GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Mariniradius saccharolyticus AK6

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_040480655.1 C943_RS13315 acetate kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>NCBI__GCF_000330725.2:WP_040480655.1
          Length = 403

 Score =  421 bits (1081), Expect = e-122
 Identities = 215/407 (52%), Positives = 288/407 (70%), Gaps = 9/407 (2%)

Query: 1   MRVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRV----GDEKHVIEREL 56
           M++LV+NSGSSS+KYQL E   E  LC G+ ERIG++GS + H+V    G+ K  I+R++
Sbjct: 1   MKILVLNSGSSSLKYQLFEFPNESPLCTGLVERIGLDGSIITHKVARDGGEAKFTIKRKI 60

Query: 57  PDHEEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVS 116
            +HEEAL  +   L+++  GV+ D+ E+ A+GHRVVHGGE+F  + L+ +EV   IEE+ 
Sbjct: 61  QNHEEALVTVTEILLEKDKGVLSDMSEVIAIGHRVVHGGEQFASTTLISDEVKDKIEELF 120

Query: 117 PLAPLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRY 176
            LAPLHNP NL+GI+ A ++ P    VAVFDTAFHQT+P +AY +A+P E YEK  IR Y
Sbjct: 121 ALAPLHNPPNLLGIQVAERIFPQAKQVAVFDTAFHQTMPARAYRFAVPKEMYEKMGIRAY 180

Query: 177 GFHGTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLV 236
           GFHG+SH+YVSK A + L  +   +K+I+ H+GNG+SV A++ GK VD SMG  P+ GLV
Sbjct: 181 GFHGSSHQYVSKMAMKFL--QNPGVKLISIHLGNGSSVTAIEAGKSVDHSMGLGPMGGLV 238

Query: 237 MGTRSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDE 296
           MGTR GD+DP+I F ++ + GIS  E+ DILNKKSG+ GL     SDMRD+++A   GD+
Sbjct: 239 MGTRCGDIDPSIIFHLINERGISAHELNDILNKKSGLLGLCG--HSDMRDVKDAIAAGDK 296

Query: 297 WCKLVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDK 356
              L  E+Y YRI KYIG YAAAMNG+DAI+FTAG+GEN    RE VC+ +EFLG++LD+
Sbjct: 297 DAALAYELYAYRIQKYIGMYAAAMNGLDAIIFTAGIGENDTDMREKVCANMEFLGIRLDQ 356

Query: 357 QKNEETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIVEKIGR 403
             N     G    I+  DS+VKV+VVPTNEEL I + T  +V+ I R
Sbjct: 357 SLNTARSSGIRE-INRSDSKVKVIVVPTNEELEIGQQTYHLVQAISR 402


Lambda     K      H
   0.318    0.138    0.391 

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: 455
Number of extensions: 19
Number of successful extensions: 5
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: 403
Length of database: 403
Length adjustment: 31
Effective length of query: 372
Effective length of database: 372
Effective search space:   138384
Effective search space used:   138384
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_040480655.1 C943_RS13315 (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.67084.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.4e-150  486.7   0.7   2.7e-150  486.5   0.7    1.0  1  NCBI__GCF_000330725.2:WP_040480655.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000330725.2:WP_040480655.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  486.5   0.7  2.7e-150  2.7e-150       4     404 ..       1     397 [.       1     398 [. 0.96

  Alignments for each domain:
  == domain 1  score: 486.5 bits;  conditional E-value: 2.7e-150
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktv...edgekkeeeklaiedheeavkklln 73 
                                           +kilvln+Gssslk++l++  n e+ l+ glveri l++++i+ +     ge k ++k +i++heea+ ++ +
  NCBI__GCF_000330725.2:WP_040480655.1   1 MKILVLNSGSSSLKYQLFEFPN-ESPLCTGLVERIGLDGSIITHKvarDGGEAKFTIKRKIQNHEEALVTVTE 72 
                                           69*******************7.8889*************9987733233566778899************** PP

                             TIGR00016  74 tlkk.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllk 145
                                            l + dk +l ++se+ +iGHRvvhGge+f++++++ dev +ki+++  lAPlHnp++l gi+ +    + ++
  NCBI__GCF_000330725.2:WP_040480655.1  73 ILLEkDKGVLSDMSEVIAIGHRVVHGGEQFASTTLISDEVKDKIEELFALAPLHNPPNLLGIQVAE--RIFPQ 143
                                           99887999*********************************************************9..78888 PP

                             TIGR00016 146 aknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGa 218
                                           ak+vavFDtafHqt+p +ay +a+P+++y+++g+R YGfHG sh+yv++ a k l+     ++li++HlGnG+
  NCBI__GCF_000330725.2:WP_040480655.1 144 AKQVAVFDTAFHQTMPARAYRFAVPKEMYEKMGIRAYGFHGSSHQYVSKMAMKFLQN--PGVKLISIHLGNGS 214
                                           99*****************************************************99..689*********** PP

                             TIGR00016 219 svsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRd 291
                                           sv+a++ Gks+d smGl P+ GlvmGtR+GdiDp+ii++l +++g s++e++++lnkksGllg+ g  sD+Rd
  NCBI__GCF_000330725.2:WP_040480655.1 215 SVTAIEAGKSVDHSMGLGPMGGLVMGTRCGDIDPSIIFHLINERGISAHELNDILNKKSGLLGLCG-HSDMRD 286
                                           ******************************************************************.99**** PP

                             TIGR00016 292 ildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlel 364
                                           + d++++g+++a+lA+++y++Ri+kyig y+a+++g lDai+Ft+GiGen++++re+v+ ++e+lG++ld+ l
  NCBI__GCF_000330725.2:WP_040480655.1 287 VKDAIAAGDKDAALAYELYAYRIQKYIGMYAAAMNG-LDAIIFTAGIGENDTDMREKVCANMEFLGIRLDQSL 358
                                           **********************************88.************************************ PP

                             TIGR00016 365 nnaarsgkesvisteeskvkvlviptneelviaeDalrla 404
                                           n+ ars   + i+ ++skvkv+v+ptneel i + +++l+
  NCBI__GCF_000330725.2:WP_040480655.1 359 NT-ARSSGIREINRSDSKVKVIVVPTNEELEIGQQTYHLV 397
                                           *9.999999****************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (403 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 18.71
//
[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