Alignments for a candidate for ackA in Sinorhizobium meliloti 1021

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.948.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.19
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources