Alignments for a candidate for ackA in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Desulfovibrio vulgaris Miyazaki F

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate 8501129 DvMF_1865 acetate kinase (RefSeq)

Query= BRENDA::Q9WYB1
         (403 letters)



>FitnessBrowser__Miya:8501129
          Length = 404

 Score =  422 bits (1085), Expect = e-123
 Identities = 216/403 (53%), Positives = 283/403 (70%), Gaps = 8/403 (1%)

Query: 1   MRVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRV-----GDEKHVIERE 55
           M VLVINSGSSSIKYQLI+M  EK LC G+ ERIG    +L H++      +EK V+E+ 
Sbjct: 1   MNVLVINSGSSSIKYQLIDMTTEKALCSGLVERIGEGMGKLTHKIKPDTDAEEKIVLEQA 60

Query: 56  LPDHEEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEV 115
             +H E +K +++ + D   GVI D  EI AVGHRV+ GGE  K+SV +DE     I + 
Sbjct: 61  FANHVEGMKKVVDLITDADKGVIADKGEIYAVGHRVLLGGEEIKQSVKIDEWAKGIIRDY 120

Query: 116 SPLAPLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRR 175
            PL PLHNPANL GI+ A +L P  P+V VFDT FHQT+P+KAYLY +PY+ Y+  +IRR
Sbjct: 121 IPLGPLHNPANLAGIEVAEELFPHAPSVGVFDTEFHQTMPKKAYLYPLPYDLYKTLRIRR 180

Query: 176 YGFHGTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGL 235
           YGFHGTSHRY++K+ AE LGK L+EL IITCH+GNG S+AAVK G+CVDT+MG TPLEGL
Sbjct: 181 YGFHGTSHRYITKKTAEFLGKPLDELNIITCHLGNGCSMAAVKNGRCVDTTMGITPLEGL 240

Query: 236 VMGTRSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGD 295
           +MGTR GD+DPA+  F+MEK+G S  E+  ++NK+SG+ G+     +DMRDI  A  KGD
Sbjct: 241 MMGTRCGDIDPALVPFLMEKKGWSGAEIDTVMNKQSGLKGICG--MNDMRDIHAAREKGD 298

Query: 296 EWCKLVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLD 355
           E  +L  +++ YRI KYIG++A  +  +DAIVFTAG+GEN  + R  VC  ++ LG+ +D
Sbjct: 299 EMAELAFQMFVYRIRKYIGSFAVVVGKLDAIVFTAGIGENDDLVRAAVCKDMDILGIDID 358

Query: 356 KQKNEETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIV 398
           +  N +   G+   I  P  RV VLVVPTNEEL IA+ T  ++
Sbjct: 359 EAVNAKR-SGQARHIGKPGQRVPVLVVPTNEELEIAQTTVAVL 400


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: 498
Number of extensions: 16
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: 404
Length adjustment: 31
Effective length of query: 372
Effective length of database: 373
Effective search space:   138756
Effective search space used:   138756
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 8501129 DvMF_1865 (acetate kinase (RefSeq))
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.20463.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.4e-148  480.9   0.0   1.6e-148  480.7   0.0    1.0  1  lcl|FitnessBrowser__Miya:8501129  DvMF_1865 acetate kinase (RefSeq


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501129  DvMF_1865 acetate kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  480.7   0.0  1.6e-148  1.6e-148       5     402 ..       2     398 ..       1     401 [. 0.95

  Alignments for each domain:
  == domain 1  score: 480.7 bits;  conditional E-value: 1.6e-148
                         TIGR00016   5 kilvlnaGssslkfalldaensekvllsglverikle..eariktv..edgekkeeeklaiedheeavkkllntlkk 77 
                                        +lv+n+Gsss+k++l+d++ +ek l+sglveri     + + k++  +d+e+k   ++a+++h e++kk+++ +++
  lcl|FitnessBrowser__Miya:8501129   2 NVLVINSGSSSIKYQLIDMT-TEKALCSGLVERIGEGmgKLTHKIKpdTDAEEKIVLEQAFANHVEGMKKVVDLITD 77 
                                       79******************.69999*******97541133223333388899999999*****************9 PP

                         TIGR00016  78 .dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFD 153
                                        dk ++ ++ ei ++GHRv  Gge+ ++sv +++ +   i+d ++l PlHnpa+l gie +   +  ++a+ v vFD
  lcl|FitnessBrowser__Miya:8501129  78 aDKGVIADKGEIYAVGHRVLLGGEEIKQSVKIDEWAKGIIRDYIPLGPLHNPANLAGIEVAE--ELFPHAPSVGVFD 152
                                       999***********************************************************..7778899****** PP

                         TIGR00016 154 tafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGksid 230
                                       t fHqt+p++aylY+lPy+lyk l +RrYGfHGtsh+y+t+++a+ l+kpld+ln+i+cHlGnG s++avknG+++d
  lcl|FitnessBrowser__Miya:8501129 153 TEFHQTMPKKAYLYPLPYDLYKTLRIRRYGFHGTSHRYITKKTAEFLGKPLDELNIITCHLGNGCSMAAVKNGRCVD 229
                                       ***************************************************************************** PP

                         TIGR00016 231 tsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegneeaklAl 307
                                       t+mG+tPLeGl+mGtR+GdiDpa++ +l+e++g s +ei +++nk+sGl gi g  +D+Rdi ++ e+g+e a+lA+
  lcl|FitnessBrowser__Miya:8501129 230 TTMGITPLEGLMMGTRCGDIDPALVPFLMEKKGWSGAEIDTVMNKQSGLKGICG-MNDMRDIHAAREKGDEMAELAF 305
                                       ******************************************************.89******************** PP

                         TIGR00016 308 kvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvk 384
                                       +++v+Ri+kyig+++  + g+lDaivFt+GiGen+  vr+ v++++++lG+++d++ n   rsg+ + i ++  +v 
  lcl|FitnessBrowser__Miya:8501129 306 QMFVYRIRKYIGSFAVVV-GKLDAIVFTAGIGENDDLVRAAVCKDMDILGIDIDEAVNA-KRSGQARHIGKPGQRVP 380
                                       **************9999.66***********************************999.99*************** PP

                         TIGR00016 385 vlviptneelviaeDalr 402
                                       vlv+ptneel ia+ ++ 
  lcl|FitnessBrowser__Miya:8501129 381 VLVVPTNEELEIAQTTVA 398
                                       *************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (404 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: 10.43
//
[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