GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Pseudomonas fluorescens FW300-N2E3

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate AO353_21605 AO353_21605 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 AO353_21605
           bifunctional aconitate hydratase 2/2-methylisocitrate
           dehydratase
          Length = 866

 Score = 1386 bits (3587), Expect = 0.0
 Identities = 668/856 (78%), Positives = 760/856 (88%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           +LE YRKH+ ERAA GI P+PL+A Q A LVELLKNPPAGEE FL+DL+TNRVPPGVDEA
Sbjct: 1   VLEAYRKHIEERAALGIVPQPLNAEQTAGLVELLKNPPAGEEAFLVDLITNRVPPGVDEA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AYVKAGFL+A+AKGEA SPL+  ++A+ELLGTMQGGYNI  L+D LD A+LA +AA  L 
Sbjct: 61  AYVKAGFLSALAKGEATSPLIDKKRAVELLGTMQGGYNIVTLVDLLDSAELAAVAAAQLK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
           HTLLMFD F+DV EKAK GN +A+ V+QSWAD EWF NRP LA+K+++ VFKVTGETNTD
Sbjct: 121 HTLLMFDAFHDVAEKAKNGNVHAQGVLQSWADGEWFKNRPVLADKISLRVFKVTGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHALAMLK AR+GI PD+ GV GP+KQIE ++ +GFP+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKMARDGIVPDEQGVTGPMKQIETMRGEGFPIAYVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWF GDD+P+VPNKR GG C G KIAPIF+NTMEDAGALPIE DV+N
Sbjct: 241 GTGSSRKSATNSVLWFFGDDVPYVPNKRAGGFCFGSKIAPIFYNTMEDAGALPIEFDVTN 300

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           +NMGDVID+YP+ G+V  H + E+L TFE+KT VL+DEVRAGGRIPLIIGRGLT KAR  
Sbjct: 301 MNMGDVIDLYPHAGKVTKHNSDEILTTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARAE 360

Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
           LGLP SD+F++ +  AES +GF+LAQKMVG+ACGV G+RPG YCEPKMT+VGSQDTTGPM
Sbjct: 361 LGLPPSDLFKKPEAPAESTKGFTLAQKMVGKACGVAGVRPGTYCEPKMTTVGSQDTTGPM 420

Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
           TRDELKDLACLGFS DLVMQSFCHTAAYPKP+DV THHTLPDFIM RGGVSLRPGDG+IH
Sbjct: 421 TRDELKDLACLGFSTDLVMQSFCHTAAYPKPIDVTTHHTLPDFIMTRGGVSLRPGDGIIH 480

Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
           SWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPES+LVRFKGKM
Sbjct: 481 SWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESILVRFKGKM 540

Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
           QPG+TLRDLVHAIP YAI+ GLLTVEKKGKKN FSGRILEIEGL +L +EQAFEL+DASA
Sbjct: 541 QPGVTLRDLVHAIPYYAIQAGLLTVEKKGKKNAFSGRILEIEGLDNLSIEQAFELSDASA 600

Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660
           ERSAAGCTIKL+KE I EYL+SNI LL+WMI EGYGD RTLERR Q ME W+ANPEL+ A
Sbjct: 601 ERSAAGCTIKLSKESITEYLSSNITLLRWMIGEGYGDARTLERRAQAMEAWIANPELMVA 660

Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
           DADAEYA +I+IDLADIKEP+LCAPNDPDDAR LS+V GEKIDEVFIGSCMTNIGHFRAA
Sbjct: 661 DADAEYAEIIEIDLADIKEPVLCAPNDPDDARLLSSVAGEKIDEVFIGSCMTNIGHFRAA 720

Query: 721 GKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780
           GKLLD  KGQLPTRLW++PPT+MDA QLTEEGYY ++GK+GAR+E+PGCSLCMGNQARV 
Sbjct: 721 GKLLDQVKGQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQARVE 780

Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840
             +TVVSTSTRNFPNRLG GANV+LASAELA+VA+++G+LPT EEY  Y  ++D  A D 
Sbjct: 781 PNSTVVSTSTRNFPNRLGDGANVYLASAELASVASILGRLPTVEEYMAYAKEIDTMASDV 840

Query: 841 YRYLNFNQLSQYTEKA 856
           YRYL+F+Q++++ E A
Sbjct: 841 YRYLSFDQIAEFREAA 856


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: 2149
Number of extensions: 82
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: 866
Length adjustment: 42
Effective length of query: 823
Effective length of database: 824
Effective search space:   678152
Effective search space used:   678152
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 AO353_21605 AO353_21605 (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.14511.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 1536.0   0.0          0 1535.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605  AO353_21605 bifunctional aconita


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605  AO353_21605 bifunctional aconitate hydratase 2/2-methylisocitrate dehyd
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1535.8   0.0         0         0       1     844 []       1     854 [.       1     854 [. 0.99

  Alignments for each domain:
  == domain 1  score: 1535.8 bits;  conditional E-value: 0
                                     TIGR00117   1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvka 65 
                                                   +le+yrkh+ eraa+gi p+plna+q+a lvellkn+p++ee+fl++l+++rvppgvdeaayvka
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605   1 VLEAYRKHIEERAALGIVPQPLNAEQTAGLVELLKNPPAGEEAFLVDLITNRVPPGVDEAAYVKA 65 
                                                   69*************************************************************** PP

                                     TIGR00117  66 gflaaiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfda 130
                                                   gfl+a+akge++spli  ++avellgtm+ggyn+ +l+++l+   +++a +aa  l++tll+fda
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605  66 GFLSALAKGEATSPLIDKKRAVELLGTMQGGYNIVTLVDLLD--SAELAAVAAAQLKHTLLMFDA 128
                                                   ******************************************..689****************** PP

                                     TIGR00117 131 fddveelskt.neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpd 194
                                                   f+dv+e++k  n +a+ vl+swa++ewf n++ la+ki+  vfkv+getntddlspapda++rpd
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 129 FHDVAEKAKNgNVHAQGVLQSWADGEWFKNRPVLADKISLRVFKVTGETNTDDLSPAPDAWSRPD 193
                                                   ********998****************************************************** PP

                                     TIGR00117 195 iplhalamlknkieeieq..........rikalkqkgvpvayvgdvvgtgssrksatnsvlwflg 249
                                                   iplhalamlk ++++i +          +i++++  g+p+ayvgdvvgtgssrksatnsvlwf+g
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 194 IPLHALAMLKMARDGIVPdeqgvtgpmkQIETMRGEGFPIAYVGDVVGTGSSRKSATNSVLWFFG 258
                                                   ***************999999******************************************** PP

                                     TIGR00117 250 kdipfvpnkragglvlggkiapiffntaedsgalpievdvkdlnegdvikiypykgeitnket.e 313
                                                   +d+p+vpnkragg+++g kiapif+nt+ed+galpie dv ++n+gdvi++yp+ g++t++++ e
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 259 DDVPYVPNKRAGGFCFGSKIAPIFYNTMEDAGALPIEFDVTNMNMGDVIDLYPHAGKVTKHNSdE 323
                                                   ************************************************************99989 PP

                                     TIGR00117 314 vvatfklkpetlldevraggripliigrgltdkarealglsesevfkkakapaesakgftlaqkl 378
                                                   +++tf++k+ +lldevraggripliigrglt+kar  lgl++s++fkk++apaes+kgftlaqk+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 324 ILTTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARAELGLPPSDLFKKPEAPAESTKGFTLAQKM 388
                                                   ***************************************************************** PP

                                     TIGR00117 379 vgkacgvkgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvd 443
                                                   vgkacgv g+rpgtycepk+ttvgsqdttg+mtrdelk+la+lgf++dlv+qsfchtaaypkp+d
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 389 VGKACGVAGVRPGTYCEPKMTTVGSQDTTGPMTRDELKDLACLGFSTDLVMQSFCHTAAYPKPID 453
                                                   ***************************************************************** PP

                                     TIGR00117 444 vkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafa 508
                                                   v th+tlpdfi++rggv+lrpgdg+ihswlnrmllpdtvgtggdshtrfp+gisfpagsglvafa
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 454 VTTHHTLPDFIMTRGGVSLRPGDGIIHSWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFA 518
                                                   ***************************************************************** PP

                                     TIGR00117 509 aatgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileieg 573
                                                   aatgvmpldmpes+lvrfkg++qpg+tlrdlv+aipyyai+ glltvekkgk+n f+grileieg
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 519 AATGVMPLDMPESILVRFKGKMQPGVTLRDLVHAIPYYAIQAGLLTVEKKGKKNAFSGRILEIEG 583
                                                   ***************************************************************** PP

                                     TIGR00117 574 lpdlkveqafeltdasaersaagctiklnkepvieylksnivllkemiaegyedkrtlkrridam 638
                                                   l +l +eqafel+dasaersaagctikl+ke++ eyl sni ll++mi egy+d+rtl+rr +am
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 584 LDNLSIEQAFELSDASAERSAAGCTIKLSKESITEYLSSNITLLRWMIGEGYGDARTLERRAQAM 648
                                                   ***************************************************************** PP

                                     TIGR00117 639 ekwlanpelleadadaeyaavieidlaeikepilaapndpddvkllsevagdaidevfigscmtn 703
                                                   e+w+anpel+ adadaeya++ieidla+ikep+l+apndpdd++lls vag++idevfigscmtn
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 649 EAWIANPELMVADADAEYAEIIEIDLADIKEPVLCAPNDPDDARLLSSVAGEKIDEVFIGSCMTN 713
                                                   ***************************************************************** PP

                                     TIGR00117 704 ighfraagkileaak.tvkarlwvvpptrmdeqqlieegyyaifgaagartevpgcslcmgnqar 767
                                                   ighfraagk+l++ k ++++rlw+ ppt+md++ql+eegyy+i+g+agar+e+pgcslcmgnqar
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 714 IGHFRAAGKLLDQVKgQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQAR 778
                                                   ************9988************************************************* PP

                                     TIGR00117 768 vedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkeeylalvsekvesakdklyr 832
                                                   ve ++tv+ststrnf+nrlg ga+vyl+saela+va++lg++pt+eey+a+  e +  a d +yr
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 779 VEPNSTVVSTSTRNFPNRLGDGANVYLASAELASVASILGRLPTVEEYMAYAKEIDTMASD-VYR 842
                                                   ***************************************************9998887777.*** PP

                                     TIGR00117 833 ylnfnelenfee 844
                                                   yl f+++ +f+e
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 843 YLSFDQIAEFRE 854
                                                   *********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (844 nodes)
Target sequences:                          1  (866 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: 8.95
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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