GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Magnetospirillum magneticum AMB-1

Align Aconitate hydratase B; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_011386745.1 AMB_RS22255 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= SwissProt::Q8ZRS8
         (865 letters)



>lcl|NCBI__GCF_000009985.1:WP_011386745.1 AMB_RS22255 bifunctional
           aconitate hydratase 2/2-methylisocitrate dehydratase
          Length = 861

 Score = 1248 bits (3230), Expect = 0.0
 Identities = 620/859 (72%), Positives = 720/859 (83%), Gaps = 6/859 (0%)

Query: 1   MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60
           MLE YR+HVAERAA GI P PL A Q  ALV LL+ PP GEE+ L+DL+  RVP GVD+A
Sbjct: 1   MLEAYRQHVAERAALGIPPLPLSAEQTEALVGLLQNPPKGEEQALVDLITYRVPAGVDDA 60

Query: 61  AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           A +KA FL  VAKG     L+S E A +LLGTM GG+N+ PLI+ L DAK+  +AA+ L 
Sbjct: 61  AKIKAEFLDKVAKGTVACALISRETATQLLGTMLGGFNVKPLIELLSDAKVGAVAAEGLK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETNTD 180
            TLL+FD F+DV+E A  GN  AK V+QSWADAEWF SRP + + +TVT+FKVTGETNTD
Sbjct: 121 KTLLVFDFFHDVKELADKGNANAKAVLQSWADAEWFTSRPEVPKSLTVTIFKVTGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHAQAMLKNAREGIEPDQPGVVGPIKQIEALQKKGYPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHA AMLKN R GIE D+PG  GP+KQ++AL KKG  +AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKNPRPGIEADEPGNRGPLKQLDALAKKGNLVAYVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWF G+DIP VPNKR GG+CLG KIAPIF+NTMEDAGALPIE+DV+ 
Sbjct: 241 GTGSSRKSATNSVLWFTGEDIPYVPNKRFGGVCLGTKIAPIFYNTMEDAGALPIELDVNQ 300

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           +NMGDV+++ PY+G+    + G+++A F +K++V+ DEVRAGGRIPLIIGRGLT KAREA
Sbjct: 301 MNMGDVVELRPYEGKAL--KDGKVIAEFTVKSEVIFDEVRAGGRIPLIIGRGLTAKAREA 358

Query: 361 LGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
           LGLP S +FR      ++ +GFSLAQKMVGRACG+   KG+RPG YCEPKMT+VGSQDTT
Sbjct: 359 LGLPVSTLFRLPAVPKDTGKGFSLAQKMVGRACGLPEGKGMRPGTYCEPKMTTVGSQDTT 418

Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDG 477
           GPMTRDELKDLACLGFSAD+VMQSFCHTAAYPK VDV TH  LP FI  RGGV+LRPGDG
Sbjct: 419 GPMTRDELKDLACLGFSADMVMQSFCHTAAYPKLVDVKTHRELPGFISTRGGVALRPGDG 478

Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
           VIHSWLNR+LLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK
Sbjct: 479 VIHSWLNRLLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 538

Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
           GKMQPG+TLRDLV+AIPLYAI+ GLLTVEKKGKKN+FSGRILEIEGLPDLKVEQAFEL+D
Sbjct: 539 GKMQPGVTLRDLVNAIPLYAIRAGLLTVEKKGKKNVFSGRILEIEGLPDLKVEQAFELSD 598

Query: 598 ASAERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADPQL 657
           A+AERSAA C+++L+K PI+EY+TSNI L+KWMIA GY D RTL RRI+ ME W+  P L
Sbjct: 599 AAAERSAAACSVRLDKAPIIEYMTSNITLMKWMIANGYEDARTLGRRIKAMEAWIKKPDL 658

Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIGHF 717
           L  DADAEYAAVI+IDLAD+KEPI+  PNDPDD +LLS+V G KIDEVFIGSCMTNIGHF
Sbjct: 659 LAPDADAEYAAVIEIDLADVKEPIVACPNDPDDVKLLSEVAGAKIDEVFIGSCMTNIGHF 718

Query: 718 RAAGKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
           RAAGK+L+  K  +PTRLW+APPT+MDA  L EEGYYSV GKSGAR+E+PGCSLCMGNQA
Sbjct: 719 RAAGKVLEG-KSDIPTRLWIAPPTKMDAMILNEEGYYSVLGKSGARMEMPGCSLCMGNQA 777

Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
           ++  G+T +STSTRNFPNRLG   NV+L SAELAAV AL+GK+PT  EY   V  V+  A
Sbjct: 778 QIRKGSTAMSTSTRNFPNRLGIDTNVYLGSAELAAVCALMGKIPTVAEYLEQVNVVNAKA 837

Query: 838 VDTYRYLNFDQLSQYTEKA 856
            D YRY+NFD+++++++ A
Sbjct: 838 ADVYRYMNFDKIAEFSDVA 856


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: 2079
Number of extensions: 81
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: 861
Length adjustment: 42
Effective length of query: 823
Effective length of database: 819
Effective search space:   674037
Effective search space used:   674037
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 WP_011386745.1 AMB_RS22255 (bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase)
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.27676.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 1489.7   0.1          0 1489.5   0.1    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011386745.1  AMB_RS22255 bifunctional aconita


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011386745.1  AMB_RS22255 bifunctional aconitate hydratase 2/2-methylisocitrate dehydrata
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1489.5   0.1         0         0       1     843 [.       1     853 [.       1     854 [. 0.99

  Alignments for each domain:
  == domain 1  score: 1489.5 bits;  conditional E-value: 0
                                 TIGR00117   1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagfla 69 
                                               +le+yr+hvaeraa+gi+plpl a+q++alv ll+n+p++ee+ l++l++ rvp gvd+aa++ka+fl 
  lcl|NCBI__GCF_000009985.1:WP_011386745.1   1 MLEAYRQHVAERAALGIPPLPLSAEQTEALVGLLQNPPKGEEQALVDLITYRVPAGVDDAAKIKAEFLD 69 
                                               79******************************************************************* PP

                                 TIGR00117  70 aiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveels 138
                                               ++akg v ++lis e a++llgtmlgg+nv+plie+l   d+++  +aa+ l+ktllvfd f+dv+el+
  lcl|NCBI__GCF_000009985.1:WP_011386745.1  70 KVAKGTVACALISRETATQLLGTMLGGFNVKPLIELLS--DAKVGAVAAEGLKKTLLVFDFFHDVKELA 136
                                               *************************************9..****************************9 PP

                                 TIGR00117 139 kt.neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknk 206
                                               +  n+ ak vl+swa+aewf  ++e+++ +tvt+fkv+getntddlspapda++rpdiplhalamlkn 
  lcl|NCBI__GCF_000009985.1:WP_011386745.1 137 DKgNANAKAVLQSWADAEWFTSRPEVPKSLTVTIFKVTGETNTDDLSPAPDAWSRPDIPLHALAMLKNP 205
                                               988****************************************************************** PP

                                 TIGR00117 207 ieeieq..........rikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvl 265
                                               +++ie           +++al +kg  vayvgdvvgtgssrksatnsvlwf g+dip+vpnkr gg++l
  lcl|NCBI__GCF_000009985.1:WP_011386745.1 206 RPGIEAdepgnrgplkQLDALAKKGNLVAYVGDVVGTGSSRKSATNSVLWFTGEDIPYVPNKRFGGVCL 274
                                               ****9999************************************************************* PP

                                 TIGR00117 266 ggkiapiffntaedsgalpievdvkdlnegdvikiypykgeitnketevvatfklkpetlldevraggr 334
                                               g kiapif+nt+ed+galpie dv+++n+gdv+++ py+g+  +k+++v+a f +k+e+++devraggr
  lcl|NCBI__GCF_000009985.1:WP_011386745.1 275 GTKIAPIFYNTMEDAGALPIELDVNQMNMGDVVELRPYEGKA-LKDGKVIAEFTVKSEVIFDEVRAGGR 342
                                               ****************************************96.7889********************** PP

                                 TIGR00117 335 ipliigrgltdkarealglsesevfkkakapaesakgftlaqklvgkacgv...kgirpgtycepkvtt 400
                                               ipliigrglt karealgl+ s +f+ ++ p++++kgf+laqk+vg+acg+   kg+rpgtycepk+tt
  lcl|NCBI__GCF_000009985.1:WP_011386745.1 343 IPLIIGRGLTAKAREALGLPVSTLFRLPAVPKDTGKGFSLAQKMVGRACGLpegKGMRPGTYCEPKMTT 411
                                               **************************************************87779************** PP

                                 TIGR00117 401 vgsqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvi 469
                                               vgsqdttg+mtrdelk+la+lgf+ad+v+qsfchtaaypk vdvkth++lp+fis+rggvalrpgdgvi
  lcl|NCBI__GCF_000009985.1:WP_011386745.1 412 VGSQDTTGPMTRDELKDLACLGFSADMVMQSFCHTAAYPKLVDVKTHRELPGFISTRGGVALRPGDGVI 480
                                               ********************************************************************* PP

                                 TIGR00117 470 hswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrd 538
                                               hswlnr+llpdtvgtggdshtrfp+gisfpagsglvafaaatgvmpldmpesvlvrfkg++qpg+tlrd
  lcl|NCBI__GCF_000009985.1:WP_011386745.1 481 HSWLNRLLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGVTLRD 549
                                               ********************************************************************* PP

                                 TIGR00117 539 lvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkepvi 607
                                               lvnaip+yai+ glltvekkgk+nvf+grileieglpdlkveqafel+da+aersaa+c ++l+k p+i
  lcl|NCBI__GCF_000009985.1:WP_011386745.1 550 LVNAIPLYAIRAGLLTVEKKGKKNVFSGRILEIEGLPDLKVEQAFELSDAAAERSAAACSVRLDKAPII 618
                                               ********************************************************************* PP

                                 TIGR00117 608 eylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapn 676
                                               ey+ sni l+k+mia+gyed+rtl rri+ame+w++ p+ll +dadaeyaavieidla++kepi+a+pn
  lcl|NCBI__GCF_000009985.1:WP_011386745.1 619 EYMTSNITLMKWMIANGYEDARTLGRRIKAMEAWIKKPDLLAPDADAEYAAVIEIDLADVKEPIVACPN 687
                                               ********************************************************************* PP

                                 TIGR00117 677 dpddvkllsevagdaidevfigscmtnighfraagkileaaktvkarlwvvpptrmdeqqlieegyyai 745
                                               dpddvkllsevag +idevfigscmtnighfraagk+le+++++++rlw++ppt+md+  l eegyy++
  lcl|NCBI__GCF_000009985.1:WP_011386745.1 688 DPDDVKLLSEVAGAKIDEVFIGSCMTNIGHFRAAGKVLEGKSDIPTRLWIAPPTKMDAMILNEEGYYSV 756
                                               ********************************************************************* PP

                                 TIGR00117 746 fgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkee 814
                                               +g++gar+e+pgcslcmgnqa+++ g+t +ststrnf+nrlg  ++vylgsaelaav+al+gkipt+ e
  lcl|NCBI__GCF_000009985.1:WP_011386745.1 757 LGKSGARMEMPGCSLCMGNQAQIRKGSTAMSTSTRNFPNRLGIDTNVYLGSAELAAVCALMGKIPTVAE 825
                                               ********************************************************************* PP

                                 TIGR00117 815 ylalvsekvesakdklyrylnfnelenfe 843
                                               yl+ v  + + a d +yry+nf+++ +f 
  lcl|NCBI__GCF_000009985.1:WP_011386745.1 826 YLEQVNVVNAKAAD-VYRYMNFDKIAEFS 853
                                               *****988888887.**********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (844 nodes)
Target sequences:                          1  (861 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.07
# Mc/sec: 9.31
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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