Alignments for a candidate for ackA in Flavobacterium glycines Gm-149

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Flavobacterium glycines Gm-149

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_066323543.1 BLR17_RS10645 acetate kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>NCBI__GCF_900100165.1:WP_066323543.1
          Length = 394

 Score =  391 bits (1004), Expect = e-113
 Identities = 205/399 (51%), Positives = 280/399 (70%), Gaps = 8/399 (2%)

Query: 1   MRVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRVGDEKHVIERELPDHE 60
           M++++INSGSSSIKYQLI+M   +V+C G+ +RIG+E S   ++   +       +P+H+
Sbjct: 1   MKIVIINSGSSSIKYQLIDMPAREVICSGMIDRIGLETSNFSYKTNKDSLEEILPIPNHK 60

Query: 61  EALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVSPLAP 120
             L+ I + L+DEKLGVIK   EI+AVGHRVVHGG  F ++VL+ EEV + I+++  LAP
Sbjct: 61  IGLEKISSLLMDEKLGVIKSTAEIEAVGHRVVHGGASFSDTVLITEEVKEKIKQLFELAP 120

Query: 121 LHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRYGFHG 180
           LHNPANL GI  A ++      +AVFDTAFHQT+P+ AY YAIP     + KIR YGFHG
Sbjct: 121 LHNPANLEGIIVAEEVFSSAKQIAVFDTAFHQTMPEVAYRYAIPNYLLTENKIRAYGFHG 180

Query: 181 TSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLVMGTR 240
           TSH+YVS++A   L K     KIIT H+GNG S+ AVK GK +D SMGF P+ GL+MGTR
Sbjct: 181 TSHKYVSEKAIGFLEK---SSKIITVHLGNGCSITAVKDGKSIDHSMGFGPMNGLIMGTR 237

Query: 241 SGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDEWCKL 300
           SGD+D ++ F+++   G    E+  +L K+SG+ GL+    SD+RDI+  A KGD  C+L
Sbjct: 238 SGDIDQSVIFYMVNTLGYQLNEVNTVLQKQSGMLGLTG--HSDLRDIQANAEKGDLNCQL 295

Query: 301 VLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDKQKNE 360
            L++  YRI KYIG+YAA +NG+DAIVFTAG+GENS   R+ VC+ ++FLG++LD+ KN 
Sbjct: 296 ALDMNVYRIKKYIGSYAAVLNGIDAIVFTAGIGENSAYIRKSVCADMQFLGLELDEAKN- 354

Query: 361 ETIRGKE-GIISTPDSRVKVLVVPTNEELMIARDTKEIV 398
             IR  E   I+T +S+ K+LVVPTNEEL IA    +++
Sbjct: 355 -AIRSSEIREINTVNSKTKILVVPTNEELEIANQVYDLI 392


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: 446
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: 394
Length adjustment: 31
Effective length of query: 372
Effective length of database: 363
Effective search space:   135036
Effective search space used:   135036
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_066323543.1 BLR17_RS10645 (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.609721.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-148  480.6   7.3   1.9e-148  480.4   7.3    1.0  1  NCBI__GCF_900100165.1:WP_066323543.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900100165.1:WP_066323543.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  480.4   7.3  1.9e-148  1.9e-148       4     403 ..       1     391 [.       1     393 [. 0.97

  Alignments for each domain:
  == domain 1  score: 480.4 bits;  conditional E-value: 1.9e-148
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 
                                           +ki+++n+Gsss+k++l+d+  +++v++sg+++ri le +  +  +++++  ee+l i++h+ +++k+ + l+
  NCBI__GCF_900100165.1:WP_066323543.1   1 MKIVIINSGSSSIKYQLIDMP-AREVICSGMIDRIGLETS-NFSYKTNKDSLEEILPIPNHKIGLEKISSLLM 71 
                                           69*******************.68999************9.5557788899999******************9 PP

                             TIGR00016  77 k.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkakn 148
                                           + +  ++k+++ei+++GHRvvhGg +f+++v++t+ev +kik++ elAPlHnpa+legi  +   +v  +ak+
  NCBI__GCF_900100165.1:WP_066323543.1  72 DeKLGVIKSTAEIEAVGHRVVHGGASFSDTVLITEEVKEKIKQLFELAPLHNPANLEGIIVAE--EVFSSAKQ 142
                                           87889******************************************************9998..899999** PP

                             TIGR00016 149 vavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvs 221
                                           +avFDtafHqt+pe ay Ya+P  l +e+++R YGfHGtshkyv+++a   l+k   ++++i++HlGnG s++
  NCBI__GCF_900100165.1:WP_066323543.1 143 IAVFDTAFHQTMPEVAYRYAIPNYLLTENKIRAYGFHGTSHKYVSEKAIGFLEK---SSKIITVHLGNGCSIT 212
                                           ***************************************************999...99************** PP

                             TIGR00016 222 avknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdild 294
                                           avk+Gksid smG+ P++Gl+mGtRsGdiD ++i+y+ +tlg  l+e++++l+k+sG+lg++g  sDlRdi +
  NCBI__GCF_900100165.1:WP_066323543.1 213 AVKDGKSIDHSMGFGPMNGLIMGTRSGDIDQSVIFYMVNTLGYQLNEVNTVLQKQSGMLGLTG-HSDLRDIQA 284
                                           ***************************************************************.99******* PP

                             TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367
                                           + e+g+ +++lAl++ v+Ri+kyig+y+a l+g +DaivFt+GiGen+a++r+ v+ ++++lGl+ld+++n  
  NCBI__GCF_900100165.1:WP_066323543.1 285 NAEKGDLNCQLALDMNVYRIKKYIGSYAAVLNG-IDAIVFTAGIGENSAYIRKSVCADMQFLGLELDEAKNA- 355
                                           *******************************88.************************************99. PP

                             TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDalrl 403
                                            rs + + i+t +sk+k+lv+ptneel ia+ ++ l
  NCBI__GCF_900100165.1:WP_066323543.1 356 IRSSEIREINTVNSKTKILVVPTNEELEIANQVYDL 391
                                           899999************************999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (394 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: 00:00:00.00
# Mc/sec: 22.61
//
[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:

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