Aligments for a candidate for acn in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Aligments 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.7330.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: 0.07u 0.02s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 8.42
//
[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, or view the source code.

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