Alignments for a candidate for ackA in Sulfuritalea hydrogenivorans sk43H DSM 22779

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Sulfuritalea hydrogenivorans sk43H DSM 22779

Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate WP_041099069.1 SUTH_RS10370 acetate/propionate family kinase

Query= curated2:Q6N143
         (398 letters)



>NCBI__GCF_000828635.1:WP_041099069.1
          Length = 400

 Score =  394 bits (1012), Expect = e-114
 Identities = 215/400 (53%), Positives = 268/400 (67%), Gaps = 9/400 (2%)

Query: 1   MSDVLLVLNAGSSSIKFALYEAHTE-PTADHLICE-GGIGSLGHRP-HFKVVNSDGSTRY 57
           M+D +L LNAGSSSIKFAL+      P    L+ +  GIG+ G +P HF   ++      
Sbjct: 1   MADAILTLNAGSSSIKFALFAYSAAIPQQPELVGQIDGIGAAGGQPAHFNARDAARHVLD 60

Query: 58  DTYL----PEGTSHDDAMAVLIGWIETTFPEHRLSAVGHRVVHGGALFDGPVDVTPEVIA 113
           D  L    P  T H  A+  L+ W+       R+  VGHRVVHG   F  P+ +   ++ 
Sbjct: 61  DLDLDLDGPTETPHKVALHFLVDWLHQREAGWRIRGVGHRVVHGAQKFSQPIVLDAAMVD 120

Query: 114 QLRAFDRLAPLHQPHNVSAIEALAKLHPSLPQIACFDTAFHHRLPEVATAFALPRELTEQ 173
            LR F  LAPLHQPHN++ I+A+    P++PQ+ACFDTAFH   PE+A  FALPR +T Q
Sbjct: 121 ALRGFIPLAPLHQPHNLAGIDAMTAALPAIPQVACFDTAFHRSQPELAQLFALPRAITAQ 180

Query: 174 GVRRYGFHGLSYEYIAGRLPDVAGQAVADGRVVVAHLGAGASMCAMLRCRSIATTMGFTA 233
           GVRRYGFHGLSYEYIA  LP   G   A GRV+VAHLG GASMCAM   +S A+TMGFTA
Sbjct: 181 GVRRYGFHGLSYEYIAEVLPRHLGPQKARGRVIVAHLGNGASMCAMKDLKSQASTMGFTA 240

Query: 234 LDGLMMGSRCGELDPGVVLYLLEEKSMTAREIEDLLYRESGLLGVSGISDDMRTLLASDD 293
           +DGLMMGSR G LDPGV+LYL++   M A+ +  LLY+ESGLLGVSGIS DMR LL S  
Sbjct: 241 VDGLMMGSRTGNLDPGVLLYLMDYHQMDAKALTRLLYKESGLLGVSGISQDMRILLDSPA 300

Query: 294 PHACEAIELFVYRIARELGSLAAALGGLDALVFTGGIGEHASEIRRRVCEQAAWLGVTLD 353
           P A EA++LF YR+ RE+GSL AALGGLDALVFTGGIGEH + +R  VC++  WLG+ L+
Sbjct: 301 PEAREAVDLFCYRVVREIGSLTAALGGLDALVFTGGIGEHGAPVRGMVCDRLGWLGLRLN 360

Query: 354 PDANASLSGAGRISAPDSKVSAWAIPTDEDLMIARHVWRL 393
             AN   + A +ISA DS++    IPT+E+ +IARH   L
Sbjct: 361 SAAND--ANASKISAADSEIEVCVIPTNEEWIIARHTANL 398


Lambda     K      H
   0.321    0.137    0.413 

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: 499
Number of extensions: 20
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: 398
Length of database: 400
Length adjustment: 31
Effective length of query: 367
Effective length of database: 369
Effective search space:   135423
Effective search space used:   135423
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate WP_041099069.1 SUTH_RS10370 (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.2590844.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.8e-112  360.6   0.0   6.8e-112  360.1   0.0    1.2  1  NCBI__GCF_000828635.1:WP_041099069.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000828635.1:WP_041099069.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  360.1   0.0  6.8e-112  6.8e-112       4     404 ..       3     399 ..       1     400 [] 0.90

  Alignments for each domain:
  == domain 1  score: 360.1 bits;  conditional E-value: 6.8e-112
                             TIGR00016   4 kkilvlnaGssslkfalldaen..sekvllsglverikleeariktv..edgekkeeekla.......iedhe 65 
                                             il lnaGsss+kfal+ ++   +++  l g ++ i  ++ +       d+ ++  + l+        + h+
  NCBI__GCF_000828635.1:WP_041099069.1   3 DAILTLNAGSSSIKFALFAYSAaiPQQPELVGQIDGIGAAGGQPAHFnaRDAARHVLDDLDldldgptETPHK 75 
                                           579***************9998665555667888888777654332211333333333222111111145699 PP

                             TIGR00016  66 eavkkllntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavl 138
                                            a+++l++ l++    ++    i+ +GHRvvhG++kf++ +++++ ++++++ +++lAPlH p +l gi+a++
  NCBI__GCF_000828635.1:WP_041099069.1  76 VALHFLVDWLHQ----REAGWRIRGVGHRVVHGAQKFSQPIVLDAAMVDALRGFIPLAPLHQPHNLAGIDAMT 144
                                           9*********97....78999**************************************************** PP

                             TIGR00016 139 klkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnliv 211
                                               l+  ++va+FDtafH+  pe a l+alP ++ + +gvRrYGfHG+s++y+++ + ++l+ + +  ++iv
  NCBI__GCF_000828635.1:WP_041099069.1 145 --AALPAIPQVACFDTAFHRSQPELAQLFALP-RAITAQGVRRYGFHGLSYEYIAEVLPRHLGPQKARGRVIV 214
                                           ..8899999***********************.778999********************************** PP

                             TIGR00016 212 cHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisg 284
                                           +HlGnGas++a+k+ ks   +mG+t ++Gl+mG+R+G++Dp+++ yl++ +++ +++++++l k+sGllg+sg
  NCBI__GCF_000828635.1:WP_041099069.1 215 AHLGNGASMCAMKDLKSQASTMGFTAVDGLMMGSRTGNLDPGVLLYLMDYHQMDAKALTRLLYKESGLLGVSG 287
                                           ************************************************************************* PP

                             TIGR00016 285 lssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlG 357
                                           +s D+R +ld +     ea+ A++++++R+ + ig+ +a+l g lDa+vFtgGiGe  a vr +v+++l  lG
  NCBI__GCF_000828635.1:WP_041099069.1 288 ISQDMRILLDSP---APEAREAVDLFCYRVVREIGSLTAALGG-LDALVFTGGIGEHGAPVRGMVCDRLGWLG 356
                                           ***********9...6679**********************76.***************************** PP

                             TIGR00016 358 lkldlelnnaarsgkesvisteeskvkvlviptneelviaeDalrla 404
                                           l+l+++ n      + s is  +s+++v+viptnee++ia+ +++l+
  NCBI__GCF_000828635.1:WP_041099069.1 357 LRLNSAAND----ANASKISAADSEIEVCVIPTNEEWIIARHTANLI 399
                                           ***999998....67889***********************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (400 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: 00:00:00.01
# Mc/sec: 14.02
//
[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:

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 2024 update 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