GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Sedimenticola selenatireducens DSM 17993

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_029132406.1 A3GO_RS0104620 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= SwissProt::Q8ZRS8
         (865 letters)



>NCBI__GCF_000428045.1:WP_029132406.1
          Length = 862

 Score = 1388 bits (3592), Expect = 0.0
 Identities = 681/861 (79%), Positives = 757/861 (87%), Gaps = 1/861 (0%)

Query: 1   MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60
           MLE YRKHV ERAA+GI P PL+  Q A LVELLK PP GEE +LLDL+I+RVP GVD++
Sbjct: 1   MLESYRKHVEERAAEGIPPLPLNPEQTAQLVELLKNPPAGEEAYLLDLIIHRVPAGVDQS 60

Query: 61  AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AYVKA FLA VAKG    PL+   KA ELLGTM GGYNI PL++ALDD  LAP A KALS
Sbjct: 61  AYVKAAFLADVAKGSCNCPLIDRVKATELLGTMLGGYNIAPLVEALDDEALAPTAVKALS 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETNTD 180
           HTLL+FD F DV+EKA AGN++AK ++QSWA+ EWF  +P LAEK+T+TVFKVTGETNTD
Sbjct: 121 HTLLVFDAFNDVKEKADAGNDHAKAILQSWAEGEWFTQKPELAEKVTLTVFKVTGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHAQAMLKNAREGIEPDQPGVVGPIKQIEALQKKGYPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHA AMLK  REGI PDQPGV+GPIK IE L++KG+P+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHANAMLKMEREGITPDQPGVIGPIKFIEELKQKGHPVAYVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLW MGDDIP +PNKR GG CLGGKIAPIFFNTMEDAGALP E DVSN
Sbjct: 241 GTGSSRKSATNSVLWHMGDDIPFIPNKRAGGFCLGGKIAPIFFNTMEDAGALPFECDVSN 300

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           LNMGDVIDVYPY+G V+NHE+GE L  FELKTDVL+DEVRAGGRIPLIIGRGLT +AREA
Sbjct: 301 LNMGDVIDVYPYEGVVKNHESGEELCRFELKTDVLLDEVRAGGRIPLIIGRGLTARAREA 360

Query: 361 LGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
           LGL  S +F+     A+S++G+SLAQKMVGRACGV+G+RPGAYCEP+MT+VGSQDTTGPM
Sbjct: 361 LGLDPSTLFKSPAPAADSTKGYSLAQKMVGRACGVEGVRPGAYCEPRMTTVGSQDTTGPM 420

Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDGVIH 480
           TRDELKDLACLGFSADLVMQSFCHTAAYPKPVD+TTHHTLPDFI +RGGV+LRPGDG+IH
Sbjct: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDITTHHTLPDFISSRGGVALRPGDGIIH 480

Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
           SWLNRMLLPDT+GTGGDSHTRFPIG+SFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM
Sbjct: 481 SWLNRMLLPDTLGTGGDSHTRFPIGLSFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540

Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
           QPGITLRDLV+AIP YAIKQGLLTV K GKKNIFSGR+LEIEGLPDLKVEQAFEL+DASA
Sbjct: 541 QPGITLRDLVNAIPYYAIKQGLLTVAKAGKKNIFSGRVLEIEGLPDLKVEQAFELSDASA 600

Query: 601 ERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADPQLLEA 660
           ERSAAGCTIKL+K PI+EYL SNI LLKWMIA  Y D RTL+RRI+GMEKWLADPQLLE 
Sbjct: 601 ERSAAGCTIKLDKAPIIEYLQSNITLLKWMIANDYQDPRTLQRRIEGMEKWLADPQLLEG 660

Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIGHFRAA 720
           DADAEYAAVI+IDLAD+KEPIL  PNDPDD + LS+V G+KIDEVFIGSCMTNIGHFRAA
Sbjct: 661 DADAEYAAVIEIDLADVKEPILACPNDPDDVKQLSEVAGQKIDEVFIGSCMTNIGHFRAA 720

Query: 721 GKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780
           GKLL+  K  +PTRLW+APPT+MDA  L EEGYY+ FGK+GAR+E+PGCSLCMGNQARV 
Sbjct: 721 GKLLEG-KHDIPTRLWMAPPTKMDAYVLNEEGYYATFGKAGARMEMPGCSLCMGNQARVK 779

Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840
           D ATVVSTSTRNFPNRLGTGANV+L+SAELAAVAA+IGKLPT EEY  Y  Q+D  + D 
Sbjct: 780 DNATVVSTSTRNFPNRLGTGANVYLSSAELAAVAAIIGKLPTVEEYMVYADQIDAMSADI 839

Query: 841 YRYLNFDQLSQYTEKADGVIF 861
           +RY+NFDQ+  Y   A+ V F
Sbjct: 840 FRYMNFDQIEAYQSVANRVEF 860


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: 2125
Number of extensions: 72
Number of successful extensions: 2
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: 862
Length adjustment: 42
Effective length of query: 823
Effective length of database: 820
Effective search space:   674860
Effective search space used:   674860
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_029132406.1 A3GO_RS0104620 (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.3313384.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 1575.8   0.0          0 1575.6   0.0    1.0  1  NCBI__GCF_000428045.1:WP_029132406.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000428045.1:WP_029132406.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1575.6   0.0         0         0       1     843 [.       1     852 [.       1     853 [. 0.99

  Alignments for each domain:
  == domain 1  score: 1575.6 bits;  conditional E-value: 0
                             TIGR00117   1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiak 73 
                                           +le yrkhv eraaegi+plpln +q+a+lvellkn+p++ee++ll+l+i+rvp gvd++ayvka fla +ak
  NCBI__GCF_000428045.1:WP_029132406.1   1 MLESYRKHVEERAAEGIPPLPLNPEQTAQLVELLKNPPAGEEAYLLDLIIHRVPAGVDQSAYVKAAFLADVAK 73 
                                           79*********************************************************************** PP

                             TIGR00117  74 gevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyak 145
                                           g  ++pli   +a+ellgtmlggyn+ pl+eal+  d+ +a++a kals+tllvfdaf+dv+e++++ n++ak
  NCBI__GCF_000428045.1:WP_029132406.1  74 GSCNCPLIDRVKATELLGTMLGGYNIAPLVEALD--DEALAPTAVKALSHTLLVFDAFNDVKEKADAgNDHAK 144
                                           **********************************..*******************************9***** PP

                             TIGR00117 146 qvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq...... 212
                                            +l+swae+ewf +k+elaek+t tvfkv+getntddlspapda++rpdiplha amlk ++e+i +      
  NCBI__GCF_000428045.1:WP_029132406.1 145 AILQSWAEGEWFTQKPELAEKVTLTVFKVTGETNTDDLSPAPDAWSRPDIPLHANAMLKMEREGITPdqpgvi 217
                                           *****************************************************************9999**** PP

                             TIGR00117 213 ....rikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsg 281
                                                i++lkqkg+pvayvgdvvgtgssrksatnsvlw++g+dipf+pnkragg++lggkiapiffnt+ed+g
  NCBI__GCF_000428045.1:WP_029132406.1 218 gpikFIEELKQKGHPVAYVGDVVGTGSSRKSATNSVLWHMGDDIPFIPNKRAGGFCLGGKIAPIFFNTMEDAG 290
                                           ***99******************************************************************** PP

                             TIGR00117 282 alpievdvkdlnegdvikiypykgeitnket.evvatfklkpetlldevraggripliigrgltdkarealgl 353
                                           alp e+dv++ln+gdvi++ypy+g ++n+e+ e ++ f+lk+++lldevraggripliigrglt +arealgl
  NCBI__GCF_000428045.1:WP_029132406.1 291 ALPFECDVSNLNMGDVIDVYPYEGVVKNHESgEELCRFELKTDVLLDEVRAGGRIPLIIGRGLTARAREALGL 363
                                           *****************************988***************************************** PP

                             TIGR00117 354 sesevfkkakapaesakgftlaqklvgkacgvkgirpgtycepkvttvgsqdttgamtrdelkelaslgfdad 426
                                            +s +fk ++ +a+s+kg++laqk+vg+acgv+g+rpg+ycep++ttvgsqdttg+mtrdelk+la+lgf+ad
  NCBI__GCF_000428045.1:WP_029132406.1 364 DPSTLFKSPAPAADSTKGYSLAQKMVGRACGVEGVRPGAYCEPRMTTVGSQDTTGPMTRDELKDLACLGFSAD 436
                                           ************************************************************************* PP

                             TIGR00117 427 lvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfp 499
                                           lv+qsfchtaaypkpvd+ th+tlpdfis+rggvalrpgdg+ihswlnrmllpdt+gtggdshtrfp+g+sfp
  NCBI__GCF_000428045.1:WP_029132406.1 437 LVMQSFCHTAAYPKPVDITTHHTLPDFISSRGGVALRPGDGIIHSWLNRMLLPDTLGTGGDSHTRFPIGLSFP 509
                                           ************************************************************************* PP

                             TIGR00117 500 agsglvafaaatgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileie 572
                                           agsglvafaaatgvmpldmpesvlvrfkg++qpgitlrdlvnaipyyaik+glltv k gk+n+f+gr+leie
  NCBI__GCF_000428045.1:WP_029132406.1 510 AGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGITLRDLVNAIPYYAIKQGLLTVAKAGKKNIFSGRVLEIE 582
                                           ************************************************************************* PP

                             TIGR00117 573 glpdlkveqafeltdasaersaagctiklnkepvieylksnivllkemiaegyedkrtlkrridamekwlanp 645
                                           glpdlkveqafel+dasaersaagctikl+k p+ieyl+sni llk+mia+ y+d rtl+rri++mekwla+p
  NCBI__GCF_000428045.1:WP_029132406.1 583 GLPDLKVEQAFELSDASAERSAAGCTIKLDKAPIIEYLQSNITLLKWMIANDYQDPRTLQRRIEGMEKWLADP 655
                                           ************************************************************************* PP

                             TIGR00117 646 elleadadaeyaavieidlaeikepilaapndpddvkllsevagdaidevfigscmtnighfraagkileaak 718
                                           +lle+dadaeyaavieidla++kepila+pndpddvk+lsevag++idevfigscmtnighfraagk+le+++
  NCBI__GCF_000428045.1:WP_029132406.1 656 QLLEGDADAEYAAVIEIDLADVKEPILACPNDPDDVKQLSEVAGQKIDEVFIGSCMTNIGHFRAAGKLLEGKH 728
                                           ************************************************************************* PP

                             TIGR00117 719 tvkarlwvvpptrmdeqqlieegyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgak 791
                                           ++++rlw++ppt+md+  l eegyya fg+agar+e+pgcslcmgnqarv+d+atv+ststrnf+nrlg+ga+
  NCBI__GCF_000428045.1:WP_029132406.1 729 DIPTRLWMAPPTKMDAYVLNEEGYYATFGKAGARMEMPGCSLCMGNQARVKDNATVVSTSTRNFPNRLGTGAN 801
                                           ************************************************************************* PP

                             TIGR00117 792 vylgsaelaavaallgkiptkeeylalvsekvesakdklyrylnfnelenfe 843
                                           vyl+saelaavaa++gk+pt+eey+ +  + ++   d ++ry+nf+++e ++
  NCBI__GCF_000428045.1:WP_029132406.1 802 VYLSSAELAAVAAIIGKLPTVEEYMVYADQIDAMSAD-IFRYMNFDQIEAYQ 852
                                           *************************998888877777.***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (844 nodes)
Target sequences:                          1  (862 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 42.86
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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