GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Lactobacillus shenzhenensis LY-73

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_022530736.1 L248_RS13095 acetate kinase

Query= BRENDA::Q9F1X7
         (397 letters)



>NCBI__GCF_000469325.1:WP_022530736.1
          Length = 396

 Score =  438 bits (1126), Expect = e-127
 Identities = 214/394 (54%), Positives = 292/394 (74%), Gaps = 1/394 (0%)

Query: 3   KIIAVNAGSSTLKFKLYEMPEENVLAEGVIERIALPASHVEIKYGDGKKYEKTTDVKNHE 62
           KI+AVN GSSTLK+KLY+MP E+VLAEG+++R+ L  S   +K+ +G K ++  D+KN E
Sbjct: 2   KILAVNTGSSTLKWKLYDMPAEHVLAEGMLDRMGLGDSVFTVKF-NGSKTKEVGDIKNAE 60

Query: 63  QAIQILLDQLLDLDIIKEYSEINGVGHRVVAGGEYFDKSVVITPDVLKKIESLTELAPLH 122
           +A++ L+  L+D  II  + EI G+GHR+VAGGE F +S ++TP+ +KK+  L + APLH
Sbjct: 61  EAVKKLMATLIDRKIIGSFDEIAGIGHRIVAGGETFTESALMTPENIKKVRGLADFAPLH 120

Query: 123 EPANVLGIKAFKKVLPDIISVAVFDTAFHATLPEKNFLYSLPYEYYEKYSARKYGFHGIG 182
            PA   GI+AF K+LP++  V VFDTAFH T+P++N+LYS+P EYY KY ARKYG HG  
Sbjct: 121 NPAEAGGIEAFAKILPNVPQVGVFDTAFHTTMPKENYLYSIPMEYYRKYGARKYGAHGTS 180

Query: 183 NRYVSQRAAELLGKPAEDLKMIITHLGAGASICPVKNGKSFDTSMGFTPVTGITMATRSG 242
           +RYVS RAAELL    + LKMI  H+G+G S+  +K+GKS DTSMGFTP+ G+TM+TRSG
Sbjct: 181 HRYVSARAAELLHADLKSLKMITLHMGSGVSVTAIKDGKSLDTSMGFTPLAGVTMSTRSG 240

Query: 243 DVDPSLLAYVMEKEGMTDINEMIKVLNTKSGLLGISGVSADMREVEAAQATNPRAKVARE 302
           D+D SL+AY+M K  +TD N+MI +LNTKSG+ GIS +S DMR++E    T P++K+A +
Sbjct: 241 DIDASLVAYLMGKLKITDPNQMIDILNTKSGIYGISELSPDMRQLEQTIDTRPQSKLAID 300

Query: 303 IYVNRIIRYVGAYLAEMGGADAIVFTAGVGENSITIRKEVAEGLNYFGIGVDNEKNDVRG 362
           I+VNRII+Y+G+Y A MGG D +VFTAG+GE  I +R  + + LNY G  +D E+NDV  
Sbjct: 301 IFVNRIIKYIGSYTAIMGGLDVLVFTAGIGEGDIKMRDRIVKKLNYMGAKIDPERNDVMA 360

Query: 363 VVRDISAKDSKIKTLLVPTDEELMIVRDVQTLAN 396
             R IS  DS +K +LVPT+EELMI RD   +A+
Sbjct: 361 KERLISTDDSSVKVMLVPTNEELMIARDTVRVAH 394


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: 478
Number of extensions: 20
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: 397
Length of database: 396
Length adjustment: 31
Effective length of query: 366
Effective length of database: 365
Effective search space:   133590
Effective search space used:   133590
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_022530736.1 L248_RS13095 (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.811962.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.1e-151  488.7   0.6   6.9e-151  488.5   0.6    1.0  1  NCBI__GCF_000469325.1:WP_022530736.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000469325.1:WP_022530736.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  488.5   0.6  6.9e-151  6.9e-151       4     404 ..       1     393 [.       1     394 [. 0.98

  Alignments for each domain:
  == domain 1  score: 488.5 bits;  conditional E-value: 6.9e-151
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 
                                           +kil +n+Gss lk++l+d+  +e+vl++g+ +r+ l ++ ++tv++++ k++e+ +i++ eeavkkl+ tl 
  NCBI__GCF_000469325.1:WP_022530736.1   1 MKILAVNTGSSTLKWKLYDMP-AEHVLAEGMLDRMGLGDS-VFTVKFNGSKTKEVGDIKNAEEAVKKLMATLI 71 
                                           69*******************.7****************9.999***************************** PP

                             TIGR00016  77 kdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknv 149
                                            d+ki+ + +eia iGHR+v Gge+ftes+++t e +kk++ ++++APlHnpae+ giea+   k+l+++++v
  NCBI__GCF_000469325.1:WP_022530736.1  72 -DRKIIGSFDEIAGIGHRIVAGGETFTESALMTPENIKKVRGLADFAPLHNPAEAGGIEAFA--KILPNVPQV 141
                                           .8************************************************************..99******* PP

                             TIGR00016 150 avFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsa 222
                                            vFDtafH+t+p+e+ylY++P+++y+++g R+YG+HGtsh+yv+ raa+ll   l++l++i++H+G G sv+a
  NCBI__GCF_000469325.1:WP_022530736.1 142 GVFDTAFHTTMPKENYLYSIPMEYYRKYGARKYGAHGTSHRYVSARAAELLHADLKSLKMITLHMGSGVSVTA 214
                                           ************************************************************************* PP

                             TIGR00016 223 vknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlgls.ldeieetlnkksGllgisglssDlRdild 294
                                           +k+Gks+dtsmG+tPL+G+ m tRsGdiD +++ yl+ +l+ +  +++ ++ln ksG+ gis+ls D+R++++
  NCBI__GCF_000469325.1:WP_022530736.1 215 IKDGKSLDTSMGFTPLAGVTMSTRSGDIDASLVAYLMGKLKITdPNQMIDILNTKSGIYGISELSPDMRQLEQ 287
                                           ***************************************99884799************************** PP

                             TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367
                                            + +++ ++klA++++v+Ri kyig+y+a + g lD +vFt+GiGe + ++r+++++kl+ +G k+d+e+n  
  NCBI__GCF_000469325.1:WP_022530736.1 288 TI-DTRPQSKLAIDIFVNRIIKYIGSYTAIMGG-LDVLVFTAGIGEGDIKMRDRIVKKLNYMGAKIDPERND- 357
                                           **.8999************************76.**************************************. PP

                             TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDalrla 404
                                             + ke++ist++s+vkv+ +ptneel+ia+D++r+a
  NCBI__GCF_000469325.1:WP_022530736.1 358 -VMAKERLISTDDSSVKVMLVPTNEELMIARDTVRVA 393
                                           .99*******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (396 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: 00:00:00.00
# Mc/sec: 24.32
//
[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