GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Pontibacillus litoralis JSM 072002

Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate WP_036831492.1 N784_RS01950 acetate kinase

Query= SwissProt::P37877
         (395 letters)



>NCBI__GCF_000775615.1:WP_036831492.1
          Length = 398

 Score =  631 bits (1627), Expect = 0.0
 Identities = 299/393 (76%), Positives = 360/393 (91%)

Query: 1   MSKIIAINAGSSSLKFQLFEMPSETVLTKGLVERIGIADSVFTISVNGEKNTEVTDIPDH 60
           MSKI++INAGSSSLKFQL EMP+E V+TKGLVERIG+ +++FTI VNGEK+  VTDIP+H
Sbjct: 1   MSKILSINAGSSSLKFQLIEMPAEEVVTKGLVERIGLDNAIFTIEVNGEKDKMVTDIPNH 60

Query: 61  AVAVKMLLNKLTEFGIIKDLNEIDGIGHRVVHGGEKFSDSVLLTDETIKEIEDISELAPL 120
             AV++L++KLT  GI++ L+EI+GIGHRVVHGGE+FSDS L+T+E +KEIE++SELAPL
Sbjct: 61  QRAVEILVDKLTSTGIVQSLDEIEGIGHRVVHGGERFSDSALVTEEVMKEIEEVSELAPL 120

Query: 121 HNPANIVGIKAFKEVLPNVPAVAVFDTAFHQTMPEQSYLYSLPYEYYEKFGIRKYGFHGT 180
           HNPAN+ GI+AF+++LPNVPAV VFDTAFHQ+MPEQSYLYSLPY+YYE +GIRKYGFHGT
Sbjct: 121 HNPANLTGIRAFQQILPNVPAVVVFDTAFHQSMPEQSYLYSLPYDYYEDYGIRKYGFHGT 180

Query: 181 SHKYVTERAAELLGRPLKDLRLISCHLGNGASIAAVEGGKSIDTSMGFTPLAGVAMGTRS 240
           SHKYV++RAAE++ RPL  +R++SCHLGNGASIAA+EGGKS+DTSMGFTPLAGV MGTRS
Sbjct: 181 SHKYVSQRAAEMVNRPLDQMRILSCHLGNGASIAAIEGGKSVDTSMGFTPLAGVTMGTRS 240

Query: 241 GNIDPALIPYIMEKTGQTADEVLNTLNKKSGLLGISGFSSDLRDIVEATKEGNERAETAL 300
           GNIDPALIPYIMEKTG++A+EV++ LNK+SG+L +SGFSSDLRDI E  ++G+ERAE AL
Sbjct: 241 GNIDPALIPYIMEKTGKSAEEVIHVLNKESGMLALSGFSSDLRDIEEKAEQGDERAELAL 300

Query: 301 EVFASRIHKYIGSYAARMSGVDAIIFTAGIGENSVEVRERVLRGLEFMGVYWDPALNNVR 360
           +VFA RIHKYIGSYAARM GVDAI+FTAG+GENS  +RERVL+GLEFMGVYWDP+LN  R
Sbjct: 301 QVFADRIHKYIGSYAARMHGVDAIVFTAGVGENSTAIRERVLKGLEFMGVYWDPSLNQTR 360

Query: 361 GEEAFISYPHSPVKVMIIPTDEEVMIARDVVRL 393
           G+EAFISYPHSPVKVM+IPT+EEVMIARD VRL
Sbjct: 361 GKEAFISYPHSPVKVMVIPTNEEVMIARDTVRL 393


Lambda     K      H
   0.317    0.136    0.381 

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: 513
Number of extensions: 14
Number of successful extensions: 1
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: 395
Length of database: 398
Length adjustment: 31
Effective length of query: 364
Effective length of database: 367
Effective search space:   133588
Effective search space used:   133588
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_036831492.1 N784_RS01950 (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.120556.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.2e-181  588.0   0.1   4.7e-181  587.8   0.1    1.0  1  NCBI__GCF_000775615.1:WP_036831492.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000775615.1:WP_036831492.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  587.8   0.1  4.7e-181  4.7e-181       4     404 ..       2     394 ..       1     395 [. 0.99

  Alignments for each domain:
  == domain 1  score: 587.8 bits;  conditional E-value: 4.7e-181
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 
                                           +kil +naGssslkf+l+++  +e+v+++glveri l++a i+t+e +++k++ +++i++h++av+ l+++l+
  NCBI__GCF_000775615.1:WP_036831492.1   2 SKILSINAGSSSLKFQLIEMP-AEEVVTKGLVERIGLDNA-IFTIEVNGEKDKMVTDIPNHQRAVEILVDKLT 72 
                                           79*******************.79999*************.999***************************** PP

                             TIGR00016  77 kdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknv 149
                                             + i ++l+ei+ iGHRvvhGge+f++s++vt+ev+k+i+++selAPlHnpa+l+gi+a++  ++l+++++v
  NCBI__GCF_000775615.1:WP_036831492.1  73 -STGIVQSLDEIEGIGHRVVHGGERFSDSALVTEEVMKEIEEVSELAPLHNPANLTGIRAFQ--QILPNVPAV 142
                                           .699**********************************************************..999****** PP

                             TIGR00016 150 avFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsa 222
                                           +vFDtafHq +pe++ylY+lPy++y+++g+R+YGfHGtshkyv+qraa+++n+pld++++++cHlGnGas++a
  NCBI__GCF_000775615.1:WP_036831492.1 143 VVFDTAFHQSMPEQSYLYSLPYDYYEDYGIRKYGFHGTSHKYVSQRAAEMVNRPLDQMRILSCHLGNGASIAA 215
                                           ************************************************************************* PP

                             TIGR00016 223 vknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildk 295
                                           ++ Gks+dtsmG+tPL+G+ mGtRsG+iDpa+i y++e++g+s++e+ ++lnk+sG+l++sg+ssDlRdi++k
  NCBI__GCF_000775615.1:WP_036831492.1 216 IEGGKSVDTSMGFTPLAGVTMGTRSGNIDPALIPYIMEKTGKSAEEVIHVLNKESGMLALSGFSSDLRDIEEK 288
                                           ************************************************************************* PP

                             TIGR00016 296 keegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaa 368
                                            e+g+e+a+lAl+v++ Ri+kyig+y+a+++g +DaivFt+G+Gen++ +re+vl++le++G+++d+ ln+  
  NCBI__GCF_000775615.1:WP_036831492.1 289 AEQGDERAELALQVFADRIHKYIGSYAARMHG-VDAIVFTAGVGENSTAIRERVLKGLEFMGVYWDPSLNQ-- 358
                                           ******************************88.**************************************.. PP

                             TIGR00016 369 rsgkesvisteeskvkvlviptneelviaeDalrla 404
                                           ++gke++is+++s vkv+viptnee++ia+D++rl+
  NCBI__GCF_000775615.1:WP_036831492.1 359 TRGKEAFISYPHSPVKVMVIPTNEEVMIARDTVRLI 394
                                           99********************************97 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 19.69
//
[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