GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Rhizobium etli CFN 42

Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate WP_011426667.1 RHE_RS17585 acetate/propionate family kinase

Query= curated2:Q1QPW6
         (404 letters)



>NCBI__GCF_000092045.1:WP_011426667.1
          Length = 392

 Score =  300 bits (767), Expect = 6e-86
 Identities = 173/393 (44%), Positives = 232/393 (59%), Gaps = 6/393 (1%)

Query: 2   DSILVVNAGSSSVKFQVFSAEGEGKLLRQIKGQVDGIGSRPRLRASGADNEPLADRAYPI 61
           D +L  NAGSS+VK  VFS +G   + R +   V  + + P L           D     
Sbjct: 5   DLLLTFNAGSSTVKVGVFSIDGA--VARHLGRGVIDLRAEP-LSLGLTRGSQTFDMPLKA 61

Query: 62  ESVSDVPAAMGVAGGWLRDELRISP-MAVGHRVVHGGPDYDRPVLIDHGVVARLERFVAL 120
           E   D+   +      L DE  ++  +AVGHRVVHGG  +   V +D      +E  + L
Sbjct: 62  EVTDDLHGVIDETFALLADEFDMAAAVAVGHRVVHGGERFTSAVALDDAATDGIEALIPL 121

Query: 121 APLHQPNNLDPIRSLLANFPALPQVACFDTAFHRTHDAVADYYAIPYQFYVEGVRRYGFH 180
           APLHQP  L  IR+L    P L Q A FDTAFH T D +    AIP   + EG++RYGFH
Sbjct: 122 APLHQPQALRFIRALRHLKPHLVQTASFDTAFHATQDDLVRRLAIPRSLHEEGIKRYGFH 181

Query: 181 GLSYEYVAKTLPHVAPEIAKGRVIVAHLGSGASMCALKGGRSIESTMGFTALDGLPMGTR 240
           GLSY+++A  L   AP  AK   +VAHLGSGAS+CA++ G S + +MGF+ LDG+PM TR
Sbjct: 182 GLSYKFIASELARKAPHAAKA--VVAHLGSGASLCAMEDGISRDCSMGFSTLDGIPMATR 239

Query: 241 PGQIDPGVVLYLVSEKGMSPAKAQDFLYRDCGLKGLSGVSNDMRELEASEDPKAKLAVDY 300
           PG +DPGV+L+L  E+  S  + +D LY   GL G+SG+S D R+L     P+A+ A+D 
Sbjct: 240 PGCLDPGVILHLAGERKRSLGEIEDLLYHRSGLLGVSGISADTRDLLTDGRPEARQAIDL 299

Query: 301 FVYRVGLNAGMLAAALQGLDAFVFTAGIGENSMRIRARIADQLAWLGVTLDPTQNSRHAR 360
           F  R+    G +AA L GLDA VFTAGIGE+   IRA +A +L WLG+++D T N+  + 
Sbjct: 300 FTLRIAGEIGRMAATLGGLDAVVFTAGIGEHQPEIRAGVAKRLFWLGLSIDETANAADSF 359

Query: 361 LISGSDSRIPVYVIPTDEELMIAQHTLSLLLDR 393
            IS  +SRI  +V+ TDEE +IA   LS+L  R
Sbjct: 360 TISTGESRIAAHVVATDEEQVIADEALSVLRAR 392


Lambda     K      H
   0.320    0.137    0.403 

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: 423
Number of extensions: 15
Number of successful extensions: 3
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: 404
Length of database: 392
Length adjustment: 31
Effective length of query: 373
Effective length of database: 361
Effective search space:   134653
Effective search space used:   134653
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_011426667.1 RHE_RS17585 (acetate/propionate family 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.71106.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.6e-94  302.8   0.0      2e-94  302.5   0.0    1.0  1  NCBI__GCF_000092045.1:WP_011426667.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000092045.1:WP_011426667.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.5   0.0     2e-94     2e-94       4     402 ..       5     387 ..       2     390 .. 0.88

  Alignments for each domain:
  == domain 1  score: 302.5 bits;  conditional E-value: 2e-94
                             TIGR00016   4 kkilvlnaGssslkfalldaen.sekvllsglverikleeariktvedgekkeee..klaie.dheeavkkll 72 
                                            ++l  naGss +k  ++   +   + l +g+++    + +    ++ g+++     k +++ d +  +++ +
  NCBI__GCF_000092045.1:WP_011426667.1   5 DLLLTFNAGSSTVKVGVFSIDGaVARHLGRGVIDLRAEPLS--LGLTRGSQTFDMplKAEVTdDLHGVIDETF 75 
                                           57899**************9973456699****98877766..445666665544114444414444555555 PP

                             TIGR00016  73 ntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllk 145
                                             l +      +++   ++GHRvvhGge+ft++v ++d + ++i+ +++lAPlH p++l  i+a+ +lk++l 
  NCBI__GCF_000092045.1:WP_011426667.1  76 ALLAD----EFDMAAAVAVGHRVVHGGERFTSAVALDDAATDGIEALIPLAPLHQPQALRFIRALRHLKPHLV 144
                                           55554....345666778************************************************7766665 PP

                             TIGR00016 146 aknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGa 218
                                             + a FDtafH t  +     a+P+sl+ e g++rYGfHG+s+k+++ ++a++     +  + +v+HlG Ga
  NCBI__GCF_000092045.1:WP_011426667.1 145 --QTASFDTAFHATQDDLVRRLAIPRSLH-EEGIKRYGFHGLSYKFIASELARKA---PHAAKAVVAHLGSGA 211
                                           ..9**********************8776.679**************99888755...558899********* PP

                             TIGR00016 219 svsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRd 291
                                           s++a+++G s d smG+  L+G+ m tR G +Dp++i +la ++++sl eie++l  +sGllg+sg+s+D Rd
  NCBI__GCF_000092045.1:WP_011426667.1 212 SLCAMEDGISRDCSMGFSTLDGIPMATRPGCLDPGVILHLAGERKRSLGEIEDLLYHRSGLLGVSGISADTRD 284
                                           ************************************************************************* PP

                             TIGR00016 292 ildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlel 364
                                           +l +   g+ ea+ A+++++ Ria  ig+++a+l g lDa+vFt+GiGe + e+r+ v ++l  lGl +d+  
  NCBI__GCF_000092045.1:WP_011426667.1 285 LLTD---GRPEARQAIDLFTLRIAGEIGRMAATLGG-LDAVVFTAGIGEHQPEIRAGVAKRLFWLGLSIDETA 353
                                           9975...5889***********************76.*********************************999 PP

                             TIGR00016 365 nnaarsgkesvisteeskvkvlviptneelviaeDalr 402
                                           n      ++  ist es++ + v+ t+ee via +al 
  NCBI__GCF_000092045.1:WP_011426667.1 354 NA----ADSFTISTGESRIAAHVVATDEEQVIADEALS 387
                                           98....89999**********************99876 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 16.95
//
[ok]

This GapMind analysis is from Apr 09 2024. 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