GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Dechlorosoma suillum PS

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate Dsui_2205 Dsui_2205 aconitate hydratase 2

Query= BRENDA::P36683
         (865 letters)



>FitnessBrowser__PS:Dsui_2205
          Length = 865

 Score = 1245 bits (3222), Expect = 0.0
 Identities = 626/864 (72%), Positives = 716/864 (82%), Gaps = 6/864 (0%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           MLE YR+HVAERAA GI P PL A Q   LV LL+NPP GEE+ L++L+T RVP GVD+A
Sbjct: 1   MLEAYRQHVAERAALGIPPLPLSAAQTKDLVALLQNPPKGEEQALVELITYRVPAGVDDA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           A VKA FLA +AKGE    L++  KA ELLGTM GGYN+ P+ID L DA++  +AA+ L 
Sbjct: 61  AKVKAEFLAKVAKGELSCALISRAKATELLGTMLGGYNVKPMIDLLGDAEVGAVAAEGLK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
            TLL+FD F+DV E AK GN  AK VMQSWADAEWF +RP +     +TVFKVTGETNTD
Sbjct: 121 KTLLVFDFFHDVAELAKGGNANAKAVMQSWADAEWFTSRPEVPASQKLTVFKVTGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHALAMLKN R GIE D+ G  GP+KQ+EAL +KG  +AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKNPRPGIEADKAGERGPVKQLEALAKKGNLIAYVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWF G+DIP VPNKR GG+CLG KIAPIFFNTMEDAGALPIE+DV  
Sbjct: 241 GTGSSRKSATNSVLWFTGEDIPFVPNKRFGGVCLGSKIAPIFFNTMEDAGALPIELDVGQ 300

Query: 301 LNMGDVID--VYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAR 358
           ++MGD I+  +     +V   + G ++A  +LKT V++DEVRAGGRIPLIIGRGLTTKAR
Sbjct: 301 MDMGDEIELKIDQATAKVTALKNGAVIAESQLKTPVILDEVRAGGRIPLIIGRGLTTKAR 360

Query: 359 EALGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQD 415
           EALGL  S +FR  +   +  +G+SLAQKMVGRACG+   KGI PG YCEPKMT+VGSQD
Sbjct: 361 EALGLAPSTLFRLPQQPNDPGKGYSLAQKMVGRACGLPEGKGILPGTYCEPKMTTVGSQD 420

Query: 416 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPG 475
           TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPK VDV  H  LP FI  RGGV+LRPG
Sbjct: 421 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKLVDVRMHRELPSFISTRGGVALRPG 480

Query: 476 DGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR 535
           DGVIHSWLNR+LLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR
Sbjct: 481 DGVIHSWLNRLLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR 540

Query: 536 FKGKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFEL 595
           FKGKMQPGITLRDLV+AIPLYAIKQGLLTVEKKGKKN+FSGRILEIEGLPDLKVEQAFEL
Sbjct: 541 FKGKMQPGITLRDLVNAIPLYAIKQGLLTVEKKGKKNVFSGRILEIEGLPDLKVEQAFEL 600

Query: 596 TDASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANP 655
           +DA+AERSAA C I LNKEPI+EYL SNI L+KWMIAEGY D RTL+RRI+ ME+W+AN 
Sbjct: 601 SDAAAERSAAACAIALNKEPIVEYLRSNITLMKWMIAEGYQDARTLKRRIKAMEEWIANG 660

Query: 656 ELLEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIG 715
            LL+AD DA+YAAVI+IDLAD+KEPI+  PNDPDD + LS V G+KIDEVFIGSCMTNIG
Sbjct: 661 TLLKADTDAQYAAVIEIDLADVKEPIVACPNDPDDVKVLSEVAGDKIDEVFIGSCMTNIG 720

Query: 716 HFRAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGN 775
           HFRAAGK+LD  K  +PTRLW+APPT+MDA  LTEEGYYSV GK+GAR+E+PGCSLCMGN
Sbjct: 721 HFRAAGKVLDG-KSDIPTRLWIAPPTKMDALILTEEGYYSVLGKAGARMEMPGCSLCMGN 779

Query: 776 QARVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDK 835
           QA++  G+T +STSTRNFPNRLG    V+L SAELAA+ +L+GK+PT  EY  Y+  V+ 
Sbjct: 780 QAQIRKGSTAMSTSTRNFPNRLGIDTRVYLGSAELAAMCSLLGKIPTVAEYMEYIQVVNA 839

Query: 836 TAVDTYRYLNFNQLSQYTEKADGV 859
            A D YRY+NF+Q+ ++ E A+ V
Sbjct: 840 KAADIYRYMNFDQIPEFVEVAETV 863


Lambda     K      H
   0.317    0.136    0.400 

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: 2064
Number of extensions: 83
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: 865
Length of database: 865
Length adjustment: 42
Effective length of query: 823
Effective length of database: 823
Effective search space:   677329
Effective search space used:   677329
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 (21.7 bits)
S2: 56 (26.2 bits)

Align candidate Dsui_2205 Dsui_2205 (aconitate hydratase 2)
to HMM TIGR00117 (acnB: aconitate hydratase 2 (EC 4.2.1.3))

# 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/TIGR00117.hmm
# target sequence database:        /tmp/gapView.2855966.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00117  [M=844]
Accession:   TIGR00117
Description: acnB: aconitate hydratase 2
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                     -----------
          0 1484.0   0.1          0 1483.8   0.1    1.0  1  FitnessBrowser__PS:Dsui_2205  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__PS:Dsui_2205  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1483.8   0.1         0         0       1     843 [.       1     857 [.       1     858 [. 0.98

  Alignments for each domain:
  == domain 1  score: 1483.8 bits;  conditional E-value: 0
                     TIGR00117   1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiakgevkspli 81 
                                   +le+yr+hvaeraa+gi+plpl a q+++lv ll+n+p++ee+ l+el++ rvp gvd+aa+vka+fla++akge+ ++li
  FitnessBrowser__PS:Dsui_2205   1 MLEAYRQHVAERAALGIPPLPLSAAQTKDLVALLQNPPKGEEQALVELITYRVPAGVDDAAKVKAEFLAKVAKGELSCALI 81 
                                   79******************************************************************************* PP

                     TIGR00117  82 saeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyakqvleswaeaewflnke 161
                                   s  +a+ellgtmlggynv+p+i++l   d+++  +aa+ l+ktllvfd f+dv+el+k  n+ ak v++swa+aewf  ++
  FitnessBrowser__PS:Dsui_2205  82 SRAKATELLGTMLGGYNVKPMIDLLG--DAEVGAVAAEGLKKTLLVFDFFHDVAELAKGgNANAKAVMQSWADAEWFTSRP 160
                                   *************************9..******************************99********************* PP

                     TIGR00117 162 elaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq..........rikalkqkgvpvayvgdvvg 232
                                   e++   + tvfkv+getntddlspapda++rpdiplhalamlkn +++ie           +++al +kg  +ayvgdvvg
  FitnessBrowser__PS:Dsui_2205 161 EVPASQKLTVFKVTGETNTDDLSPAPDAWSRPDIPLHALAMLKNPRPGIEAdkagergpvkQLEALAKKGNLIAYVGDVVG 241
                                   **************************************************999**************************** PP

                     TIGR00117 233 tgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdvkdlnegdvik..iypykgeit.nk 310
                                   tgssrksatnsvlwf g+dipfvpnkr gg++lg kiapiffnt+ed+galpie dv ++++gd i+  i     ++t +k
  FitnessBrowser__PS:Dsui_2205 242 TGSSRKSATNSVLWFTGEDIPFVPNKRFGGVCLGSKIAPIFFNTMEDAGALPIELDVGQMDMGDEIElkIDQATAKVTaLK 322
                                   ****************************************************************99722556677887357 PP

                     TIGR00117 311 etevvatfklkpetlldevraggripliigrgltdkarealglsesevfkkakapaesakgftlaqklvgkacgv...kgi 388
                                   ++ v+a  +lk+ ++ldevraggripliigrglt+karealgl++s +f+ +++p++ +kg++laqk+vg+acg+   kgi
  FitnessBrowser__PS:Dsui_2205 323 NGAVIAESQLKTPVILDEVRAGGRIPLIIGRGLTTKAREALGLAPSTLFRLPQQPNDPGKGYSLAQKMVGRACGLpegKGI 403
                                   78************************************************************************87779** PP

                     TIGR00117 389 rpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvi 469
                                   +pgtycepk+ttvgsqdttg+mtrdelk+la+lgf+adlv+qsfchtaaypk vdv++h++lp fis+rggvalrpgdgvi
  FitnessBrowser__PS:Dsui_2205 404 LPGTYCEPKMTTVGSQDTTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKLVDVRMHRELPSFISTRGGVALRPGDGVI 484
                                   ********************************************************************************* PP

                     TIGR00117 470 hswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikk 550
                                   hswlnr+llpdtvgtggdshtrfp+gisfpagsglvafaaatgvmpldmpesvlvrfkg++qpgitlrdlvnaip+yaik+
  FitnessBrowser__PS:Dsui_2205 485 HSWLNRLLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGITLRDLVNAIPLYAIKQ 565
                                   ********************************************************************************* PP

                     TIGR00117 551 glltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkepvieylksnivllkemiaegyedkrtl 631
                                   glltvekkgk+nvf+grileieglpdlkveqafel+da+aersaa+c+i lnkep++eyl+sni l+k+miaegy+d+rtl
  FitnessBrowser__PS:Dsui_2205 566 GLLTVEKKGKKNVFSGRILEIEGLPDLKVEQAFELSDAAAERSAAACAIALNKEPIVEYLRSNITLMKWMIAEGYQDARTL 646
                                   ********************************************************************************* PP

                     TIGR00117 632 krridamekwlanpelleadadaeyaavieidlaeikepilaapndpddvkllsevagdaidevfigscmtnighfraagk 712
                                   krri+ame+w+an +ll+ad+da+yaavieidla++kepi+a+pndpddvk+lsevagd+idevfigscmtnighfraagk
  FitnessBrowser__PS:Dsui_2205 647 KRRIKAMEEWIANGTLLKADTDAQYAAVIEIDLADVKEPIVACPNDPDDVKVLSEVAGDKIDEVFIGSCMTNIGHFRAAGK 727
                                   ********************************************************************************* PP

                     TIGR00117 713 ileaaktvkarlwvvpptrmdeqqlieegyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvy 793
                                   +l++++++++rlw++ppt+md+  l+eegyy+++g+agar+e+pgcslcmgnqa+++ g+t +ststrnf+nrlg  ++vy
  FitnessBrowser__PS:Dsui_2205 728 VLDGKSDIPTRLWIAPPTKMDALILTEEGYYSVLGKAGARMEMPGCSLCMGNQAQIRKGSTAMSTSTRNFPNRLGIDTRVY 808
                                   ********************************************************************************* PP

                     TIGR00117 794 lgsaelaavaallgkiptkeeylalvsekvesakdklyrylnfnelenfe 843
                                   lgsaelaa+++llgkipt+ ey++++  + + a d +yry+nf+++ +f 
  FitnessBrowser__PS:Dsui_2205 809 LGSAELAAMCSLLGKIPTVAEYMEYIQVVNAKAAD-IYRYMNFDQIPEFV 857
                                   *************************9877777777.**********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (844 nodes)
Target sequences:                          1  (865 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 18.41
//
[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:

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