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.30105.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: 10.11
//
[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:

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