GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Shewanella amazonensis SB2B

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate 6936193 Sama_0382 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase (RefSeq)

Query= BRENDA::P36683
         (865 letters)



>FitnessBrowser__SB2B:6936193
          Length = 865

 Score = 1456 bits (3769), Expect = 0.0
 Identities = 712/865 (82%), Positives = 787/865 (90%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           MLE YRKHV ERAAEG+ PKPLDA+Q+A LVEL+KNPPAGEE F+LDLL NR+PPGVDEA
Sbjct: 1   MLEAYRKHVEERAAEGVVPKPLDAHQVAELVELVKNPPAGEEAFILDLLENRIPPGVDEA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AYVKAGFL AIAKG A SP+L  E+A+ELLGTMQGGYNI PLI  LD+ KLAP+A KALS
Sbjct: 61  AYVKAGFLDAIAKGTATSPILNAERAVELLGTMQGGYNIEPLIHQLDNDKLAPLAVKALS 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
           HTLLMFD+F+DV EK  AGN +AKQV++SWA+AEWFL+RP LA+K+++TVFKVTGETNTD
Sbjct: 121 HTLLMFDSFHDVVEKMNAGNAHAKQVVESWANAEWFLSRPKLADKISLTVFKVTGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHALAMLKNAR+GI PD+PGVVGPIK+IE L+ +GFPL YVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKNARDGIVPDEPGVVGPIKKIEELKTQGFPLVYVGDVV 240

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

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           + MGDVID+YPY+G+VR H + E+++ FELKTDVL+DEVRAGGRIPLIIGRGLT KARE 
Sbjct: 301 MEMGDVIDIYPYEGKVRRHGSDEVISEFELKTDVLLDEVRAGGRIPLIIGRGLTDKAREV 360

Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
           LGL  S  F + +DVA++ +GF+LAQKMVG+ACGV G+RPG YCEPKMTSVGSQDTTGPM
Sbjct: 361 LGLGASKEFVRPQDVADTGKGFTLAQKMVGKACGVAGVRPGQYCEPKMTSVGSQDTTGPM 420

Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
           TRDELKDLACLGFSADL MQSFCHTAAYPKPVDVNTHHTLPDFIMNRGG+SLRPGDGVIH
Sbjct: 421 TRDELKDLACLGFSADLTMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGISLRPGDGVIH 480

Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
           SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKG+M
Sbjct: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGQM 540

Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
           QPGITLRDLVHAIP  AI+ GLLTVEKKGKKNIFSGRILEIEGL  LKVEQAFEL+DASA
Sbjct: 541 QPGITLRDLVHAIPHKAIEMGLLTVEKKGKKNIFSGRILEIEGLEHLKVEQAFELSDASA 600

Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660
           ERSAAGCTIKL+K+PIIEYLNSNIV+LKWMIAEGYGDRRT+ERRI+GME+WL NPEL+EA
Sbjct: 601 ERSAAGCTIKLDKDPIIEYLNSNIVMLKWMIAEGYGDRRTIERRIKGMEEWLKNPELMEA 660

Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
           D DAEYAAVI+IDL +IKEPILCAPNDPDDA  LSAV   KIDEVF+GSCMTNIGHFRA 
Sbjct: 661 DKDAEYAAVIEIDLNNIKEPILCAPNDPDDAVLLSAVANTKIDEVFVGSCMTNIGHFRAT 720

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

Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840
           DGATVVSTSTRNFPNRLGTGANV+LASAELAAVAAL+G+LP+PEEYQ Y  ++D TA DT
Sbjct: 781 DGATVVSTSTRNFPNRLGTGANVYLASAELAAVAALLGRLPSPEEYQVYAKEIDATAADT 840

Query: 841 YRYLNFNQLSQYTEKADGVIFQTAV 865
           YRYLNF+++  YT+KA  VIFQ+AV
Sbjct: 841 YRYLNFDEIESYTKKAGEVIFQSAV 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: 2208
Number of extensions: 79
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 6936193 Sama_0382 (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.29370.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 1580.4   0.0          0 1580.2   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6936193  Sama_0382 bifunctional aconitate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6936193  Sama_0382 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 ! 1580.2   0.0         0         0       1     843 [.       1     853 [.       1     854 [. 0.99

  Alignments for each domain:
  == domain 1  score: 1580.2 bits;  conditional E-value: 0
                         TIGR00117   1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiakgevk 77 
                                       +le+yrkhv eraaeg+ p+pl+a+qva+lvel+kn+p++ee+f+l+ll +r+ppgvdeaayvkagfl aiakg ++
  lcl|FitnessBrowser__SB2B:6936193   1 MLEAYRKHVEERAAEGVVPKPLDAHQVAELVELVKNPPAGEEAFILDLLENRIPPGVDEAAYVKAGFLDAIAKGTAT 77 
                                       79*************************************************************************** PP

                         TIGR00117  78 splisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyakqvleswae 153
                                       sp + ae+avellgtm+ggyn+epli++l+  + ++a+ a kals+tll+fd+f+dv e+ ++ n++akqv+eswa+
  lcl|FitnessBrowser__SB2B:6936193  78 SPILNAERAVELLGTMQGGYNIEPLIHQLD--NDKLAPLAVKALSHTLLMFDSFHDVVEKMNAgNAHAKQVVESWAN 152
                                       ******************************..789*********************99988888************* PP

                         TIGR00117 154 aewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq..........rikalkqk 220
                                       aewfl +++la+ki+ tvfkv+getntddlspapda++rpdiplhalamlkn++++i +          +i++lk++
  lcl|FitnessBrowser__SB2B:6936193 153 AEWFLSRPKLADKISLTVFKVTGETNTDDLSPAPDAWSRPDIPLHALAMLKNARDGIVPdepgvvgpikKIEELKTQ 229
                                       *********************************************************9999**************** PP

                         TIGR00117 221 gvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdvkdlnegdv 297
                                       g+p+ yvgdvvgtgssrksatnsvlwf+g+dipfvpnkragg++lggkiapiffnt+ed+galpie dv+++++gdv
  lcl|FitnessBrowser__SB2B:6936193 230 GFPLVYVGDVVGTGSSRKSATNSVLWFMGDDIPFVPNKRAGGFCLGGKIAPIFFNTMEDAGALPIELDVSKMEMGDV 306
                                       ***************************************************************************** PP

                         TIGR00117 298 ikiypykgeitnket.evvatfklkpetlldevraggripliigrgltdkarealglsesevfkkakapaesakgft 373
                                       i+iypy+g+++ + + ev++ f+lk+++lldevraggripliigrgltdkare+lgl+ s+ f++++++a+++kgft
  lcl|FitnessBrowser__SB2B:6936193 307 IDIYPYEGKVRRHGSdEVISEFELKTDVLLDEVRAGGRIPLIIGRGLTDKAREVLGLGASKEFVRPQDVADTGKGFT 383
                                       *************9889************************************************************ PP

                         TIGR00117 374 laqklvgkacgvkgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvkthktl 450
                                       laqk+vgkacgv g+rpg ycepk+t+vgsqdttg+mtrdelk+la+lgf+adl++qsfchtaaypkpvdv+th+tl
  lcl|FitnessBrowser__SB2B:6936193 384 LAQKMVGKACGVAGVRPGQYCEPKMTSVGSQDTTGPMTRDELKDLACLGFSADLTMQSFCHTAAYPKPVDVNTHHTL 460
                                       ***************************************************************************** PP

                         TIGR00117 451 pdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfk 527
                                       pdfi++rgg++lrpgdgvihswlnrmllpdtvgtggdshtrfp+gisfpagsglvafaaatgvmpldmpesvlvrfk
  lcl|FitnessBrowser__SB2B:6936193 461 PDFIMNRGGISLRPGDGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
                                       ***************************************************************************** PP

                         TIGR00117 528 gelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnke 604
                                       g++qpgitlrdlv+aip+ ai+ glltvekkgk+n+f+grileiegl  lkveqafel+dasaersaagctikl+k+
  lcl|FitnessBrowser__SB2B:6936193 538 GQMQPGITLRDLVHAIPHKAIEMGLLTVEKKGKKNIFSGRILEIEGLEHLKVEQAFELSDASAERSAAGCTIKLDKD 614
                                       ***************************************************************************** PP

                         TIGR00117 605 pvieylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapndpddv 681
                                       p+ieyl+sniv+lk+miaegy+d+rt++rri++me+wl+npel+ead daeyaavieidl++ikepil+apndpdd+
  lcl|FitnessBrowser__SB2B:6936193 615 PIIEYLNSNIVMLKWMIAEGYGDRRTIERRIKGMEEWLKNPELMEADKDAEYAAVIEIDLNNIKEPILCAPNDPDDA 691
                                       ***************************************************************************** PP

                         TIGR00117 682 kllsevagdaidevfigscmtnighfraagkilea.aktvkarlwvvpptrmdeqqlieegyyaifgaagartevpg 757
                                        lls+va  +idevf+gscmtnighfra+gk+l++ ak++++rlw++ppt+md++ql+eegyy+ifg+ gar+e+pg
  lcl|FitnessBrowser__SB2B:6936193 692 VLLSAVANTKIDEVFVGSCMTNIGHFRATGKVLDKfAKSLPTRLWIAPPTKMDKDQLTEEGYYGIFGRVGARIEIPG 768
                                       *********************************9835699************************************* PP

                         TIGR00117 758 cslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkeeylalvsekvesakdklyryl 834
                                       cslcmgnqarv+dgatv+ststrnf+nrlg+ga+vyl+saelaavaallg++p++eey+ +  e +++a d +yryl
  lcl|FitnessBrowser__SB2B:6936193 769 CSLCMGNQARVADGATVVSTSTRNFPNRLGTGANVYLASAELAAVAALLGRLPSPEEYQVYAKEIDATAAD-TYRYL 844
                                       ********************************************************************999.***** PP

                         TIGR00117 835 nfnelenfe 843
                                       nf+e+e ++
  lcl|FitnessBrowser__SB2B:6936193 845 NFDEIESYT 853
                                       ******997 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 0.02s 00:00:00.08 Elapsed: 00:00:00.08
# Mc/sec: 8.35
//
[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