GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Sinorhizobium meliloti 1021

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate SM_b21184 SM_b21184 acetate kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>FitnessBrowser__Smeli:SM_b21184
          Length = 392

 Score =  257 bits (656), Expect = 5e-73
 Identities = 161/402 (40%), Positives = 235/402 (58%), Gaps = 22/402 (5%)

Query: 3   VLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGS-RLVHRVGDEKHVIEREL----- 56
           +LVIN+GSSS+K+Q+  +    +  +  A+  GI    RL     D   +I R L     
Sbjct: 4   LLVINAGSSSLKFQIFGIATAGLERQVRAKLDGIATQPRLKATAADGTELINRRLDATAV 63

Query: 57  PDHEEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVS 116
           PD  EAL     ++  + L  ++   ++ A+GHRVVHGG  +   VL++  VL  +    
Sbjct: 64  PDLPEAL-----SVARDWLATLRGF-DLRAIGHRVVHGGPDYVRPVLIETTVLDRLASYQ 117

Query: 117 PLAPLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRY 176
            LAPLH P NL  I+ AM + P VP VA FDTAFH+   +    YA+P  +YE+  +RRY
Sbjct: 118 DLAPLHQPNNLAPIRLAMDIKPDVPQVACFDTAFHRGRTEHTDCYALPRTFYEQ-GVRRY 176

Query: 177 GFHGTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLV 236
           GFHG S+ Y++ R  E+   ++   ++I  H+G+GAS+ A+K G+ V+T+MGFT L+GL 
Sbjct: 177 GFHGISYEYIAGRLREV-APEVARGRVIVAHLGSGASMCALKDGRSVETTMGFTALDGLP 235

Query: 237 MGTRSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDE 296
           MGTR G LDP +   ++  +G+S Q + D+L  +SG+ GLS G S+DMR++  +    D 
Sbjct: 236 MGTRPGQLDPGVVLHLLTDQGMSAQAVSDLLYHRSGLKGLS-GISNDMRELLGS---DDP 291

Query: 297 WCKLVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDK 356
                ++ + +R A   G  AAA+ G+DA VFTAG+GENS   R  V   L +LG +LD 
Sbjct: 292 RASFAIDHFVHRCALDAGMLAAALGGLDAFVFTAGIGENSAPIRARVSEGLAWLGAELDP 351

Query: 357 QKNEETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIV 398
             N+        +IS   SRV + V+PT+EELMIAR T  I+
Sbjct: 352 AAND----AGASVISKAGSRVALHVMPTDEELMIARHTLAII 389


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: 360
Number of extensions: 17
Number of successful extensions: 6
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: 392
Length adjustment: 31
Effective length of query: 372
Effective length of database: 361
Effective search space:   134292
Effective search space used:   134292
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 SM_b21184 SM_b21184 (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.3682015.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   2.1e-107  345.3   0.0   2.4e-107  345.1   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SM_b21184  SM_b21184 acetate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SM_b21184  SM_b21184 acetate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.1   0.0  2.4e-107  2.4e-107       5     402 ..       3     387 ..       1     390 [. 0.89

  Alignments for each domain:
  == domain 1  score: 345.1 bits;  conditional E-value: 2.4e-107
                            TIGR00016   5 kilvlnaGssslkfalldaen.sekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkk 77 
                                           +lv+naGssslkf+++  ++ + +  +++  + i  +     t  dg     e  + +  ++av  l ++l  
  lcl|FitnessBrowser__Smeli:SM_b21184   3 ALLVINAGSSSLKFQIFGIATaGLERQVRAKLDGIATQPRLKATAADGT----ELINRRLDATAVPDLPEALSV 72 
                                          68***************99874334448888999998888555555553....334444445566666666665 PP

                            TIGR00016  78 dkkilk..elseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknv 149
                                           ++ l      ++++iGHRvvhGg ++   v++++ vl++++   +lAPlH p++l  i+ ++   +++++++v
  lcl|FitnessBrowser__Smeli:SM_b21184  73 ARDWLAtlRGFDLRAIGHRVVHGGPDYVRPVLIETTVLDRLASYQDLAPLHQPNNLAPIRLAM--DIKPDVPQV 144
                                          33333300345899***********************************************99..88999**** PP

                            TIGR00016 150 avFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsav 223
                                          a+FDtafH+   e++  YalP+ +y e+gvRrYGfHG+s++y++ r+ ++    ++  ++iv+HlG Gas++a+
  lcl|FitnessBrowser__Smeli:SM_b21184 145 ACFDTAFHRGRTEHTDCYALPRTFY-EQGVRRYGFHGISYEYIAGRLREVAPE-VARGRVIVAHLGSGASMCAL 216
                                          *********************8877.57*******************998776.999***************** PP

                            TIGR00016 224 knGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkke 297
                                          k+G+s++t+mG+t L+Gl mGtR G++Dp+++ +l + +g+s++++ ++l  +sGl g+sg+s+D+R++l    
  lcl|FitnessBrowser__Smeli:SM_b21184 217 KDGRSVETTMGFTALDGLPMGTRPGQLDPGVVLHLLTDQGMSAQAVSDLLYHRSGLKGLSGISNDMRELLGSD- 289
                                          *********************************************************************9987. PP

                            TIGR00016 298 egneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsg 371
                                            + +a+ A++ +vhR a   g  +a+l g lDa vFt+GiGen+a +r++v e+l+ lG +ld++ n      
  lcl|FitnessBrowser__Smeli:SM_b21184 290 --DPRASFAIDHFVHRCALDAGMLAAALGG-LDAFVFTAGIGENSAPIRARVSEGLAWLGAELDPAAND----A 356
                                          ..7899**********************76.***********************************999....7 PP

                            TIGR00016 372 kesvisteeskvkvlviptneelviaeDalr 402
                                            svis+  s+v + v+pt+eel+ia+ +l 
  lcl|FitnessBrowser__Smeli:SM_b21184 357 GASVISKAGSRVALHVMPTDEELMIARHTLA 387
                                          889***********************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (392 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: 24.20
//
[ok]

This GapMind analysis is from Sep 17 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