GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Shewanella loihica PV-4

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate 5210998 Shew_3424 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase (RefSeq)

Query= BRENDA::P36683
         (865 letters)



>lcl|FitnessBrowser__PV4:5210998 Shew_3424 bifunctional aconitate
           hydratase 2/2-methylisocitrate dehydratase (RefSeq)
          Length = 865

 Score = 1438 bits (3723), Expect = 0.0
 Identities = 704/865 (81%), Positives = 785/865 (90%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           MLE YRKHVAERAAEG+ PKPLDA+Q+A L+EL+KNPPAGEEEF+LDLL NR+PPGVDEA
Sbjct: 1   MLEAYRKHVAERAAEGVVPKPLDAHQVAELIELVKNPPAGEEEFILDLLENRIPPGVDEA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AYVKAGFL A+AKGEA SP+L+  +A+ELLGTMQGGYNI PLI  LD+   AP+A KALS
Sbjct: 61  AYVKAGFLDAVAKGEATSPILSAARAVELLGTMQGGYNIEPLIAQLDNDVQAPLAVKALS 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
           +TLLMFD ++DV EK +AGN +AKQV++SWA+AEWFL+RP LA+K+T+TVFKVTGETNTD
Sbjct: 121 NTLLMFDAYHDVVEKMQAGNAHAKQVVESWANAEWFLSRPKLADKVTLTVFKVTGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHALAMLKNAR+GI PD+ GV GPI +IEAL+QKG PL YVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKNARDGIVPDEAGVKGPINEIEALKQKGHPLVYVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWFMGDDIP VPNKR GG CLGGKIAPIFFNTMEDAGALPIE+DVS 
Sbjct: 241 GTGSSRKSATNSVLWFMGDDIPFVPNKRAGGFCLGGKIAPIFFNTMEDAGALPIELDVSK 300

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           +NMGDVID+YPY+G V+ H + E+++ F+LKTDVL+DEVRAGGRIPLIIGRGLT +ARE 
Sbjct: 301 MNMGDVIDIYPYEGVVKLHGSDEVISEFKLKTDVLLDEVRAGGRIPLIIGRGLTDRARET 360

Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
           LGLP SDVF + +DVA+S +G++LAQKMVG+ACGV G+RPG YCEPKMTSVGSQDTTGPM
Sbjct: 361 LGLPASDVFVRPQDVADSGKGYTLAQKMVGKACGVAGVRPGQYCEPKMTSVGSQDTTGPM 420

Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
           TRDELKDLACLGFSADL MQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH
Sbjct: 421 TRDELKDLACLGFSADLTMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480

Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
           SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPES+LVRFKG+M
Sbjct: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESILVRFKGEM 540

Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
           QPGITLRDLVHAIP  AI+ GLLTVEKKGK N FSGRILEIEGL  LKVEQAFEL+DASA
Sbjct: 541 QPGITLRDLVHAIPHKAIEMGLLTVEKKGKINAFSGRILEIEGLEKLKVEQAFELSDASA 600

Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660
           ERSAAGCTIKL+KEPIIEYLNSNIV+LKWMIAEGYGDRRT+ERRI  ME+WLANPEL+ A
Sbjct: 601 ERSAAGCTIKLDKEPIIEYLNSNIVMLKWMIAEGYGDRRTIERRIAAMEEWLANPELMAA 660

Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
           DADAEYA VI+IDL +IKEPILCAPNDPDDA  LS V+  +IDEVF+GSCMTNIGHFRA 
Sbjct: 661 DADAEYAEVIEIDLNEIKEPILCAPNDPDDAVLLSQVKDTQIDEVFVGSCMTNIGHFRAT 720

Query: 721 GKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780
           GK+LD     LPTRLW+APPT+MD  QLTEEGYY++FG+ GARIEIPGCSLCMGNQARVA
Sbjct: 721 GKMLDKFAKTLPTRLWIAPPTKMDRDQLTEEGYYAIFGRVGARIEIPGCSLCMGNQARVA 780

Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840
           +GATVVSTSTRNFPNRLGTGANV+LASAELAAVAAL+G+LP+ EEYQ Y  ++D TA DT
Sbjct: 781 EGATVVSTSTRNFPNRLGTGANVYLASAELAAVAALLGRLPSVEEYQEYAKEIDATAADT 840

Query: 841 YRYLNFNQLSQYTEKADGVIFQTAV 865
           YRYLNF+Q+  YT+KA  VIFQ+AV
Sbjct: 841 YRYLNFDQIDSYTQKAGEVIFQSAV 865


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: 2167
Number of extensions: 77
Number of successful extensions: 1
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: 865
Length adjustment: 42
Effective length of query: 823
Effective length of database: 823
Effective search space:   677329
Effective search space used:   677329
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 5210998 Shew_3424 (bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase (RefSeq))
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.487.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 1581.0   0.0          0 1580.8   0.0    1.0  1  lcl|FitnessBrowser__PV4:5210998  Shew_3424 bifunctional aconitate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210998  Shew_3424 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1580.8   0.0         0         0       1     843 [.       1     853 [.       1     854 [. 0.99

  Alignments for each domain:
  == domain 1  score: 1580.8 bits;  conditional E-value: 0
                        TIGR00117   1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiakgevks 78 
                                      +le+yrkhvaeraaeg+ p+pl+a+qva+l+el+kn+p++eeef+l+ll +r+ppgvdeaayvkagfl a+akge++s
  lcl|FitnessBrowser__PV4:5210998   1 MLEAYRKHVAERAAEGVVPKPLDAHQVAELIELVKNPPAGEEEFILDLLENRIPPGVDEAAYVKAGFLDAVAKGEATS 78 
                                      79**************************************************************************** PP

                        TIGR00117  79 plisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyakqvleswaeae 155
                                      p +sa +avellgtm+ggyn+epli +l+  +   a+ a kals+tll+fda++dv e+ ++ n++akqv+eswa+ae
  lcl|FitnessBrowser__PV4:5210998  79 PILSAARAVELLGTMQGGYNIEPLIAQLD--NDVQAPLAVKALSNTLLMFDAYHDVVEKMQAgNAHAKQVVESWANAE 154
                                      *****************************..44569*******************99998888*************** PP

                        TIGR00117 156 wflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq..........rikalkqkgvp 223
                                      wfl +++la+k+t tvfkv+getntddlspapda++rpdiplhalamlkn++++i +          +i+alkqkg+p
  lcl|FitnessBrowser__PV4:5210998 155 WFLSRPKLADKVTLTVFKVTGETNTDDLSPAPDAWSRPDIPLHALAMLKNARDGIVPdeagvkgpinEIEALKQKGHP 232
                                      *******************************************************9999******************* PP

                        TIGR00117 224 vayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdvkdlnegdvikiy 301
                                      + yvgdvvgtgssrksatnsvlwf+g+dipfvpnkragg++lggkiapiffnt+ed+galpie dv+++n+gdvi+iy
  lcl|FitnessBrowser__PV4:5210998 233 LVYVGDVVGTGSSRKSATNSVLWFMGDDIPFVPNKRAGGFCLGGKIAPIFFNTMEDAGALPIELDVSKMNMGDVIDIY 310
                                      ****************************************************************************** PP

                        TIGR00117 302 pykgeitnket.evvatfklkpetlldevraggripliigrgltdkarealglsesevfkkakapaesakgftlaqkl 378
                                      py+g ++++ + ev++ fklk+++lldevraggripliigrgltd+are+lgl+ s+vf++++++a+s+kg+tlaqk+
  lcl|FitnessBrowser__PV4:5210998 311 PYEGVVKLHGSdEVISEFKLKTDVLLDEVRAGGRIPLIIGRGLTDRARETLGLPASDVFVRPQDVADSGKGYTLAQKM 388
                                      *********9889***************************************************************** PP

                        TIGR00117 379 vgkacgvkgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvkthktlpdfisq 456
                                      vgkacgv g+rpg ycepk+t+vgsqdttg+mtrdelk+la+lgf+adl++qsfchtaaypkpvdv+th+tlpdfi++
  lcl|FitnessBrowser__PV4:5210998 389 VGKACGVAGVRPGQYCEPKMTSVGSQDTTGPMTRDELKDLACLGFSADLTMQSFCHTAAYPKPVDVNTHHTLPDFIMN 466
                                      ****************************************************************************** PP

                        TIGR00117 457 rggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgi 534
                                      rggv+lrpgdgvihswlnrmllpdtvgtggdshtrfp+gisfpagsglvafaaatgvmpldmpes+lvrfkge+qpgi
  lcl|FitnessBrowser__PV4:5210998 467 RGGVSLRPGDGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESILVRFKGEMQPGI 544
                                      ****************************************************************************** PP

                        TIGR00117 535 tlrdlvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkepvieylks 612
                                      tlrdlv+aip+ ai+ glltvekkgk+n f+grileiegl  lkveqafel+dasaersaagctikl+kep+ieyl+s
  lcl|FitnessBrowser__PV4:5210998 545 TLRDLVHAIPHKAIEMGLLTVEKKGKINAFSGRILEIEGLEKLKVEQAFELSDASAERSAAGCTIKLDKEPIIEYLNS 622
                                      ****************************************************************************** PP

                        TIGR00117 613 nivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapndpddvkllsevagd 690
                                      niv+lk+miaegy+d+rt++rri+ame+wlanpel+ adadaeya+vieidl+eikepil+apndpdd+ lls+v+  
  lcl|FitnessBrowser__PV4:5210998 623 NIVMLKWMIAEGYGDRRTIERRIAAMEEWLANPELMAADADAEYAEVIEIDLNEIKEPILCAPNDPDDAVLLSQVKDT 700
                                      ****************************************************************************** PP

                        TIGR00117 691 aidevfigscmtnighfraagkilea.aktvkarlwvvpptrmdeqqlieegyyaifgaagartevpgcslcmgnqar 767
                                      +idevf+gscmtnighfra+gk+l++ akt+++rlw++ppt+md +ql+eegyyaifg+ gar+e+pgcslcmgnqar
  lcl|FitnessBrowser__PV4:5210998 701 QIDEVFVGSCMTNIGHFRATGKMLDKfAKTLPTRLWIAPPTKMDRDQLTEEGYYAIFGRVGARIEIPGCSLCMGNQAR 778
                                      ************************983569************************************************ PP

                        TIGR00117 768 vedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkeeylalvsekvesakdklyrylnfnelenfe 843
                                      v++gatv+ststrnf+nrlg+ga+vyl+saelaavaallg++p++eey+++  e +++a d +yrylnf++++ ++
  lcl|FitnessBrowser__PV4:5210998 779 VAEGATVVSTSTRNFPNRLGTGANVYLASAELAAVAALLGRLPSVEEYQEYAKEIDATAAD-TYRYLNFDQIDSYT 853
                                      **********************************************************999.************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (844 nodes)
Target sequences:                          1  (865 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: 0.06u 0.03s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 8.58
//
[ok]

This GapMind analysis is from Sep 17 2021. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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