GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Desulfovibrio vulgaris Hildenborough

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate 208544 DVU3030 acetate kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>MicrobesOnline__882:208544
          Length = 402

 Score =  433 bits (1114), Expect = e-126
 Identities = 222/404 (54%), Positives = 285/404 (70%), Gaps = 8/404 (1%)

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

Query: 56  LPDHEEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEV 115
             +H E +K ++  + D   GVIKD  EI A+GHRV+ GGE  K+SV +D+     I + 
Sbjct: 61  FTNHVEGMKRVVELITDADKGVIKDKSEIGAIGHRVLLGGEEIKQSVRIDDWAKGVIRDY 120

Query: 116 SPLAPLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRR 175
            PL PLHNPANL GI+ A +L PG+PNV VFDT FHQ++P KAYLY +P E YE+ KIRR
Sbjct: 121 IPLGPLHNPANLAGIEVAEELFPGLPNVGVFDTEFHQSMPAKAYLYPLPIELYEELKIRR 180

Query: 176 YGFHGTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGL 235
           YGFHGTSHRY++KR A+ LGK L+EL IITCH+GNG S+AAVK GKCVDT+MG TPLEGL
Sbjct: 181 YGFHGTSHRYITKRTAQYLGKPLDELNIITCHLGNGCSMAAVKNGKCVDTTMGITPLEGL 240

Query: 236 VMGTRSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGD 295
           +MGTR GD+DPAI  F+MEK+ +SP E   ++NK+SG+ G+     +DMRD+  A   G+
Sbjct: 241 MMGTRCGDIDPAIVPFLMEKKNLSPAEADTLMNKQSGLKGMCG--MNDMRDLHAARENGN 298

Query: 296 EWCKLVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLD 355
           E  +L  E++ YRI KYIGAY A +  VDA+VFTAG+GEN    R +VC+ L+ LG+ +D
Sbjct: 299 ERAQLAFEMFTYRIKKYIGAYYAVLGRVDAVVFTAGIGENDDFVRAEVCAGLDSLGIAVD 358

Query: 356 KQKNEETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIVE 399
             +N     G+   IS   SRV VLVVPTNEEL IA+ T ++++
Sbjct: 359 PARN-AVRNGQPRHISPDGSRVAVLVVPTNEELEIAQATLDVLK 401


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: 484
Number of extensions: 23
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: 402
Length adjustment: 31
Effective length of query: 372
Effective length of database: 371
Effective search space:   138012
Effective search space used:   138012
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 208544 DVU3030 (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.8319.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   7.1e-150  485.1   0.0   7.9e-150  485.0   0.0    1.0  1  lcl|MicrobesOnline__882:208544  DVU3030 acetate kinase


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:208544  DVU3030 acetate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  485.0   0.0  7.9e-150  7.9e-150       5     402 ..       2     398 ..       1     401 [. 0.95

  Alignments for each domain:
  == domain 1  score: 485.0 bits;  conditional E-value: 7.9e-150
                       TIGR00016   5 kilvlnaGssslkfalldaensekvllsglverikleeariktv....edgekkeeeklaiedheeavkkllntlkk.d 78 
                                      +lv+n+Gsss+k++l+d+e  e  l+sglveri  +  +++ +     +ge+k ++++ +++h e++k++++ +++ d
  lcl|MicrobesOnline__882:208544   2 NVLVINSGSSSIKYQLIDME-REVPLCSGLVERIGEPMGKLTHKirpdAEGEEKLTFEQPFTNHVEGMKRVVELITDaD 79 
                                     79******************.5888*********98765544432343678888999999****************999 PP

                       TIGR00016  79 kkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFDtafH 157
                                     k ++k++sei +iGHRv  Gge+ ++sv ++d +   i+d ++l PlHnpa+l gie + +l+  +  +nv vFDt fH
  lcl|MicrobesOnline__882:208544  80 KGVIKDKSEIGAIGHRVLLGGEEIKQSVRIDDWAKGVIRDYIPLGPLHNPANLAGIEVAEELF--PGLPNVGVFDTEFH 156
                                     ************************************************************555..5567********** PP

                       TIGR00016 158 qtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGksidtsmGlt 236
                                     q +p +aylY+lP +ly+el++RrYGfHGtsh+y+t+r+a++l+kpld+ln+i+cHlGnG s++avknGk++dt+mG+t
  lcl|MicrobesOnline__882:208544 157 QSMPAKAYLYPLPIELYEELKIRRYGFHGTSHRYITKRTAQYLGKPLDELNIITCHLGNGCSMAAVKNGKCVDTTMGIT 235
                                     ******************************************************************************* PP

                       TIGR00016 237 PLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegneeaklAlkvyvhRia 315
                                     PLeGl+mGtR+GdiDpai+ +l+e+++ls +e  +++nk+sGl g+ g  +D+Rd+ ++ e+gne+a+lA++++++Ri+
  lcl|MicrobesOnline__882:208544 236 PLEGLMMGTRCGDIDPAIVPFLMEKKNLSPAEADTLMNKQSGLKGMCG-MNDMRDLHAARENGNERAQLAFEMFTYRIK 313
                                     ************************************************.89**************************** PP

                       TIGR00016 316 kyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneel 394
                                     kyig+y a l g++Da+vFt+GiGen+  vr++v+ +l++lG+++d+++n   r+g+ + is + s+v vlv+ptneel
  lcl|MicrobesOnline__882:208544 314 KYIGAYYAVL-GRVDAVVFTAGIGENDDFVRAEVCAGLDSLGIAVDPARNA-VRNGQPRHISPDGSRVAVLVVPTNEEL 390
                                     **********.67*************************************9.999************************ PP

                       TIGR00016 395 viaeDalr 402
                                      ia+ +l 
  lcl|MicrobesOnline__882:208544 391 EIAQATLD 398
                                     ***98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (402 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: 11.34
//
[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