GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Pseudomonas fluorescens GW456-L13

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate PfGW456L13_3378 Aconitate hydratase 2 (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99)

Query= BRENDA::P36683
         (865 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 Aconitate
           hydratase 2 (EC 4.2.1.3) @ 2-methylisocitrate
           dehydratase (EC 4.2.1.99)
          Length = 866

 Score = 1387 bits (3591), Expect = 0.0
 Identities = 672/856 (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+AIAKGEAKSPL+  ++A+ELLGTMQGGYNI  L++ LDDA+LAP+AA+ L 
Sbjct: 61  AYVKAGFLSAIAKGEAKSPLIDKKRAVELLGTMQGGYNIVTLVNLLDDAELAPVAAEELK 120

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

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

Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWF GDD+P+VPNKR GG C G KIAPIF+NTMEDAGALPIE DVSN
Sbjct: 241 GTGSSRKSATNSVLWFFGDDVPYVPNKRAGGFCFGSKIAPIFYNTMEDAGALPIEFDVSN 300

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           ++MGDVID+YP+ G+V  H T E+L TFE+KT VL+DEVRAGGRIPLIIGRGLT KAR  
Sbjct: 301 MHMGDVIDLYPHAGKVCKHGTDEVLTTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARTE 360

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

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

Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
           SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPES+LVRFKG++
Sbjct: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESILVRFKGEL 540

Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
           QPG+TLRDLVHAIP YAI+ GLLTVEKKGKKN FSGRILEIEGLP L VEQAFEL+DASA
Sbjct: 541 QPGVTLRDLVHAIPYYAIQAGLLTVEKKGKKNAFSGRILEIEGLPKLTVEQAFELSDASA 600

Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660
           ERSAAGCTI+L+KE I EYL SNI LL+WMI EGYGD RTLERR Q ME WLANPELLEA
Sbjct: 601 ERSAAGCTIQLSKESIAEYLQSNITLLRWMIGEGYGDARTLERRAQAMEAWLANPELLEA 660

Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
           D DAEYA VI+IDLADIKEP+LCAPNDPDDAR LS+V GEKIDEVFIGSCMTNIGHFRAA
Sbjct: 661 DKDAEYAEVIEIDLADIKEPVLCAPNDPDDARLLSSVAGEKIDEVFIGSCMTNIGHFRAA 720

Query: 721 GKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780
           GKLL+  KGQLPTRLW++PPT+MDA QLTEEGYY ++GK+GAR+E+PGCSLCMGNQARV 
Sbjct: 721 GKLLEQVKGQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQARVE 780

Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840
             +TVVSTSTRNFPNRLG GANV+LASAELA+VA+++G+LPT EEY  Y  ++D  A D 
Sbjct: 781 PNSTVVSTSTRNFPNRLGDGANVYLASAELASVASILGRLPTVEEYMEYAGKIDSMAADV 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: 2168
Number of extensions: 75
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 PfGW456L13_3378 (Aconitate hydratase 2 (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99))
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.3057.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 1541.2   0.0          0 1541.0   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378  Aconitate hydratase 2 (EC 4.2.1.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378  Aconitate hydratase 2 (EC 4.2.1.3) @ 2-methylisocitrate dehyd
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1541.0   0.0         0         0       1     844 []       1     854 [.       1     854 [. 0.99

  Alignments for each domain:
  == domain 1  score: 1541.0 bits;  conditional E-value: 0
                                               TIGR00117   1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvpp 55 
                                                             +le+yrkh+ eraa+gi p+plna+q+a lvellkn+p++ee+fl++l+++rvpp
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378   1 VLEAYRKHIEERAALGIVPQPLNAEQTAGLVELLKNPPAGEEAFLVDLITNRVPP 55 
                                                             69***************************************************** PP

                                               TIGR00117  56 gvdeaayvkagflaaiakgevksplisaeeavellgtmlggynvepliealeskd 110
                                                             gvdeaayvkagfl+aiakge+kspli  ++avellgtm+ggyn+ +l+++l+  d
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378  56 GVDEAAYVKAGFLSAIAKGEAKSPLIDKKRAVELLGTMQGGYNIVTLVNLLD--D 108
                                                             ****************************************************..* PP

                                               TIGR00117 111 kniakaaakalsktllvfdafddveelskt.neyakqvleswaeaewflnkeela 164
                                                             +++a++aa+ l++tll+fdaf+dv+e++k  n +a+ vl+swa++ewf+ +++la
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 109 AELAPVAAEELKHTLLMFDAFHDVAEKAKNgNVHAQGVLQSWADGEWFVKRPTLA 163
                                                             ****************************998************************ PP

                                               TIGR00117 165 ekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq....... 212
                                                             +ki+  vfkv+getntddlspapda++rpdiplhalamlk ++++i +       
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 164 DKISLRVFKVTGETNTDDLSPAPDAWSRPDIPLHALAMLKMARDGIVPdaqgvtg 218
                                                             **********************************************99999**** PP

                                               TIGR00117 213 ...rikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglv 264
                                                                +i+++++ g+p+ayvgdvvgtgssrksatnsvlwf+g+d+p+vpnkragg++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 219 pmkQIEEMRNAGFPIAYVGDVVGTGSSRKSATNSVLWFFGDDVPYVPNKRAGGFC 273
                                                             ******************************************************* PP

                                               TIGR00117 265 lggkiapiffntaedsgalpievdvkdlnegdvikiypykgeitnket.evvatf 318
                                                             +g kiapif+nt+ed+galpie dv+++++gdvi++yp+ g++ ++ t ev++tf
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 274 FGSKIAPIFYNTMEDAGALPIEFDVSNMHMGDVIDLYPHAGKVCKHGTdEVLTTF 328
                                                             **********************************************9999***** PP

                                               TIGR00117 319 klkpetlldevraggripliigrgltdkarealglsesevfkkakapaesakgft 373
                                                             ++k+ +lldevraggripliigrglt+kar  lgl++s +fkk++apaes+kgft
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 329 EMKTPVLLDEVRAGGRIPLIIGRGLTEKARTELGLPPSTLFKKPEAPAESTKGFT 383
                                                             ******************************************************* PP

                                               TIGR00117 374 laqklvgkacgvkgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlv 428
                                                             laqk+vgkacgv g+rpgtycepk+ttvgsqdttg+mtrdelk+la+lgf++dlv
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 384 LAQKMVGKACGVTGVRPGTYCEPKMTTVGSQDTTGPMTRDELKDLACLGFSTDLV 438
                                                             ******************************************************* PP

                                               TIGR00117 429 lqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvg 483
                                                             +qsfchtaaypkp+dv th+tlpdfi++rggv+lrpgdg+ihswlnrmllpdtvg
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 439 MQSFCHTAAYPKPIDVTTHHTLPDFIMTRGGVSLRPGDGIIHSWLNRMLLPDTVG 493
                                                             ******************************************************* PP

                                               TIGR00117 484 tggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrd 538
                                                             tggdshtrfp+gisfpagsglvafaaatgvmpldmpes+lvrfkgelqpg+tlrd
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 494 TGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESILVRFKGELQPGVTLRD 548
                                                             ******************************************************* PP

                                               TIGR00117 539 lvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaers 593
                                                             lv+aipyyai+ glltvekkgk+n f+grileieglp l veqafel+dasaers
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 549 LVHAIPYYAIQAGLLTVEKKGKKNAFSGRILEIEGLPKLTVEQAFELSDASAERS 603
                                                             ******************************************************* PP

                                               TIGR00117 594 aagctiklnkepvieylksnivllkemiaegyedkrtlkrridamekwlanpell 648
                                                             aagcti+l+ke+++eyl+sni ll++mi egy+d+rtl+rr +ame+wlanpell
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 604 AAGCTIQLSKESIAEYLQSNITLLRWMIGEGYGDARTLERRAQAMEAWLANPELL 658
                                                             ******************************************************* PP

                                               TIGR00117 649 eadadaeyaavieidlaeikepilaapndpddvkllsevagdaidevfigscmtn 703
                                                             ead daeya+vieidla+ikep+l+apndpdd++lls vag++idevfigscmtn
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 659 EADKDAEYAEVIEIDLADIKEPVLCAPNDPDDARLLSSVAGEKIDEVFIGSCMTN 713
                                                             ******************************************************* PP

                                               TIGR00117 704 ighfraagkileaak.tvkarlwvvpptrmdeqqlieegyyaifgaagartevpg 757
                                                             ighfraagk+le+ k ++++rlw+ ppt+md++ql+eegyy+i+g+agar+e+pg
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 714 IGHFRAAGKLLEQVKgQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPG 768
                                                             ************9988*************************************** PP

                                               TIGR00117 758 cslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptk 812
                                                             cslcmgnqarve ++tv+ststrnf+nrlg ga+vyl+saela+va++lg++pt+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 769 CSLCMGNQARVEPNSTVVSTSTRNFPNRLGDGANVYLASAELASVASILGRLPTV 823
                                                             ******************************************************* PP

                                               TIGR00117 813 eeylalvsekvesakdklyrylnfnelenfee 844
                                                             eey+++  + +  a d +yryl f+++ +f+e
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 824 EEYMEYAGKIDSMAAD-VYRYLSFDQIAEFRE 854
                                                             ******8877766666.************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: 00:00:00.07
# Mc/sec: 9.70
//
[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