GapMind for catabolism of small carbon sources

 

Alignments 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)



>NCBI__GCF_000009985.1:WP_011386745.1
          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.31868.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 0.03s 00:00:00.08 Elapsed: 00:00:00.06
# Mc/sec: 11.11
//
[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