k+lvln+Gssslk++ +d+  +e  l++g+v+ri l++a+i   ++++++  ++++i+dh+ a+k +l+ l+
  NCBI__GCF_000166775.1:WP_013430189.1   1 MKVLVLNSGSSSLKYQFIDTD-TEVALCKGVVDRIGLPGAFIRH-QKNGQEIVKEQEINDHNVAIKLVLEMLT 71 
                                           69*****************99.6999**************8885.5666899999****************** PP

                             TIGR00016  77 k.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkakn 148
                                           + +  i+++++ei++iGHRvvhGge+f+++viv++ev k+i++ +elAPlHnpa+l giea    k+++ ++n
  NCBI__GCF_000166775.1:WP_013430189.1  72 HeEAGIIHSMDEIDAIGHRVVHGGEYFSDAVIVNEEVKKAIRECIELAPLHNPANLMGIEACE--KEIPGKPN 142
                                           98899**********************************************************..999999** PP

                             TIGR00016 149 vavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvs 221
                                           vavFDtafHqt+p+ ay+Y+lPy++y+++++R+YGfHGtshkyv+ +aa++l +pl++l+li+cHlGnG+sv+
  NCBI__GCF_000166775.1:WP_013430189.1 143 VAVFDTAFHQTMPRYAYMYSLPYEVYEKYKIRKYGFHGTSHKYVAIKAAEYLRRPLEELKLITCHLGNGSSVC 215
                                           ************************************************************************* PP

                             TIGR00016 222 avknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdild 294
                                           a+k Gks+dtsmG+tPL+Gl+mGtRsG iDpa+i yl+e++++ ++++++ lnkksG+lgisg+ssD+Rd+++
  NCBI__GCF_000166775.1:WP_013430189.1 216 AIKYGKSVDTSMGFTPLAGLAMGTRSGTIDPAVILYLMEKEKMDVKQMNDFLNKKSGVLGISGVSSDFRDLEK 288
                                           ************************************************************************* PP

                             TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367
                                           + +egne+a+lA++++++R++kyig+y+a l g +Dai+Ft+GiGen+a vr+++l +le +G+  d e+n +
  NCBI__GCF_000166775.1:WP_013430189.1 289 AANEGNERAQLAIDMFCYRVKKYIGEYAAVLGG-VDAIIFTAGIGENNALVRDKCLTDLEYMGVLYDRERNFN 360
                                           *******************************76.**************************************9 PP

                             TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDalrla 404
                                            ++gk   i+++eskvkvl++ptneel+ia+++ rl 
  NCBI__GCF_000166775.1:WP_013430189.1 361 VEKGKVFEINKPESKVKVLIVPTNEELMIARETKRLL 397
                                           9*******************************99985 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: 00:00:00.00
# Mc/sec: 20.58
//
[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