GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Shewanella oneidensis MR-1

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate 199624 SO0432 aconitate hydratase 2 (NCBI ptt file)

Query= BRENDA::P36683
         (865 letters)



>FitnessBrowser__MR1:199624
          Length = 865

 Score = 1437 bits (3720), Expect = 0.0
 Identities = 700/865 (80%), Positives = 784/865 (90%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           MLE YRKHVAERAAEG+ PKPLDA+Q+A LV+L++NPPAGEE F+LDLL NR+PPGVDEA
Sbjct: 1   MLEAYRKHVAERAAEGVVPKPLDAHQVAELVKLVQNPPAGEEAFVLDLLENRIPPGVDEA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AYVKA FL A+AKG A SP+L+ E+A ELLGTMQGGYNI PLI  LD+  LAP+AAKAL+
Sbjct: 61  AYVKAAFLDAVAKGTATSPILSAERATELLGTMQGGYNIEPLIAQLDNPALAPLAAKALA 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
           HTLLMFD+F+DV EK +AGN++AKQV+++WA+A+W+L+RP LA+K+T+TVFKV+GETNTD
Sbjct: 121 HTLLMFDSFHDVVEKMEAGNQFAKQVVEAWANADWYLSRPKLADKVTLTVFKVSGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHALAMLKNAR+GIEPD  G VGPIK++E L+ KGFPL YVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKNARDGIEPDVAGSVGPIKKLEELKTKGFPLVYVGDVV 240

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

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           + MGDVID+YPY G V+ H + E+++ F LKTDVL+DEVRAGGRIPLIIGRGLT KAR  
Sbjct: 301 MEMGDVIDIYPYAGVVKRHGSDEVISEFSLKTDVLLDEVRAGGRIPLIIGRGLTDKARAV 360

Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
           LGLP S+VF + +D+A++ +G++LAQKMVG+ACGV G+RPG YCEPKMTSVGSQDTTGPM
Sbjct: 361 LGLPASEVFVRPQDIADNGKGYTLAQKMVGKACGVAGVRPGQYCEPKMTSVGSQDTTGPM 420

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

Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
           SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM
Sbjct: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540

Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
           QPGITLRDLVHAIPL AI+ G+LTVEKKGK NIFSGR+LEIEGL  LKVEQAFEL+DASA
Sbjct: 541 QPGITLRDLVHAIPLKAIELGMLTVEKKGKVNIFSGRVLEIEGLESLKVEQAFELSDASA 600

Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660
           ERSAAGCTIKL+KEPIIEYLNSNI +LKWMIAEGYGDRRT+ERRI+GME+WLANPEL+ A
Sbjct: 601 ERSAAGCTIKLDKEPIIEYLNSNITMLKWMIAEGYGDRRTIERRIKGMEEWLANPELMSA 660

Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
           DADAEY AVI+IDL +IKEPILCAPNDPDDA  LS+V   KIDEVF+GSCMTNIGHFRA 
Sbjct: 661 DADAEYTAVIEIDLNEIKEPILCAPNDPDDAVLLSSVAQTKIDEVFVGSCMTNIGHFRAT 720

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

Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840
           +GATVVSTSTRNFPNRLGTGANV+LASAELAAVAAL+G+LPT EEYQ Y  ++D TA DT
Sbjct: 781 EGATVVSTSTRNFPNRLGTGANVYLASAELAAVAALLGRLPTVEEYQEYAKELDATAADT 840

Query: 841 YRYLNFNQLSQYTEKADGVIFQTAV 865
           YRYLNF+Q+  YT+KA  VIFQ+AV
Sbjct: 841 YRYLNFDQIDSYTKKASQVIFQSAV 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: 2130
Number of extensions: 81
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 199624 SO0432 (aconitate hydratase 2 (NCBI ptt file))
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.31245.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 1571.2   0.0          0 1571.0   0.0    1.0  1  lcl|FitnessBrowser__MR1:199624  SO0432 aconitate hydratase 2 (NC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199624  SO0432 aconitate hydratase 2 (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1571.0   0.0         0         0       1     843 [.       1     853 [.       1     854 [. 0.99

  Alignments for each domain:
  == domain 1  score: 1571.0 bits;  conditional E-value: 0
                       TIGR00117   1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiakgevksp 79 
                                     +le+yrkhvaeraaeg+ p+pl+a+qva+lv+l++n+p++ee+f+l+ll +r+ppgvdeaayvka fl a+akg ++sp
  lcl|FitnessBrowser__MR1:199624   1 MLEAYRKHVAERAAEGVVPKPLDAHQVAELVKLVQNPPAGEEAFVLDLLENRIPPGVDEAAYVKAAFLDAVAKGTATSP 79 
                                     79***************************************************************************** PP

                       TIGR00117  80 lisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyakqvleswaeaewf 157
                                      +sae+a+ellgtm+ggyn+epli +l+  +  +a+ aakal +tll+fd+f+dv e+ ++ n++akqv+e+wa+a+w+
  lcl|FitnessBrowser__MR1:199624  80 ILSAERATELLGTMQGGYNIEPLIAQLD--NPALAPLAAKALAHTLLMFDSFHDVVEKMEAgNQFAKQVVEAWANADWY 156
                                     ****************************..899**********************9999988***************** PP

                       TIGR00117 158 lnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq..........rikalkqkgvpvay 226
                                     l +++la+k+t tvfkv+getntddlspapda++rpdiplhalamlkn++++ie+          ++++lk+kg+p+ y
  lcl|FitnessBrowser__MR1:199624 157 LSRPKLADKVTLTVFKVSGETNTDDLSPAPDAWSRPDIPLHALAMLKNARDGIEPdvagsvgpikKLEELKTKGFPLVY 235
                                     ******************************************************************************* PP

                       TIGR00117 227 vgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdvkdlnegdvikiypykg 305
                                     vgdvvgtgssrksatnsvlwf+g+dipfvpnkragg++lggkiapiffnt+ed+galpie dv+++++gdvi+iypy g
  lcl|FitnessBrowser__MR1:199624 236 VGDVVGTGSSRKSATNSVLWFMGDDIPFVPNKRAGGFCLGGKIAPIFFNTMEDAGALPIELDVSKMEMGDVIDIYPYAG 314
                                     ******************************************************************************* PP

                       TIGR00117 306 eitnket.evvatfklkpetlldevraggripliigrgltdkarealglsesevfkkakapaesakgftlaqklvgkac 383
                                      ++ + + ev++ f lk+++lldevraggripliigrgltdkar +lgl+ sevf+++++ a+++kg+tlaqk+vgkac
  lcl|FitnessBrowser__MR1:199624 315 VVKRHGSdEVISEFSLKTDVLLDEVRAGGRIPLIIGRGLTDKARAVLGLPASEVFVRPQDIADNGKGYTLAQKMVGKAC 393
                                     ****99889********************************************************************** PP

                       TIGR00117 384 gvkgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvkthktlpdfisqrggval 462
                                     gv g+rpg ycepk+t+vgsqdttg+mtrdelk+la+lgf+adl++qsfchtaaypkpvdv+th+tlpdfi++rggv+l
  lcl|FitnessBrowser__MR1:199624 394 GVAGVRPGQYCEPKMTSVGSQDTTGPMTRDELKDLACLGFSADLTMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSL 472
                                     ******************************************************************************* PP

                       TIGR00117 463 rpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrdlvn 541
                                     rpgdgvihswlnrmllpdtvgtggdshtrfp+gisfpagsglvafaaatgvmpldmpesvlvrfkg++qpgitlrdlv+
  lcl|FitnessBrowser__MR1:199624 473 RPGDGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGITLRDLVH 551
                                     ******************************************************************************* PP

                       TIGR00117 542 aipyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkepvieylksnivllkem 620
                                     aip+ ai+ g+ltvekkgkvn+f+gr+leiegl  lkveqafel+dasaersaagctikl+kep+ieyl+sni +lk+m
  lcl|FitnessBrowser__MR1:199624 552 AIPLKAIELGMLTVEKKGKVNIFSGRVLEIEGLESLKVEQAFELSDASAERSAAGCTIKLDKEPIIEYLNSNITMLKWM 630
                                     ******************************************************************************* PP

                       TIGR00117 621 iaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapndpddvkllsevagdaidevfigs 699
                                     iaegy+d+rt++rri++me+wlanpel++adadaey+avieidl+eikepil+apndpdd+ lls va  +idevf+gs
  lcl|FitnessBrowser__MR1:199624 631 IAEGYGDRRTIERRIKGMEEWLANPELMSADADAEYTAVIEIDLNEIKEPILCAPNDPDDAVLLSSVAQTKIDEVFVGS 709
                                     ******************************************************************************* PP

                       TIGR00117 700 cmtnighfraagkilea.aktvkarlwvvpptrmdeqqlieegyyaifgaagartevpgcslcmgnqarvedgatvfst 777
                                     cmtnighfra+gk+l++ akt+++rlw++ppt+md++ql+eegyy+ifg+ gar+e+pgcslcmgnqarv++gatv+st
  lcl|FitnessBrowser__MR1:199624 710 CMTNIGHFRATGKMLDKfAKTLPTRLWIAPPTKMDKDQLTEEGYYGIFGRVGARIEIPGCSLCMGNQARVAEGATVVST 788
                                     ***************983569********************************************************** PP

                       TIGR00117 778 strnfdnrlgkgakvylgsaelaavaallgkiptkeeylalvsekvesakdklyrylnfnelenfe 843
                                     strnf+nrlg+ga+vyl+saelaavaallg++pt+eey+++  e +++a d +yrylnf++++ ++
  lcl|FitnessBrowser__MR1:199624 789 STRNFPNRLGTGANVYLASAELAAVAALLGRLPTVEEYQEYAKELDATAAD-TYRYLNFDQIDSYT 853
                                     ***********************************************9999.***********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 0.01s 00:00:00.05 Elapsed: 00:00:00.06
# Mc/sec: 11.62
//
[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