GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Marinobacter adhaerens HP15

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate GFF2253 HP15_2203 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>lcl|FitnessBrowser__Marino:GFF2253 HP15_2203 bifunctional aconitate
           hydratase 2/2-methylisocitrate dehydratase
          Length = 864

 Score = 1269 bits (3284), Expect = 0.0
 Identities = 620/859 (72%), Positives = 720/859 (83%), Gaps = 4/859 (0%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           MLE YR+HVAER A GI PKPL+A Q AALV+LLKNPPAGEE+ L+ LL NRVPPGVDEA
Sbjct: 1   MLEAYREHVAEREALGIPPKPLNAEQTAALVDLLKNPPAGEEDTLVYLLENRVPPGVDEA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AYVKA FL AI KGEA SPLL    A++LLG MQGGYNI  L+D LDD++LA +A + L 
Sbjct: 61  AYVKAAFLTAIVKGEASSPLLDKPTAVKLLGMMQGGYNIATLVDLLDDSELAELAGEQLK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
            TLLMFD F DV+EK  AGN  A+ V++SWA+ EWF N+  + E   + VFKVTGETNTD
Sbjct: 121 RTLLMFDAFNDVKEKMDAGNPVARAVIESWANGEWFTNKKKVPESTKMVVFKVTGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHA A  K  R+G++P++PGV GP+ QI+ ++ KG P+A+VGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHARAAYKMERDGLKPEEPGVTGPMSQIDEIKAKGLPVAFVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWF GDDIP VPNKR GG+C+G K+APIFFNTMEDAGAL  E  V +
Sbjct: 241 GTGSSRKSATNSVLWFFGDDIPGVPNKRAGGVCIGNKVAPIFFNTMEDAGALVFEAPVDD 300

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           +NMGDVI++ PY G++ N E GE ++ F+ K+DV++DEV+AGGRIPLIIGRGLT KAR A
Sbjct: 301 MNMGDVIEIRPYDGKILN-EAGETISEFKFKSDVILDEVQAGGRIPLIIGRGLTAKARTA 359

Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
           LG+  +D+FR  KD     +GF+LAQKMVG+ACG+   KG+RP  YCEP MT+VGSQDTT
Sbjct: 360 LGMGATDLFRLPKDPEAGTKGFTLAQKMVGKACGLEEGKGVRPNTYCEPHMTTVGSQDTT 419

Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477
           GPMTRDELKDLACLGF ADLVMQSFCHTAAYPKPVDV   HT+PDFI  RGGVSLRPGDG
Sbjct: 420 GPMTRDELKDLACLGFQADLVMQSFCHTAAYPKPVDVEMQHTMPDFIRTRGGVSLRPGDG 479

Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
           +IHSWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPESVLVRFK
Sbjct: 480 IIHSWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 539

Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
           G+MQPGITLRDLVHAIPLY IKQG+LTVEKKGK N FSGRILEIEGL  L VEQAFEL+D
Sbjct: 540 GEMQPGITLRDLVHAIPLYGIKQGMLTVEKKGKINEFSGRILEIEGLEHLTVEQAFELSD 599

Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657
           ASAERSAAGCTI L+++ + EYL SNI +L+WMIAEGYGD RTLERR Q ME+WLA+P+L
Sbjct: 600 ASAERSAAGCTINLSEDSVAEYLRSNITMLRWMIAEGYGDPRTLERRAQQMEEWLADPKL 659

Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717
           + AD DAEYA VI+IDLADIKEPI+C PNDPDDA+ LS V G+K+DEVFIGSCMTNIGHF
Sbjct: 660 MRADKDAEYAHVIEIDLADIKEPIVCCPNDPDDAKFLSEVAGDKVDEVFIGSCMTNIGHF 719

Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
           RAAGKLL+ HKG L TRLW++PPT+MD AQL EEGY++ +G +G R E+PGCSLCMGNQA
Sbjct: 720 RAAGKLLEQHKGPLSTRLWMSPPTKMDQAQLMEEGYFNTYGTAGVRTEMPGCSLCMGNQA 779

Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
           RVA  +TV+STSTRNFPNRLG GANV+L SAELAAV A++GKLP+P EY  Y   ++  +
Sbjct: 780 RVAPKSTVLSTSTRNFPNRLGDGANVYLTSAELAAVGAVLGKLPSPAEYMEYAKDLNSMS 839

Query: 838 VDTYRYLNFNQLSQYTEKA 856
            + Y+YLNF+Q+  YT+KA
Sbjct: 840 KEIYKYLNFDQMENYTKKA 858


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: 2088
Number of extensions: 72
Number of successful extensions: 3
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: 864
Length adjustment: 42
Effective length of query: 823
Effective length of database: 822
Effective search space:   676506
Effective search space used:   676506
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 GFF2253 HP15_2203 (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.1588.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 1467.3   0.0          0 1467.1   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF2253  HP15_2203 bifunctional aconitate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF2253  HP15_2203 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1467.1   0.0         0         0       1     843 [.       1     855 [.       1     856 [. 0.99

  Alignments for each domain:
  == domain 1  score: 1467.1 bits;  conditional E-value: 0
                           TIGR00117   1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiakge 75 
                                         +le+yr hvaer+a+gi+p+plna+q+aalv+llkn+p++ee+ l+ ll +rvppgvdeaayvka fl+ai kge
  lcl|FitnessBrowser__Marino:GFF2253   1 MLEAYREHVAEREALGIPPKPLNAEQTAALVDLLKNPPAGEEDTLVYLLENRVPPGVDEAAYVKAAFLTAIVKGE 75 
                                         79************************************************************************* PP

                           TIGR00117  76 vksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyakqvle 149
                                         + spl+    av+llg m+ggyn+ +l+++l+  d+++a+ a + l++tll+fdaf+dv+e+ ++ n +a+ v+e
  lcl|FitnessBrowser__Marino:GFF2253  76 ASSPLLDKPTAVKLLGMMQGGYNIATLVDLLD--DSELAELAGEQLKRTLLMFDAFNDVKEKMDAgNPVARAVIE 148
                                         ********************************..****************************9999********* PP

                           TIGR00117 150 swaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq..........ri 214
                                         swa++ewf nk++++e  +++vfkv+getntddlspapda++rpdiplha+a  k ++++ ++          +i
  lcl|FitnessBrowser__Marino:GFF2253 149 SWANGEWFTNKKKVPESTKMVVFKVTGETNTDDLSPAPDAWSRPDIPLHARAAYKMERDGLKPeepgvtgpmsQI 223
                                         ***********************************************************9999999********* PP

                           TIGR00117 215 kalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdv 289
                                         +++k kg pva+vgdvvgtgssrksatnsvlwf+g+dip vpnkragg+++g k+apiffnt+ed+gal  e+ v
  lcl|FitnessBrowser__Marino:GFF2253 224 DEIKAKGLPVAFVGDVVGTGSSRKSATNSVLWFFGDDIPGVPNKRAGGVCIGNKVAPIFFNTMEDAGALVFEAPV 298
                                         *************************************************************************** PP

                           TIGR00117 290 kdlnegdvikiypykgeitnketevvatfklkpetlldevraggripliigrgltdkarealglsesevfkkaka 364
                                         +d+n+gdvi+i py+g+i n+++e+++ fk+k++++ldev+aggripliigrglt kar alg++ +++f+ +k+
  lcl|FitnessBrowser__Marino:GFF2253 299 DDMNMGDVIEIRPYDGKILNEAGETISEFKFKSDVILDEVQAGGRIPLIIGRGLTAKARTALGMGATDLFRLPKD 373
                                         *************************************************************************** PP

                           TIGR00117 365 paesakgftlaqklvgkacgv...kgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfchta 436
                                         p+  +kgftlaqk+vgkacg+   kg+rp tycep++ttvgsqdttg+mtrdelk+la+lgf+adlv+qsfchta
  lcl|FitnessBrowser__Marino:GFF2253 374 PEAGTKGFTLAQKMVGKACGLeegKGVRPNTYCEPHMTTVGSQDTTGPMTRDELKDLACLGFQADLVMQSFCHTA 448
                                         ********************86668************************************************** PP

                           TIGR00117 437 aypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaat 511
                                         aypkpvdv++ +t+pdfi +rggv+lrpgdg+ihswlnrmllpdtvgtggdshtrfp+gisfpagsglvafaaat
  lcl|FitnessBrowser__Marino:GFF2253 449 AYPKPVDVEMQHTMPDFIRTRGGVSLRPGDGIIHSWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAAT 523
                                         *************************************************************************** PP

                           TIGR00117 512 gvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafelt 586
                                         gvmpldmpesvlvrfkge+qpgitlrdlv+aip+y ik+g+ltvekkgk+n f+grileiegl  l veqafel+
  lcl|FitnessBrowser__Marino:GFF2253 524 GVMPLDMPESVLVRFKGEMQPGITLRDLVHAIPLYGIKQGMLTVEKKGKINEFSGRILEIEGLEHLTVEQAFELS 598
                                         *************************************************************************** PP

                           TIGR00117 587 dasaersaagctiklnkepvieylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavie 661
                                         dasaersaagcti+l++++v+eyl+sni +l++miaegy+d rtl+rr ++me+wla+p+l+ ad daeya vie
  lcl|FitnessBrowser__Marino:GFF2253 599 DASAERSAAGCTINLSEDSVAEYLRSNITMLRWMIAEGYGDPRTLERRAQQMEEWLADPKLMRADKDAEYAHVIE 673
                                         *************************************************************************** PP

                           TIGR00117 662 idlaeikepilaapndpddvkllsevagdaidevfigscmtnighfraagkileaak.tvkarlwvvpptrmdeq 735
                                         idla+ikepi+++pndpdd+k lsevagd++devfigscmtnighfraagk+le++k ++ +rlw+ ppt+md++
  lcl|FitnessBrowser__Marino:GFF2253 674 IDLADIKEPIVCCPNDPDDAKFLSEVAGDKVDEVFIGSCMTNIGHFRAAGKLLEQHKgPLSTRLWMSPPTKMDQA 748
                                         ********************************************************999**************** PP

                           TIGR00117 736 qlieegyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkip 810
                                         ql+eegy++ +g+ag rte+pgcslcmgnqarv+ ++tv+ststrnf+nrlg ga+vyl+saelaav a+lgk+p
  lcl|FitnessBrowser__Marino:GFF2253 749 QLMEEGYFNTYGTAGVRTEMPGCSLCMGNQARVAPKSTVLSTSTRNFPNRLGDGANVYLTSAELAAVGAVLGKLP 823
                                         *************************************************************************** PP

                           TIGR00117 811 tkeeylalvsekvesakdklyrylnfnelenfe 843
                                         ++ ey+++  + ++s+ +++y+ylnf+++en++
  lcl|FitnessBrowser__Marino:GFF2253 824 SPAEYMEYAKD-LNSMSKEIYKYLNFDQMENYT 855
                                         *******9665.6677777*************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (844 nodes)
Target sequences:                          1  (864 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 0.04s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 8.21
//
[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