GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Thermoactinomyces daqus H-18

Align acetate kinase (EC 2.7.2.15) (characterized)
to candidate WP_033101565.1 JG50_RS0113070 acetate kinase

Query= metacyc::MONOMER-20612
         (399 letters)



>NCBI__GCF_000763315.1:WP_033101565.1
          Length = 397

 Score =  476 bits (1225), Expect = e-139
 Identities = 229/397 (57%), Positives = 302/397 (76%), Gaps = 1/397 (0%)

Query: 1   MNVLVINCGSSSLKYQFIDMTSEEVLAKGLVERIGIEGSILKHQTTGKDKVSIEQPMHDH 60
           M +LVINCGSSS+KYQ  DMT E VLA GLVE+IG E +I+KH+  G++K  I   + DH
Sbjct: 1   MKILVINCGSSSIKYQLFDMTDESVLASGLVEKIGTESAIIKHEPAGREKKVIISEILDH 60

Query: 61  KIALQLVLEALMNSEYGAIKDLKEIAAVGHRVVHGGEAFSHSALIDEHVKKAIEDCIELA 120
           ++ L+ VL+ LM+ + G IK   E++AVGHRVVHGGE F+ S ++D  V++AI +  +LA
Sbjct: 61  RVGLKKVLDLLMDEKEGVIKSADEVSAVGHRVVHGGETFARSVVVDSEVRRAIRETFDLA 120

Query: 121 PLHNPPNLIGINACQEILPNVPMVAVFDTAFHQTMPKSSYLYGLPYEYYEKYKVRRYGFH 180
           PLHNPPNLIGI+A Q  LP+   VAVFDTAFHQTMP  +Y+Y LP   Y KYKVRRYGFH
Sbjct: 121 PLHNPPNLIGIDAAQANLPHAVHVAVFDTAFHQTMPDYAYMYPLPRILYHKYKVRRYGFH 180

Query: 181 GTSHKYVAQKTAEILNKNLEDINIITCHLGNGASVTAVEKGHSVDTSMGFTPLEGLIMGT 240
           GTSHKYV+Q+ AE L K LE++ II+CH+GNGAS+TAV+ G SVDTSMG TPLEGL+MGT
Sbjct: 181 GTSHKYVSQRAAEFLGKPLEELKIISCHIGNGASITAVQGGKSVDTSMGMTPLEGLMMGT 240

Query: 241 RCGDIDPAMVTFLMEKENLSTAQINDVMNKKSGVLGISKVSSDFRDIETEAEKGNENAKI 300
           RCGDIDPA+V F++ KE L+ +++N +MNK SG+LG+S +SSD R++      GN NA++
Sbjct: 241 RCGDIDPAIVPFVIAKEELTLSEVNSMMNKHSGLLGVSGISSDMREVMEAMFDGNANARL 300

Query: 301 ALETYYKKVKKYIGAYMAEMGSVDAIVFTAGLGENSSSARLAICGGMEGIGIEIDAKEND 360
           A++ Y  K+KK IGAY+A M  VDAI+FTAG+GEN++  R  +C G+   G+++D  +N 
Sbjct: 301 AIDMYVYKIKKTIGAYVAAMDGVDAIIFTAGVGENAAQIREKVCEGLTFFGVDLDRDKNG 360

Query: 361 MRGEE-KVVSKPSSKISVLVVPTNEELMIARDTLEIV 396
           MR +E + +S   SK+ VLV+PTNEELMIAR+TL +V
Sbjct: 361 MRSKEIQRISTEKSKVEVLVIPTNEELMIARETLALV 397


Lambda     K      H
   0.315    0.133    0.371 

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: 412
Number of extensions: 11
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: 399
Length of database: 397
Length adjustment: 31
Effective length of query: 368
Effective length of database: 366
Effective search space:   134688
Effective search space used:   134688
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_033101565.1 JG50_RS0113070 (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.1825741.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-168  546.4   1.6     2e-168  546.3   1.6    1.0  1  NCBI__GCF_000763315.1:WP_033101565.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000763315.1:WP_033101565.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  546.3   1.6    2e-168    2e-168       4     403 ..       1     396 [.       1     397 [] 0.98

  Alignments for each domain:
  == domain 1  score: 546.3 bits;  conditional E-value: 2e-168
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 
                                           +kilv+n+Gsss+k++l+d+++ e+vl+sglve+i  e a+ik    g +k+ ++ +i dh+ ++kk+l+ l+
  NCBI__GCF_000763315.1:WP_033101565.1   1 MKILVINCGSSSIKYQLFDMTD-ESVLASGLVEKIGTESAIIKHEPAGREKKVIISEILDHRVGLKKVLDLLM 72 
                                           69*******************7.999**********************************************9 PP

                             TIGR00016  77 k.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkakn 148
                                           + ++ ++k+ +e++++GHRvvhGge+f+ sv+v++ev ++i++  +lAPlHnp++l+gi+a++    l++a +
  NCBI__GCF_000763315.1:WP_033101565.1  73 DeKEGVIKSADEVSAVGHRVVHGGETFARSVVVDSEVRRAIRETFDLAPLHNPPNLIGIDAAQ--ANLPHAVH 143
                                           97899**********************************************************..8999999* PP

                             TIGR00016 149 vavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvs 221
                                           vavFDtafHqt+p+ ay+Y+lP+ ly++++vRrYGfHGtshkyv+qraa+ l+kpl++l++i+cH+GnGas++
  NCBI__GCF_000763315.1:WP_033101565.1 144 VAVFDTAFHQTMPDYAYMYPLPRILYHKYKVRRYGFHGTSHKYVSQRAAEFLGKPLEELKIISCHIGNGASIT 216
                                           ************************************************************************* PP

                             TIGR00016 222 avknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdild 294
                                           av+ Gks+dtsmG+tPLeGl+mGtR+GdiDpai+ ++  +++l+l+e+++++nk+sGllg+sg+ssD+R++++
  NCBI__GCF_000763315.1:WP_033101565.1 217 AVQGGKSVDTSMGMTPLEGLMMGTRCGDIDPAIVPFVIAKEELTLSEVNSMMNKHSGLLGVSGISSDMREVME 289
                                           ************************************************************************* PP

                             TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367
                                           ++ +gn +a+lA+++yv++i+k ig+y+a+++g +Dai+Ft+G+Genaa++re+v+e+l ++G++ld ++n  
  NCBI__GCF_000763315.1:WP_033101565.1 290 AMFDGNANARLAIDMYVYKIKKTIGAYVAAMDG-VDAIIFTAGVGENAAQIREKVCEGLTFFGVDLDRDKNG- 360
                                           *******************************88.**************************************. PP

                             TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDalrl 403
                                            rs++ + iste+skv+vlviptneel+ia+++l l
  NCBI__GCF_000763315.1:WP_033101565.1 361 MRSKEIQRISTEKSKVEVLVIPTNEELMIARETLAL 396
                                           68888899***********************98866 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (397 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 14.73
//
[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