GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Catellicoccus marimammalium M35/04/3

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_009491778.1 C683_RS05475 acetate kinase

Query= BRENDA::Q9F1X7
         (397 letters)



>NCBI__GCF_000313915.1:WP_009491778.1
          Length = 397

 Score =  453 bits (1166), Expect = e-132
 Identities = 224/395 (56%), Positives = 300/395 (75%), Gaps = 1/395 (0%)

Query: 1   MSKIIAVNAGSSTLKFKLYEMPEENVLAEGVIERIALPASHVEIKYGDGKKYEKTTDVKN 60
           MS +IAVNAGSS+LK+KL+E+PEE  +A G+ ERI L    +++K  DG+  EK   + N
Sbjct: 1   MSYVIAVNAGSSSLKWKLFEVPEEKEVASGIAERIGLDMGKIKLKKADGETVEKELPIPN 60

Query: 61  HEQAIQILLDQLLDLDIIKEYSEINGVGHRVVAGGEYFDKSVVITPDVLKKIESLTELAP 120
           H +A+  +L+ L++  II     I  VGHRVVAGGE +  SVV+  +VL +IE L+ELAP
Sbjct: 61  HNEALTEILNSLIEEKIIPSLDAITAVGHRVVAGGESYKDSVVVDEEVLAEIERLSELAP 120

Query: 121 LHEPANVLGIKAFKKVLPDIISVAVFDTAFHATLPEKNFLYSLPYEYYEKYSARKYGFHG 180
           LH PA    I+ F++VLP++ +VAVFDT+FH T+P +N+LYSLP  YYE+Y AR+YG HG
Sbjct: 121 LHNPAEAKVIRVFREVLPNVQNVAVFDTSFHQTMPVENYLYSLPMRYYEEYKARRYGAHG 180

Query: 181 IGNRYVSQRAAELLGKPAEDLKMIITHLGAGASICPVKNGKSFDTSMGFTPVTGITMATR 240
             ++YVSQRAAELLGKP E+LK+I  HLG GASI  V +GKS DTSMGFTP+ G+TM TR
Sbjct: 181 TSHKYVSQRAAELLGKPIEELKIITCHLGNGASITAVDHGKSVDTSMGFTPLAGLTMGTR 240

Query: 241 SGDVDPSLLAYVMEKEGMTDINEMIKVLNTKSGLLGISGVSADMREV-EAAQATNPRAKV 299
           SGD+D SL+ ++M+KEG+TD+ E I +LN +SGLLG+SG+S+DMR++ +AA+  N +A+V
Sbjct: 241 SGDIDASLIPFIMKKEGITDVQEFIDILNNESGLLGLSGLSSDMRDLRDAARNGNEQAEV 300

Query: 300 AREIYVNRIIRYVGAYLAEMGGADAIVFTAGVGENSITIRKEVAEGLNYFGIGVDNEKND 359
           A +I+ NRII+Y+G+Y+AEM G DAIVFT G+GEN   +RK+V   L +FG+ +D EKND
Sbjct: 301 AIKIFKNRIIKYIGSYMAEMNGCDAIVFTGGIGENDRAVRKDVCASLTFFGVDLDEEKND 360

Query: 360 VRGVVRDISAKDSKIKTLLVPTDEELMIVRDVQTL 394
           VRG    IS ++SKI  LLVPT+EELMIVRDV+ L
Sbjct: 361 VRGKEGIISKENSKISVLLVPTEEELMIVRDVERL 395


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: 485
Number of extensions: 22
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: 397
Length adjustment: 31
Effective length of query: 366
Effective length of database: 366
Effective search space:   133956
Effective search space used:   133956
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_009491778.1 C683_RS05475 (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.1881071.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-165  536.6   0.3   1.9e-165  536.4   0.3    1.0  1  NCBI__GCF_000313915.1:WP_009491778.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000313915.1:WP_009491778.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  536.4   0.3  1.9e-165  1.9e-165       5     404 ..       3     396 ..       1     397 [] 0.98

  Alignments for each domain:
  == domain 1  score: 536.4 bits;  conditional E-value: 1.9e-165
                             TIGR00016   5 kilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkk 77 
                                            ++ +naGssslk++l++  + ek ++sg++eri l+  +ik ++ ++++ e++l i++h+ea++++ln+l  
  NCBI__GCF_000313915.1:WP_009491778.1   3 YVIAVNAGSSSLKWKLFEVPE-EKEVASGIAERIGLDMGKIKLKKADGETVEKELPIPNHNEALTEILNSLI- 73 
                                           6999****************7.5556******************9999************************. PP

                             TIGR00016  78 dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknva 150
                                           ++ki+ +l+ i+++GHRvv Gge++++sv+v++evl++i+++selAPlHnpae+++i+ +   +vl++++nva
  NCBI__GCF_000313915.1:WP_009491778.1  74 EEKIIPSLDAITAVGHRVVAGGESYKDSVVVDEEVLAEIERLSELAPLHNPAEAKVIRVFR--EVLPNVQNVA 144
                                           799**********************************************************..999******* PP

                             TIGR00016 151 vFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsav 223
                                           vFDt+fHqt+p e+ylY+lP+++y+e++ RrYG+HGtshkyv+qraa+ll+kp+++l++i+cHlGnGas++av
  NCBI__GCF_000313915.1:WP_009491778.1 145 VFDTSFHQTMPVENYLYSLPMRYYEEYKARRYGAHGTSHKYVSQRAAELLGKPIEELKIITCHLGNGASITAV 217
                                           ************************************************************************* PP

                             TIGR00016 224 knGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlgls.ldeieetlnkksGllgisglssDlRdildk 295
                                             Gks+dtsmG+tPL+Gl mGtRsGdiD ++i ++++++g + ++e  ++ln +sGllg+sglssD+Rd+ d+
  NCBI__GCF_000313915.1:WP_009491778.1 218 DHGKSVDTSMGFTPLAGLTMGTRSGDIDASLIPFIMKKEGITdVQEFIDILNNESGLLGLSGLSSDMRDLRDA 290
                                           ****************************************985799*************************** PP

                             TIGR00016 296 keegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaa 368
                                            ++gne+a++A+k++ +Ri kyig+y+a+++g  DaivFtgGiGen+  vr++v+ +l ++G++ld+e+n   
  NCBI__GCF_000313915.1:WP_009491778.1 291 ARNGNEQAEVAIKIFKNRIIKYIGSYMAEMNG-CDAIVFTGGIGENDRAVRKDVCASLTFFGVDLDEEKND-- 360
                                           ******************************88.**************************************.. PP

                             TIGR00016 369 rsgkesvisteeskvkvlviptneelviaeDalrla 404
                                            +gke++is+e+sk+ vl +pt+eel+i++D+ rl+
  NCBI__GCF_000313915.1:WP_009491778.1 361 VRGKEGIISKENSKISVLLVPTEEELMIVRDVERLT 396
                                           9*******************************9997 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 17.14
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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