GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Rubrivirga marina SAORIC-28

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_095512017.1 BSZ37_RS18750 acetate kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>NCBI__GCF_002283365.1:WP_095512017.1
          Length = 405

 Score =  399 bits (1025), Expect = e-116
 Identities = 211/398 (53%), Positives = 273/398 (68%), Gaps = 4/398 (1%)

Query: 1   MRVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRVGDEK-HVIERELPDH 59
           M VLV+N+GSSS+K  LI+    + L  G  ERIG   S    RVGD K   I  + PDH
Sbjct: 1   MTVLVLNAGSSSLKVDLIDAAAGQTLAAGQVERIGAVSSLASFRVGDAKPERISLKAPDH 60

Query: 60  EEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVSPLA 119
             AL  +L T+  E  G    L +++AVGHRVVHGGERF ES L+D EV+ AI +   LA
Sbjct: 61  AAALSHLLETM-READGEEDRLPDVEAVGHRVVHGGERFAESALIDGEVVDAIRDAFDLA 119

Query: 120 PLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRYGFH 179
           PLHNPANL GI+AA K  P VP VAVFDTAFHQTIP +AYLYA+P   Y ++KIRRYGFH
Sbjct: 120 PLHNPANLQGIRAAQKAFPDVPQVAVFDTAFHQTIPAEAYLYALPNRLYRRHKIRRYGFH 179

Query: 180 GTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLVMGT 239
           GTSH YVS+R  E+ G   +  +++T H+GNG S+AA++ GK VDTSMG TPLEGLVMGT
Sbjct: 180 GTSHYYVSRRLYELAGLDQQNSRVVTIHLGNGCSMAAIRDGKSVDTSMGMTPLEGLVMGT 239

Query: 240 RSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDEWCK 299
           RSGDLDP+I F +MEKE +   E++ +LN+ SG+ GLS G+++DMRD+   A  GD  C+
Sbjct: 240 RSGDLDPSIVFEVMEKEDMPLAEVHTLLNRYSGLLGLS-GYAADMRDLLAEAADGDVRCQ 298

Query: 300 LVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDKQKN 359
             ++++ YR+  Y+G Y A + G+DA+ FTAG+G  +   R  +   L  LG+ LD   N
Sbjct: 299 QAIDVFCYRVKSYLGRYLAVLGGLDAVAFTAGIGTFAAPVRAQILYGLAGLGMTLDAGAN 358

Query: 360 EETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEI 397
            E   G E +I+TPDS V V VVPTNEEL+IA+DT+++
Sbjct: 359 -EAANGTEAVITTPDSAVPVWVVPTNEELVIAQDTQKL 395


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: 411
Number of extensions: 17
Number of successful extensions: 4
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: 405
Length adjustment: 31
Effective length of query: 372
Effective length of database: 374
Effective search space:   139128
Effective search space used:   139128
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_095512017.1 BSZ37_RS18750 (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.593796.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-150  487.4   0.0   1.7e-150  487.2   0.0    1.0  1  NCBI__GCF_002283365.1:WP_095512017.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002283365.1:WP_095512017.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  487.2   0.0  1.7e-150  1.7e-150       5     403 ..       2     395 ..       1     397 [. 0.97

  Alignments for each domain:
  == domain 1  score: 487.2 bits;  conditional E-value: 1.7e-150
                             TIGR00016   5 kilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkk 77 
                                            +lvlnaGssslk  l+da+   ++l+ g veri    +  +  + + k e++ l+ +dh++a+++ll+t+ +
  NCBI__GCF_002283365.1:WP_095512017.1   2 TVLVLNAGSSSLKVDLIDAAA-GQTLAAGQVERIGAVSSLASFRVGDAKPERISLKAPDHAAALSHLLETMRE 73 
                                           79******************6.5556*********999977777777789999*******************9 PP

                             TIGR00016  78 dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknva 150
                                            +   + l +++++GHRvvhGge+f+es++++ ev+++i+d+ +lAPlHnpa+l+gi+a++  k  +++++va
  NCBI__GCF_002283365.1:WP_095512017.1  74 ADGEEDRLPDVEAVGHRVVHGGERFAESALIDGEVVDAIRDAFDLAPLHNPANLQGIRAAQ--KAFPDVPQVA 144
                                           999999*******************************************************..7788999*** PP

                             TIGR00016 151 vFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsav 223
                                           vFDtafHqtip eaylYalP +ly+++++RrYGfHGtsh+yv++r+ +l +   ++++++++HlGnG s++a+
  NCBI__GCF_002283365.1:WP_095512017.1 145 VFDTAFHQTIPAEAYLYALPNRLYRRHKIRRYGFHGTSHYYVSRRLYELAGLDQQNSRVVTIHLGNGCSMAAI 217
                                           ************************************************************************* PP

                             TIGR00016 224 knGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkk 296
                                           ++Gks+dtsmG+tPLeGlvmGtRsGd+Dp+i++ ++e++++ l+e++++ln+ sGllg+sg ++D+Rd+l++ 
  NCBI__GCF_002283365.1:WP_095512017.1 218 RDGKSVDTSMGMTPLEGLVMGTRSGDLDPSIVFEVMEKEDMPLAEVHTLLNRYSGLLGLSGYAADMRDLLAEA 290
                                           ************************************************************************* PP

                             TIGR00016 297 eegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaar 369
                                           ++g+ +++ A++v+++R+++y+g+y+a l g lDa+ Ft+GiG  aa vr+++l +l+ lG+ ld   n+ a 
  NCBI__GCF_002283365.1:WP_095512017.1 291 ADGDVRCQQAIDVFCYRVKSYLGRYLAVLGG-LDAVAFTAGIGTFAAPVRAQILYGLAGLGMTLDAGANE-AA 361
                                           *****************************76.**************************************.88 PP

                             TIGR00016 370 sgkesvisteeskvkvlviptneelviaeDalrl 403
                                           +g+e+vi+t++s+v v v+ptneelvia+D+ +l
  NCBI__GCF_002283365.1:WP_095512017.1 362 NGTEAVITTPDSAVPVWVVPTNEELVIAQDTQKL 395
                                           899****************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (405 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: 23.41
//
[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