GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Burkholderia phytofirmans PsJN

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 BPHYT_RS10160 BPHYT_RS10160 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= SwissProt::Q8ZRS8
         (865 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS10160 BPHYT_RS10160 bifunctional
           aconitate hydratase 2/2-methylisocitrate dehydratase
          Length = 861

 Score = 1270 bits (3286), Expect = 0.0
 Identities = 632/862 (73%), Positives = 724/862 (83%), Gaps = 6/862 (0%)

Query: 1   MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60
           MLE +R H A RA  GI P PL A Q A LVELL  PP GEE+ LLDL+ NRVP GVDEA
Sbjct: 1   MLENFRAHAAARATLGIPPLPLTAQQTAELVELLTNPPAGEEQTLLDLITNRVPAGVDEA 60

Query: 61  AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           A VKAGFLAAVAKG+TT  L+S  +A ELLGTM GGYNI PLI+ L DA++  +AA+AL 
Sbjct: 61  ARVKAGFLAAVAKGETTCALISRARATELLGTMLGGYNIQPLIELLSDAEVGTVAAEALK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETNTD 180
            TLLMFD F+DV+E A  GN  AK V+QSWADAEWF SRP + + +T+TVFKVTGETNTD
Sbjct: 121 KTLLMFDAFHDVKELADKGNANAKAVLQSWADAEWFTSRPEVPQSLTITVFKVTGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHAQAMLKNAREGIEPDQPGVVGPIKQIEALQKKGYPLAYVGDVV 240
           DLSPAPDA +RPDIP+HA AMLKNAR GI P++ G  GPIK I++L++KG+ +AYVGDVV
Sbjct: 181 DLSPAPDATTRPDIPMHALAMLKNARPGITPEEDGKRGPIKFIQSLKEKGHLVAYVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWF G+DIP +PNKR GG+CLG KIAPIF+NTMEDAGALPIE+DVS 
Sbjct: 241 GTGSSRKSATNSVLWFTGEDIPFIPNKRFGGVCLGSKIAPIFYNTMEDAGALPIELDVSQ 300

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           + MGDV+++ PY+G+   +  G ++A F++K+DVL DEVRAGGRIPLIIGRGLT KAREA
Sbjct: 301 MEMGDVVELRPYEGKALKN--GAVIAEFKVKSDVLFDEVRAGGRIPLIIGRGLTAKAREA 358

Query: 361 LGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
           LGL  S +FR  +  A+S +GFSLAQKMVGRACG+   +G+RPG YCEPKMTSVGSQDTT
Sbjct: 359 LGLAPSTLFRLPQQPADSGKGFSLAQKMVGRACGLPEGQGVRPGTYCEPKMTSVGSQDTT 418

Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDG 477
           GPMTRDELKDLACLGFSADLVMQSFCHTAAYPK VDV TH TLPDFI NRGG++LRPGDG
Sbjct: 419 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKSVDVKTHRTLPDFISNRGGIALRPGDG 478

Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
           VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATG MPLDMPESVLVRFK
Sbjct: 479 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGTMPLDMPESVLVRFK 538

Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
           GKMQPG+TLRDLV+AIPLYAIKQG LTV K+GKKNIFSGR+LEIEGLPDLKVEQAFEL+D
Sbjct: 539 GKMQPGVTLRDLVNAIPLYAIKQGTLTVAKQGKKNIFSGRVLEIEGLPDLKVEQAFELSD 598

Query: 598 ASAERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADPQL 657
           ASAERSAAGCT+ LNKEPI+EYL SN+ LLKWMIA+GY D R+L+RRI+ ME WLADPQL
Sbjct: 599 ASAERSAAGCTVHLNKEPIIEYLNSNVTLLKWMIAQGYQDPRSLQRRIKAMEAWLADPQL 658

Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIGHF 717
           L  DADAEYAAVI+IDLADI EPI+  PNDPDD + LSDV G KIDEVFIGSCMTNIGHF
Sbjct: 659 LSPDADAEYAAVIEIDLADIHEPIVACPNDPDDVKTLSDVAGAKIDEVFIGSCMTNIGHF 718

Query: 718 RAAGKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
           RAA KLL+  K  +P +LWVAPPT+MD  QLTEEG+Y VFG +GAR E+PGCSLCMGNQA
Sbjct: 719 RAASKLLEG-KRDIPVKLWVAPPTKMDQKQLTEEGHYGVFGTAGARTEMPGCSLCMGNQA 777

Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
           +V +GATV+STSTRNFPNRLG   NV+L SAELAA+ + +GK+PT EEY   +  +  + 
Sbjct: 778 QVREGATVMSTSTRNFPNRLGKNTNVYLGSAELAAICSRLGKIPTKEEYMADMGVLTASG 837

Query: 838 VDTYRYLNFDQLSQYTEKADGV 859
              Y+Y+NFDQ+  + + AD V
Sbjct: 838 DKIYQYMNFDQIEDFKDLADTV 859


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: 2048
Number of extensions: 75
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 BPHYT_RS10160 BPHYT_RS10160 (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.4738.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 1519.2   0.0          0 1519.0   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS10160  BPHYT_RS10160 bifunctional aconi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS10160  BPHYT_RS10160 bifunctional aconitate hydratase 2/2-methylisocitrate dehydrat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1519.0   0.0         0         0       1     844 []       1     854 [.       1     854 [. 0.99

  Alignments for each domain:
  == domain 1  score: 1519.0 bits;  conditional E-value: 0
                                TIGR00117   1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaa 70 
                                              +le++r h a ra++gi+plpl a+q+a+lvell+n+p++ee+ ll+l+++rvp gvdeaa+vkagflaa
  lcl|FitnessBrowser__BFirm:BPHYT_RS10160   1 MLENFRAHAAARATLGIPPLPLTAQQTAELVELLTNPPAGEEQTLLDLITNRVPAGVDEAARVKAGFLAA 70 
                                              79******************************************************************** PP

                                TIGR00117  71 iakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt 140
                                              +akge +++lis  +a+ellgtmlggyn++plie+l   d+++ ++aa+al+ktll+fdaf+dv+el++ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS10160  71 VAKGETTCALISRARATELLGTMLGGYNIQPLIELLS--DAEVGTVAAEALKKTLLMFDAFHDVKELADK 138
                                              ************************************9..****************************998 PP

                                TIGR00117 141 .neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkiee 209
                                               n+ ak vl+swa+aewf  ++e+++ +t+tvfkv+getntddlspapda+trpdip+halamlkn++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS10160 139 gNANAKAVLQSWADAEWFTSRPEVPQSLTITVFKVTGETNTDDLSPAPDATTRPDIPMHALAMLKNARPG 208
                                              8********************************************************************* PP

                                TIGR00117 210 ieq..........rikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggki 269
                                              i +           i++lk+kg+ vayvgdvvgtgssrksatnsvlwf g+dipf+pnkr gg++lg ki
  lcl|FitnessBrowser__BFirm:BPHYT_RS10160 209 ITPeedgkrgpikFIQSLKEKGHLVAYVGDVVGTGSSRKSATNSVLWFTGEDIPFIPNKRFGGVCLGSKI 278
                                              *99999****9999******************************************************** PP

                                TIGR00117 270 apiffntaedsgalpievdvkdlnegdvikiypykgeitnketevvatfklkpetlldevraggriplii 339
                                              apif+nt+ed+galpie dv+++++gdv+++ py+g+   k++ v+a fk+k+++l+devraggriplii
  lcl|FitnessBrowser__BFirm:BPHYT_RS10160 279 APIFYNTMEDAGALPIELDVSQMEMGDVVELRPYEGKAL-KNGAVIAEFKVKSDVLFDEVRAGGRIPLII 347
                                              *************************************75.5569************************** PP

                                TIGR00117 340 grgltdkarealglsesevfkkakapaesakgftlaqklvgkacgv...kgirpgtycepkvttvgsqdt 406
                                              grglt karealgl++s +f+ +++pa+s+kgf+laqk+vg+acg+   +g+rpgtycepk+t+vgsqdt
  lcl|FitnessBrowser__BFirm:BPHYT_RS10160 348 GRGLTAKAREALGLAPSTLFRLPQQPADSGKGFSLAQKMVGRACGLpegQGVRPGTYCEPKMTSVGSQDT 417
                                              *********************************************87679******************** PP

                                TIGR00117 407 tgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrm 476
                                              tg+mtrdelk+la+lgf+adlv+qsfchtaaypk vdvkth+tlpdfis+rgg+alrpgdgvihswlnrm
  lcl|FitnessBrowser__BFirm:BPHYT_RS10160 418 TGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKSVDVKTHRTLPDFISNRGGIALRPGDGVIHSWLNRM 487
                                              ********************************************************************** PP

                                TIGR00117 477 llpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrdlvnaipyy 546
                                              llpdtvgtggdshtrfp+gisfpagsglvafaaatg+mpldmpesvlvrfkg++qpg+tlrdlvnaip+y
  lcl|FitnessBrowser__BFirm:BPHYT_RS10160 488 LLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGTMPLDMPESVLVRFKGKMQPGVTLRDLVNAIPLY 557
                                              ********************************************************************** PP

                                TIGR00117 547 aikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkepvieylksnivl 616
                                              aik+g ltv k+gk+n+f+gr+leieglpdlkveqafel+dasaersaagct++lnkep+ieyl+sn+ l
  lcl|FitnessBrowser__BFirm:BPHYT_RS10160 558 AIKQGTLTVAKQGKKNIFSGRVLEIEGLPDLKVEQAFELSDASAERSAAGCTVHLNKEPIIEYLNSNVTL 627
                                              ********************************************************************** PP

                                TIGR00117 617 lkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapndpddvkllse 686
                                              lk+mia+gy+d r+l+rri+ame+wla+p+ll++dadaeyaavieidla+i+epi+a+pndpddvk+ls+
  lcl|FitnessBrowser__BFirm:BPHYT_RS10160 628 LKWMIAQGYQDPRSLQRRIKAMEAWLADPQLLSPDADAEYAAVIEIDLADIHEPIVACPNDPDDVKTLSD 697
                                              ********************************************************************** PP

                                TIGR00117 687 vagdaidevfigscmtnighfraagkileaaktvkarlwvvpptrmdeqqlieegyyaifgaagartevp 756
                                              vag +idevfigscmtnighfraa+k+le++++++ +lwv+ppt+md++ql+eeg y++fg+agarte+p
  lcl|FitnessBrowser__BFirm:BPHYT_RS10160 698 VAGAKIDEVFIGSCMTNIGHFRAASKLLEGKRDIPVKLWVAPPTKMDQKQLTEEGHYGVFGTAGARTEMP 767
                                              ********************************************************************** PP

                                TIGR00117 757 gcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkeeylalvsekvesa 826
                                              gcslcmgnqa+v++gatv+ststrnf+nrlgk ++vylgsaelaa+++ lgkiptkeey+a +  ++ + 
  lcl|FitnessBrowser__BFirm:BPHYT_RS10160 768 GCSLCMGNQAQVREGATVMSTSTRNFPNRLGKNTNVYLGSAELAAICSRLGKIPTKEEYMADMG-VLTAS 836
                                              ************************************************************9986.66777 PP

                                TIGR00117 827 kdklyrylnfnelenfee 844
                                               dk+y+y+nf+++e+f++
  lcl|FitnessBrowser__BFirm:BPHYT_RS10160 837 GDKIYQYMNFDQIEDFKD 854
                                              899*************85 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.08
# Mc/sec: 8.41
//
[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