Alignments for a candidate for acn in Shewanella amazonensis SB2B

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.3478.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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 12.06
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources