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.6253.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  lcl|FitnessBrowser__PS:Dsui_2205  Dsui_2205 aconitate hydratase 2


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_2205  Dsui_2205 aconitate hydratase 2
   #    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 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiakgevk 77 
                                       +le+yr+hvaeraa+gi+plpl a q+++lv ll+n+p++ee+ l+el++ rvp gvd+aa+vka+fla++akge+ 
  lcl|FitnessBrowser__PS:Dsui_2205   1 MLEAYRQHVAERAALGIPPLPLSAAQTKDLVALLQNPPKGEEQALVELITYRVPAGVDDAAKVKAEFLAKVAKGELS 77 
                                       79*************************************************************************** PP

                         TIGR00117  78 splisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyakqvleswae 153
                                       ++lis  +a+ellgtmlggynv+p+i++l   d+++  +aa+ l+ktllvfd f+dv+el+k  n+ ak v++swa+
  lcl|FitnessBrowser__PS:Dsui_2205  78 CALISRAKATELLGTMLGGYNVKPMIDLLG--DAEVGAVAAEGLKKTLLVFDFFHDVAELAKGgNANAKAVMQSWAD 152
                                       *****************************9..******************************99************* PP

                         TIGR00117 154 aewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq..........rikalkqk 220
                                       aewf  ++e++   + tvfkv+getntddlspapda++rpdiplhalamlkn +++ie           +++al +k
  lcl|FitnessBrowser__PS:Dsui_2205 153 AEWFTSRPEVPASQKLTVFKVTGETNTDDLSPAPDAWSRPDIPLHALAMLKNPRPGIEAdkagergpvkQLEALAKK 229
                                       **********************************************************999**************** PP

                         TIGR00117 221 gvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdvkdlnegdv 297
                                       g  +ayvgdvvgtgssrksatnsvlwf g+dipfvpnkr gg++lg kiapiffnt+ed+galpie dv ++++gd 
  lcl|FitnessBrowser__PS:Dsui_2205 230 GNLIAYVGDVVGTGSSRKSATNSVLWFTGEDIPFVPNKRFGGVCLGSKIAPIFFNTMEDAGALPIELDVGQMDMGDE 306
                                       ****************************************************************************9 PP

                         TIGR00117 298 ik..iypykgeit.nketevvatfklkpetlldevraggripliigrgltdkarealglsesevfkkakapaesakg 371
                                       i+  i     ++t +k++ v+a  +lk+ ++ldevraggripliigrglt+karealgl++s +f+ +++p++ +kg
  lcl|FitnessBrowser__PS:Dsui_2205 307 IElkIDQATAKVTaLKNGAVIAESQLKTPVILDEVRAGGRIPLIIGRGLTTKAREALGLAPSTLFRLPQQPNDPGKG 383
                                       972255667788735778*********************************************************** PP

                         TIGR00117 372 ftlaqklvgkacgv...kgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvk 445
                                       ++laqk+vg+acg+   kgi+pgtycepk+ttvgsqdttg+mtrdelk+la+lgf+adlv+qsfchtaaypk vdv+
  lcl|FitnessBrowser__PS:Dsui_2205 384 YSLAQKMVGRACGLpegKGILPGTYCEPKMTTVGSQDTTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKLVDVR 460
                                       *************87779*********************************************************** PP

                         TIGR00117 446 thktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesv 522
                                       +h++lp fis+rggvalrpgdgvihswlnr+llpdtvgtggdshtrfp+gisfpagsglvafaaatgvmpldmpesv
  lcl|FitnessBrowser__PS:Dsui_2205 461 MHRELPSFISTRGGVALRPGDGVIHSWLNRLLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESV 537
                                       ***************************************************************************** PP

                         TIGR00117 523 lvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagcti 599
                                       lvrfkg++qpgitlrdlvnaip+yaik+glltvekkgk+nvf+grileieglpdlkveqafel+da+aersaa+c+i
  lcl|FitnessBrowser__PS:Dsui_2205 538 LVRFKGKMQPGITLRDLVNAIPLYAIKQGLLTVEKKGKKNVFSGRILEIEGLPDLKVEQAFELSDAAAERSAAACAI 614
                                       ***************************************************************************** PP

                         TIGR00117 600 klnkepvieylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapn 676
                                        lnkep++eyl+sni l+k+miaegy+d+rtlkrri+ame+w+an +ll+ad+da+yaavieidla++kepi+a+pn
  lcl|FitnessBrowser__PS:Dsui_2205 615 ALNKEPIVEYLRSNITLMKWMIAEGYQDARTLKRRIKAMEEWIANGTLLKADTDAQYAAVIEIDLADVKEPIVACPN 691
                                       ***************************************************************************** PP

                         TIGR00117 677 dpddvkllsevagdaidevfigscmtnighfraagkileaaktvkarlwvvpptrmdeqqlieegyyaifgaagart 753
                                       dpddvk+lsevagd+idevfigscmtnighfraagk+l++++++++rlw++ppt+md+  l+eegyy+++g+agar+
  lcl|FitnessBrowser__PS:Dsui_2205 692 DPDDVKVLSEVAGDKIDEVFIGSCMTNIGHFRAAGKVLDGKSDIPTRLWIAPPTKMDALILTEEGYYSVLGKAGARM 768
                                       ***************************************************************************** PP

                         TIGR00117 754 evpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkeeylalvsekvesakdkl 830
                                       e+pgcslcmgnqa+++ g+t +ststrnf+nrlg  ++vylgsaelaa+++llgkipt+ ey++++  + + a d +
  lcl|FitnessBrowser__PS:Dsui_2205 769 EMPGCSLCMGNQAQIRKGSTAMSTSTRNFPNRLGIDTRVYLGSAELAAMCSLLGKIPTVAEYMEYIQVVNAKAAD-I 844
                                       *****************************************************************9877777777.* PP

                         TIGR00117 831 yrylnfnelenfe 843
                                       yry+nf+++ +f 
  lcl|FitnessBrowser__PS:Dsui_2205 845 YRYMNFDQIPEFV 857
                                       *********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: 0.04u 0.03s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 10.79
//
[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