GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Pseudomonas fluorescens FW300-N1B4

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate Pf1N1B4_4564 Aconitate hydratase 2 (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99)

Query= BRENDA::P36683
         (865 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564
          Length = 866

 Score = 1382 bits (3578), Expect = 0.0
 Identities = 667/856 (77%), Positives = 759/856 (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+AKGEAKSPL+  ++A+ELLGTMQGGYNI  L++ LDDA+LAP+AA+ L 
Sbjct: 61  AYVKAGFLSALAKGEAKSPLIDKKRAVELLGTMQGGYNIVTLVNLLDDAELAPVAAEELK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
           HTLLMFD F+DV E+AK GN +AK V+QSWAD EWF NRP LA+K+++ VFKVTGETNTD
Sbjct: 121 HTLLMFDAFHDVAERAKNGNVHAKGVLQSWADGEWFKNRPVLADKISLRVFKVTGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHALAMLK AR+GI PD  G +GP+KQIE ++  GFP+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKMARDGIVPDVQGSIGPMKQIEEMRNSGFPIAYVGDVV 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 T E++ TFE+KT VL+DEVRAGGRIPLIIGRGLT KAR  
Sbjct: 301 INMGDVIDLYPHAGKVCKHGTDEVITTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARAE 360

Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
           LGLP  D+F++     ES +GF+LAQKMVG+ACGV G+RPG YCEPKMT+VGSQDTTGPM
Sbjct: 361 LGLPAFDLFKKPDAPIESTKGFTLAQKMVGKACGVAGVRPGTYCEPKMTTVGSQDTTGPM 420

Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
           TRDELKDLACLGFSADLVMQSFCHTAAYPKP+DV THHTLPDFIM RGGVSLRPGDG+IH
Sbjct: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPIDVTTHHTLPDFIMTRGGVSLRPGDGIIH 480

Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
           SWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPES+LVRFKG+M
Sbjct: 481 SWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESILVRFKGEM 540

Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
           QPG+TLRDLVHAIP +AI+ GLLTVEKKGKKN FSGRILEIEGL +L +EQAFEL+DASA
Sbjct: 541 QPGVTLRDLVHAIPYFAIQAGLLTVEKKGKKNAFSGRILEIEGLDNLSIEQAFELSDASA 600

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

Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
           DADAEYA VI+IDLADIKEP+LCAPNDPDDAR LS+V GEKIDEVFIGSCMTNIGHFRAA
Sbjct: 661 DADAEYAEVIEIDLADIKEPVLCAPNDPDDARLLSSVAGEKIDEVFIGSCMTNIGHFRAA 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 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: 2150
Number of extensions: 77
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 Pf1N1B4_4564 (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.18453.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 1534.1   0.0          0 1533.9   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564  Aconitate hydratase 2 (EC 4.2.1.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564  Aconitate hydratase 2 (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1533.9   0.0         0         0       1     844 []       1     854 [.       1     854 [. 0.99

  Alignments for each domain:
  == domain 1  score: 1533.9 bits;  conditional E-value: 0
                                      TIGR00117   1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvk 64 
                                                    +le+yrkh+ eraa+gi p+plna+q+a lvellkn+p++ee+fl++l+++rvppgvdeaayvk
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564   1 VLEAYRKHIEERAALGIVPQPLNAEQTAGLVELLKNPPAGEEAFLVDLITNRVPPGVDEAAYVK 64 
                                                    69************************************************************** PP

                                      TIGR00117  65 agflaaiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvf 128
                                                    agfl+a+akge+kspli  ++avellgtm+ggyn+ +l+++l+  d+++a++aa+ l++tll+f
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564  65 AGFLSALAKGEAKSPLIDKKRAVELLGTMQGGYNIVTLVNLLD--DAELAPVAAEELKHTLLMF 126
                                                    *******************************************..******************* PP

                                      TIGR00117 129 dafddveelskt.neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaft 191
                                                    daf+dv+e +k  n +ak vl+swa++ewf n++ la+ki+  vfkv+getntddlspapda++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 127 DAFHDVAERAKNgNVHAKGVLQSWADGEWFKNRPVLADKISLRVFKVTGETNTDDLSPAPDAWS 190
                                                    **********998*************************************************** PP

                                      TIGR00117 192 rpdiplhalamlknkieeieq..........rikalkqkgvpvayvgdvvgtgssrksatnsvl 245
                                                    rpdiplhalamlk ++++i +          +i+++++ g+p+ayvgdvvgtgssrksatnsvl
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 191 RPDIPLHALAMLKMARDGIVPdvqgsigpmkQIEEMRNSGFPIAYVGDVVGTGSSRKSATNSVL 254
                                                    *******************99999**************************************** PP

                                      TIGR00117 246 wflgkdipfvpnkragglvlggkiapiffntaedsgalpievdvkdlnegdvikiypykgeitn 309
                                                    wf+g+d+p+vpnkragg+++g kiapif+nt+ed+galpie dv ++n+gdvi++yp+ g++ +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 255 WFFGDDVPYVPNKRAGGFCFGSKIAPIFYNTMEDAGALPIEFDVTNINMGDVIDLYPHAGKVCK 318
                                                    **************************************************************** PP

                                      TIGR00117 310 ket.evvatfklkpetlldevraggripliigrgltdkarealglsesevfkkakapaesakgf 372
                                                    + t ev++tf++k+ +lldevraggripliigrglt+kar  lgl+  ++fkk+ ap es+kgf
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 319 HGTdEVITTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARAELGLPAFDLFKKPDAPIESTKGF 382
                                                    *9999*********************************************************** PP

                                      TIGR00117 373 tlaqklvgkacgvkgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfchta 436
                                                    tlaqk+vgkacgv g+rpgtycepk+ttvgsqdttg+mtrdelk+la+lgf+adlv+qsfchta
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 383 TLAQKMVGKACGVAGVRPGTYCEPKMTTVGSQDTTGPMTRDELKDLACLGFSADLVMQSFCHTA 446
                                                    **************************************************************** PP

                                      TIGR00117 437 aypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpa 500
                                                    aypkp+dv th+tlpdfi++rggv+lrpgdg+ihswlnrmllpdtvgtggdshtrfp+gisfpa
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 447 AYPKPIDVTTHHTLPDFIMTRGGVSLRPGDGIIHSWLNRMLLPDTVGTGGDSHTRFPMGISFPA 510
                                                    **************************************************************** PP

                                      TIGR00117 501 gsglvafaaatgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvf 564
                                                    gsglvafaaatgvmpldmpes+lvrfkge+qpg+tlrdlv+aipy+ai+ glltvekkgk+n f
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 511 GSGLVAFAAATGVMPLDMPESILVRFKGEMQPGVTLRDLVHAIPYFAIQAGLLTVEKKGKKNAF 574
                                                    **************************************************************** PP

                                      TIGR00117 565 ngrileieglpdlkveqafeltdasaersaagctiklnkepvieylksnivllkemiaegyedk 628
                                                    +grileiegl +l +eqafel+dasaersaagctikl+ke++ eyl+sni ll++mi egy+d 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 575 SGRILEIEGLDNLSIEQAFELSDASAERSAAGCTIKLSKESITEYLQSNITLLRWMIGEGYGDV 638
                                                    **************************************************************** PP

                                      TIGR00117 629 rtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapndpddvkllsevagdai 692
                                                    rtl+rr +ame+w+anpel+ adadaeya+vieidla+ikep+l+apndpdd++lls vag++i
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 639 RTLERRAQAMEAWIANPELMVADADAEYAEVIEIDLADIKEPVLCAPNDPDDARLLSSVAGEKI 702
                                                    **************************************************************** PP

                                      TIGR00117 693 devfigscmtnighfraagkileaak.tvkarlwvvpptrmdeqqlieegyyaifgaagartev 755
                                                    devfigscmtnighfraagk+l++ k ++++rlw+ ppt+md++ql+eegyy+i+g+agar+e+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 703 DEVFIGSCMTNIGHFRAAGKLLDQVKgQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEM 766
                                                    ***********************9988************************************* PP

                                      TIGR00117 756 pgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkeeylalv 819
                                                    pgcslcmgnqarve ++tv+ststrnf+nrlg ga+vyl+saela+va++lg++pt+eey+++ 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 767 PGCSLCMGNQARVEPNSTVVSTSTRNFPNRLGDGANVYLASAELASVASILGRLPTVEEYMEYA 830
                                                    ***************************************************************8 PP

                                      TIGR00117 820 sekvesakdklyrylnfnelenfee 844
                                                     + +  a d +yryl f+++ +f+e
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 831 GKIDSMAAD-VYRYLSFDQIAEFRE 854
                                                    877766666.************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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 10.64
//
[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