GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Lactobacillus oryzae SG293

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_034525942.1 LOSG293_RS00980 acetate kinase

Query= BRENDA::Q9F1X7
         (397 letters)



>NCBI__GCF_000740055.1:WP_034525942.1
          Length = 398

 Score =  439 bits (1129), Expect = e-128
 Identities = 209/396 (52%), Positives = 300/396 (75%)

Query: 1   MSKIIAVNAGSSTLKFKLYEMPEENVLAEGVIERIALPASHVEIKYGDGKKYEKTTDVKN 60
           MSK++A+NAGSSTLK+KL+ +PEE+V+AEG+++R+ LPAS  ++K  +G+K+ +T D   
Sbjct: 1   MSKVLAINAGSSTLKWKLFNLPEESVIAEGMVDRLNLPASVFKLKLANGEKHNETRDNIT 60

Query: 61  HEQAIQILLDQLLDLDIIKEYSEINGVGHRVVAGGEYFDKSVVITPDVLKKIESLTELAP 120
           + +A  ++L +L  L I++   EI GVGHRVVAGGE F  S V+TP+VL KI++L+  AP
Sbjct: 61  NREAAAMVLTRLKSLHILEHLHEIVGVGHRVVAGGEEFKDSTVVTPEVLDKIKALSAYAP 120

Query: 121 LHEPANVLGIKAFKKVLPDIISVAVFDTAFHATLPEKNFLYSLPYEYYEKYSARKYGFHG 180
           LH P     I+ F+ +LPD   VAVFDT+    +P  N++YS+PYEYYEK+ ARKYG HG
Sbjct: 121 LHNPVQAYYIQTFQTLLPDATQVAVFDTSLFTEMPPVNYMYSIPYEYYEKFGARKYGAHG 180

Query: 181 IGNRYVSQRAAELLGKPAEDLKMIITHLGAGASICPVKNGKSFDTSMGFTPVTGITMATR 240
             +RYV+ RAAE+LGKP + LK++  HLG+G+SI    +GK+ DTSMGFTP+ G+TM TR
Sbjct: 181 TSHRYVAHRAAEILGKPFDSLKIVTLHLGSGSSITAFDHGKAIDTSMGFTPLAGVTMGTR 240

Query: 241 SGDVDPSLLAYVMEKEGMTDINEMIKVLNTKSGLLGISGVSADMREVEAAQATNPRAKVA 300
           SGD+D SL+AY+M+K  +T++ +MI +LN KSGLLGIS +S D R++E  Q +NP+AK+A
Sbjct: 241 SGDIDASLVAYLMQKLNLTNVEDMIDILNQKSGLLGISELSPDQRDLEEVQDSNPKAKLA 300

Query: 301 REIYVNRIIRYVGAYLAEMGGADAIVFTAGVGENSITIRKEVAEGLNYFGIGVDNEKNDV 360
            +I+VNR+I YVG+Y+ ++ G DA+VFTAG GEN I +R+ +A+ L+YFGI VD +KN+V
Sbjct: 301 LDIFVNRVISYVGSYIGKLNGIDALVFTAGSGENGIELRQNIADQLSYFGITVDPDKNNV 360

Query: 361 RGVVRDISAKDSKIKTLLVPTDEELMIVRDVQTLAN 396
           RG    ++ +++ +  L+VPT+EELMIVRDV+ L +
Sbjct: 361 RGKETILNKENAPVDVLIVPTNEELMIVRDVERLGH 396


Lambda     K      H
   0.316    0.135    0.372 

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: 444
Number of extensions: 12
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: 397
Length of database: 398
Length adjustment: 31
Effective length of query: 366
Effective length of database: 367
Effective search space:   134322
Effective search space used:   134322
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_034525942.1 LOSG293_RS00980 (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.1876892.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-141  458.2   0.1   1.2e-141  458.0   0.1    1.0  1  NCBI__GCF_000740055.1:WP_034525942.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000740055.1:WP_034525942.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  458.0   0.1  1.2e-141  1.2e-141       4     404 ..       2     395 ..       1     396 [. 0.97

  Alignments for each domain:
  == domain 1  score: 458.0 bits;  conditional E-value: 1.2e-141
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 
                                           +k+l +naGss lk++l++  + e+v+++g+v+r++l+ ++ k +  +++k++e+ +    +ea +++l++lk
  NCBI__GCF_000740055.1:WP_034525942.1   2 SKVLAINAGSSTLKWKLFNLPE-ESVIAEGMVDRLNLPASVFKLKLANGEKHNETRDNITNREAAAMVLTRLK 73 
                                           79*******************6.9999*************998888888888888888888889999****** PP

                             TIGR00016  77 kdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknv 149
                                              +il++l+ei  +GHRvv Gge+f++s++vt evl+kik +s +APlHnp ++  i++++  + l++a +v
  NCBI__GCF_000740055.1:WP_034525942.1  74 -SLHILEHLHEIVGVGHRVVAGGEEFKDSTVVTPEVLDKIKALSAYAPLHNPVQAYYIQTFQ--TLLPDATQV 143
                                           .699**********************************************************..8889999** PP

                             TIGR00016 150 avFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsa 222
                                           avFDt+  + +p  +y+Y++Py++y+++g R+YG+HGtsh+yv++raa++l+kp d+l+++++HlG G+s++a
  NCBI__GCF_000740055.1:WP_034525942.1 144 AVFDTSLFTEMPPVNYMYSIPYEYYEKFGARKYGAHGTSHRYVAHRAAEILGKPFDSLKIVTLHLGSGSSITA 216
                                           ************************************************************************* PP

                             TIGR00016 223 vknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlgls.ldeieetlnkksGllgisglssDlRdild 294
                                              Gk+idtsmG+tPL+G+ mGtRsGdiD +++ yl+++l+l+ ++++ ++ln+ksGllgis+ls D Rd+++
  NCBI__GCF_000740055.1:WP_034525942.1 217 FDHGKAIDTSMGFTPLAGVTMGTRSGDIDASLVAYLMQKLNLTnVEDMIDILNQKSGLLGISELSPDQRDLEE 289
                                           *****************************************984799************************99 PP

                             TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367
                                            + ++n +aklAl+++v+R+ +y+g+yi +l+g +Da+vFt+G Gen  e+r+++ ++l  +G+ +d+++nn 
  NCBI__GCF_000740055.1:WP_034525942.1 290 VQ-DSNPKAKLALDIFVNRVISYVGSYIGKLNG-IDALVFTAGSGENGIELRQNIADQLSYFGITVDPDKNN- 359
                                           87.999*************************88.**************************************. PP

                             TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDalrla 404
                                             +gke+++++e++ v vl++ptneel+i++D+ rl 
  NCBI__GCF_000740055.1:WP_034525942.1 360 -VRGKETILNKENAPVDVLIVPTNEELMIVRDVERLG 395
                                           .9*******************************9985 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: 19.58
//
[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