GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Pseudomonas putida KT2440

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate PP_2339 PP_2339 bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>FitnessBrowser__Putida:PP_2339
          Length = 869

 Score = 1386 bits (3588), Expect = 0.0
 Identities = 677/859 (78%), Positives = 758/859 (88%), Gaps = 3/859 (0%)

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

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AYVKA FL+A+AKGEAKSPL+  + A ELLGTMQGGYNI  L+  LDDA+L  IAA+ L 
Sbjct: 61  AYVKAAFLSAVAKGEAKSPLIDRKHATELLGTMQGGYNIETLVALLDDAELGAIAAEQLK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
           HTLLMFD F+DV EKAKAGN +AK V++SWA  EWF +RPA+A+K T+TVFKV GETNTD
Sbjct: 121 HTLLMFDAFHDVAEKAKAGNTHAKAVLESWAAGEWFTSRPAIADKYTLTVFKVPGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHALAMLK AR+GIEP QPG VGP+ QIEA++ KGFP+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKMARDGIEPQQPGSVGPLAQIEAVKAKGFPVAYVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWF GDDIP+VPNKR GG C G KIAPIF+NTMEDAGALPIE D +N
Sbjct: 241 GTGSSRKSATNSVLWFFGDDIPYVPNKRAGGFCFGTKIAPIFYNTMEDAGALPIEFDCTN 300

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           L MGDVIDVYPYKGEVR H++ EL+ TFELKT+VL+DEVRAGGRIPLI+GRGLT KAR  
Sbjct: 301 LGMGDVIDVYPYKGEVRRHDSDELVTTFELKTEVLLDEVRAGGRIPLIVGRGLTEKARAE 360

Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
           LGL  SD+F++ +  A+S +GF+LAQKMVGRACG+   +G+RPGAYCEPKMT+VGSQDTT
Sbjct: 361 LGLGASDLFKKPEQPADSGKGFTLAQKMVGRACGLPEGQGVRPGAYCEPKMTTVGSQDTT 420

Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477
           GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKP+DV THHTLPDFI  RGGVSLRPGDG
Sbjct: 421 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPIDVTTHHTLPDFIRTRGGVSLRPGDG 480

Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
           +IHSWLNRML+PDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPES+LVRFK
Sbjct: 481 IIHSWLNRMLMPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESILVRFK 540

Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
           GK+QPGITLRDLVHAIP YAI++GLLTVEKKGKKN FSGRILEIEGL DL VEQAFEL+D
Sbjct: 541 GKLQPGITLRDLVHAIPYYAIQKGLLTVEKKGKKNAFSGRILEIEGLDDLTVEQAFELSD 600

Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657
           ASAERSAAGCTIKL ++ I EYL SNI LL+WMI EGYGD RTLERR Q ME WLA PEL
Sbjct: 601 ASAERSAAGCTIKLPEKAIAEYLQSNITLLRWMIGEGYGDARTLERRAQAMEAWLAKPEL 660

Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717
           L ADADAEYA +I+IDLAD+KEP+LCAPNDPDDAR LS+VQGEKIDEVFIGSCMTNIGHF
Sbjct: 661 LSADADAEYAEIIEIDLADVKEPVLCAPNDPDDARLLSSVQGEKIDEVFIGSCMTNIGHF 720

Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
           RAAGKLL+  KG +PTRLW+APPT+MDA QLTEEGYY ++GK+GAR+E+PGCSLCMGNQA
Sbjct: 721 RAAGKLLEKVKGGIPTRLWLAPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQA 780

Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
           RV  G+TVVSTSTRNFPNRLG   NV+LASAELAAVA++IGKLPT EEY  Y   +D  A
Sbjct: 781 RVQTGSTVVSTSTRNFPNRLGDATNVYLASAELAAVASIIGKLPTVEEYMQYAKDIDSMA 840

Query: 838 VDTYRYLNFNQLSQYTEKA 856
            D YRYL+F+Q++++ E A
Sbjct: 841 ADVYRYLSFDQIAEFREAA 859


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: 2184
Number of extensions: 74
Number of successful extensions: 2
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: 869
Length adjustment: 42
Effective length of query: 823
Effective length of database: 827
Effective search space:   680621
Effective search space used:   680621
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 PP_2339 PP_2339 (bifunctional aconitate hydratase 2 and 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.13893.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 1534.9   0.0          0 1534.7   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_2339  PP_2339 bifunctional aconitate h


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_2339  PP_2339 bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1534.7   0.0         0         0       1     844 []       1     857 [.       1     857 [. 0.99

  Alignments for each domain:
  == domain 1  score: 1534.7 bits;  conditional E-value: 0
                           TIGR00117   1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiakge 75 
                                         +le+yrkh+ eraa+gi p+plna+q+a lvellkn+p++ee+fl++l+++rvppgvdeaayvka fl+a+akge
  lcl|FitnessBrowser__Putida:PP_2339   1 MLEAYRKHIEERAALGIVPQPLNAEQTAGLVELLKNPPAGEEAFLVDLITNRVPPGVDEAAYVKAAFLSAVAKGE 75 
                                         79************************************************************************* PP

                           TIGR00117  76 vksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyakqvle 149
                                         +kspli  ++a+ellgtm+ggyn+e+l+ +l+  d+++  +aa+ l++tll+fdaf+dv+e++k+ n++ak vle
  lcl|FitnessBrowser__Putida:PP_2339  76 AKSPLIDRKHATELLGTMQGGYNIETLVALLD--DAELGAIAAEQLKHTLLMFDAFHDVAEKAKAgNTHAKAVLE 148
                                         ********************************..*******************************9********* PP

                           TIGR00117 150 swaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq..........ri 214
                                         swa +ewf  ++++a+k t tvfkv+getntddlspapda++rpdiplhalamlk ++++ie+          +i
  lcl|FitnessBrowser__Putida:PP_2339 149 SWAAGEWFTSRPAIADKYTLTVFKVPGETNTDDLSPAPDAWSRPDIPLHALAMLKMARDGIEPqqpgsvgplaQI 223
                                         **************************************************************99*********** PP

                           TIGR00117 215 kalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdv 289
                                         +a+k kg+pvayvgdvvgtgssrksatnsvlwf+g+dip+vpnkragg+++g kiapif+nt+ed+galpie d 
  lcl|FitnessBrowser__Putida:PP_2339 224 EAVKAKGFPVAYVGDVVGTGSSRKSATNSVLWFFGDDIPYVPNKRAGGFCFGTKIAPIFYNTMEDAGALPIEFDC 298
                                         *************************************************************************** PP

                           TIGR00117 290 kdlnegdvikiypykgeitnket.evvatfklkpetlldevraggripliigrgltdkarealglsesevfkkak 363
                                          +l +gdvi++ypykge++ +++ e+v+tf+lk+e+lldevraggripli+grglt+kar  lgl+ s++fkk++
  lcl|FitnessBrowser__Putida:PP_2339 299 TNLGMGDVIDVYPYKGEVRRHDSdELVTTFELKTEVLLDEVRAGGRIPLIVGRGLTEKARAELGLGASDLFKKPE 373
                                         **********************999************************************************** PP

                           TIGR00117 364 apaesakgftlaqklvgkacgv...kgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfcht 435
                                         +pa+s+kgftlaqk+vg+acg+   +g+rpg+ycepk+ttvgsqdttg+mtrdelk+la+lgf+adlv+qsfcht
  lcl|FitnessBrowser__Putida:PP_2339 374 QPADSGKGFTLAQKMVGRACGLpegQGVRPGAYCEPKMTTVGSQDTTGPMTRDELKDLACLGFSADLVMQSFCHT 448
                                         *********************87679************************************************* PP

                           TIGR00117 436 aaypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaa 510
                                         aaypkp+dv th+tlpdfi +rggv+lrpgdg+ihswlnrml+pdtvgtggdshtrfp+gisfpagsglvafaaa
  lcl|FitnessBrowser__Putida:PP_2339 449 AAYPKPIDVTTHHTLPDFIRTRGGVSLRPGDGIIHSWLNRMLMPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAA 523
                                         *************************************************************************** PP

                           TIGR00117 511 tgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafel 585
                                         tgvmpldmpes+lvrfkg+lqpgitlrdlv+aipyyai+kglltvekkgk+n f+grileiegl dl veqafel
  lcl|FitnessBrowser__Putida:PP_2339 524 TGVMPLDMPESILVRFKGKLQPGITLRDLVHAIPYYAIQKGLLTVEKKGKKNAFSGRILEIEGLDDLTVEQAFEL 598
                                         *************************************************************************** PP

                           TIGR00117 586 tdasaersaagctiklnkepvieylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavi 660
                                         +dasaersaagctikl +++++eyl+sni ll++mi egy+d+rtl+rr +ame+wla pell+adadaeya++i
  lcl|FitnessBrowser__Putida:PP_2339 599 SDASAERSAAGCTIKLPEKAIAEYLQSNITLLRWMIGEGYGDARTLERRAQAMEAWLAKPELLSADADAEYAEII 673
                                         *************************************************************************** PP

                           TIGR00117 661 eidlaeikepilaapndpddvkllsevagdaidevfigscmtnighfraagkileaak.tvkarlwvvpptrmde 734
                                         eidla++kep+l+apndpdd++lls v+g++idevfigscmtnighfraagk+le+ k  +++rlw++ppt+md+
  lcl|FitnessBrowser__Putida:PP_2339 674 EIDLADVKEPVLCAPNDPDDARLLSSVQGEKIDEVFIGSCMTNIGHFRAAGKLLEKVKgGIPTRLWLAPPTKMDA 748
                                         *******************************************************99879*************** PP

                           TIGR00117 735 qqlieegyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgki 809
                                         +ql+eegyy+i+g+agar+e+pgcslcmgnqarv+ g+tv+ststrnf+nrlg  ++vyl+saelaava+++gk+
  lcl|FitnessBrowser__Putida:PP_2339 749 HQLTEEGYYGIYGKAGARMEMPGCSLCMGNQARVQTGSTVVSTSTRNFPNRLGDATNVYLASAELAAVASIIGKL 823
                                         *************************************************************************** PP

                           TIGR00117 810 ptkeeylalvsekvesakdklyrylnfnelenfee 844
                                         pt+eey+++  + +  a d +yryl f+++ +f+e
  lcl|FitnessBrowser__Putida:PP_2339 824 PTVEEYMQYAKDIDSMAAD-VYRYLSFDQIAEFRE 857
                                         *********9888877777.************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (844 nodes)
Target sequences:                          1  (869 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: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 13.15
//
[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