GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Dyella japonica UNC79MFTsu3.2

Align Aconitate hydratase A; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate N515DRAFT_0029 N515DRAFT_0029 aconitase /2-methylcitrate dehydratase (trans-methylaconitate-forming)

Query= SwissProt::Q937N8
         (869 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0029
          Length = 869

 Score = 1511 bits (3912), Expect = 0.0
 Identities = 756/873 (86%), Positives = 808/873 (92%), Gaps = 11/873 (1%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+  R+ L GT LDYFDARAAVEAIQPGAYD LPYTSRVLAENLVRRCDPA L +SL Q
Sbjct: 1   MNTVYRQSLLGTSLDYFDARAAVEAIQPGAYDTLPYTSRVLAENLVRRCDPAILAESLKQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           ++ RKR+ DFPWFPARVVCHDILGQTALVDLAGLRDAIAD+GGDPAKVNPVVPVQLIVDH
Sbjct: 61  IIERKRERDFPWFPARVVCHDILGQTALVDLAGLRDAIADRGGDPAKVNPVVPVQLIVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVECGGFDP+AFA+NRAIEDRRNEDRFHFI+WT+QAF+NVDVIPPGNGIMHQINLEKM
Sbjct: 121 SLAVECGGFDPNAFARNRAIEDRRNEDRFHFIEWTRQAFENVDVIPPGNGIMHQINLEKM 180

Query: 181 SPVIHADN-----GVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLP 235
           SPVI   +     GVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLP
Sbjct: 181 SPVIQVQHDDQGKGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLP 240

Query: 236 DIVGVELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMA 295
           DI+GVELTGKRQPGITATDIVLALTEFLR+EKVVGAYLEFRGEGA+SLTLGDRATISNMA
Sbjct: 241 DIIGVELTGKRQPGITATDIVLALTEFLRQEKVVGAYLEFRGEGAASLTLGDRATISNMA 300

Query: 296 PEYGATAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDL 355
           PEYGATAAMFFID+QT+DYLRLTGR+DEQ++LVETYA+ AGLWAD+L  A+YER L FDL
Sbjct: 301 PEYGATAAMFFIDDQTLDYLRLTGRSDEQVRLVETYAKAAGLWADTLAAAQYERTLSFDL 360

Query: 356 SSVVRNMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTS 415
           SSVVRNMAGPSNPHKRLPT+ LA RGIA        QE  G MPDGAVIIAAITSCTNTS
Sbjct: 361 SSVVRNMAGPSNPHKRLPTADLAARGIA-----GQWQEQPGQMPDGAVIIAAITSCTNTS 415

Query: 416 NPRNVIAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAF 475
           NPRNVIAAALLARNANARGL RKPWVKSSLAPGSKAVELYL+EANLLP+LEKLGFGIVAF
Sbjct: 416 NPRNVIAAALLARNANARGLVRKPWVKSSLAPGSKAVELYLKEANLLPELEKLGFGIVAF 475

Query: 476 ACTTCNGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYA 535
           ACTTCNGMSGALDP IQQEI++RDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYA
Sbjct: 476 ACTTCNGMSGALDPAIQQEIVERDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYA 535

Query: 536 IAGTIRFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITA 595
           IAGTIRFDIE+DVLG D +G+PV LKDIWPSDEEID IVA SVKPEQFRKVYEPMFA T 
Sbjct: 536 IAGTIRFDIEQDVLGIDANGQPVTLKDIWPSDEEIDTIVAASVKPEQFRKVYEPMFARTG 595

Query: 596 ASGESVSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIM 655
            SG   +PLYDWR QSTYIRRPPYWEGALAGERTLK +R LAVLGDNITTDHLSPSNAIM
Sbjct: 596 RSGTRAAPLYDWRAQSTYIRRPPYWEGALAGERTLKGMRALAVLGDNITTDHLSPSNAIM 655

Query: 656 LNSAAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLAR 715
            +SAAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTL+NEMAVVDG+VKKGSLAR
Sbjct: 656 ADSAAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLLNEMAVVDGEVKKGSLAR 715

Query: 716 IEPEGKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFER 775
           +EPEGKV+RMWEAIETYM+RKQPLI+IAGADYGQGSSRDWAAKGVRLAGVE I AEGFER
Sbjct: 716 VEPEGKVMRMWEAIETYMERKQPLIVIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFER 775

Query: 776 IHRTNLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVP 835
           IHRTNLIGMGVLPLEF+PG +R TLG+DGTET+DV G R PRA LTLV++R+NGERVEVP
Sbjct: 776 IHRTNLIGMGVLPLEFQPGTDRKTLGIDGTETFDVTGARTPRAQLTLVIHRRNGERVEVP 835

Query: 836 VTCRLDSDEEVSIYEAGGVL-HFAQDFLESSRA 867
           VTCRLD+ EEVSIYEAGGVL  FAQDFLE+++A
Sbjct: 836 VTCRLDTAEEVSIYEAGGVLQRFAQDFLEAAQA 868


Lambda     K      H
   0.318    0.135    0.398 

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: 2239
Number of extensions: 86
Number of successful extensions: 4
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: 869
Length of database: 869
Length adjustment: 42
Effective length of query: 827
Effective length of database: 827
Effective search space:   683929
Effective search space used:   683929
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 N515DRAFT_0029 N515DRAFT_0029 (aconitase /2-methylcitrate dehydratase (trans-methylaconitate-forming))
to HMM TIGR02333 (acnD: 2-methylisocitrate dehydratase, Fe/S-dependent (EC 4.2.1.99))

# 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/TIGR02333.hmm
# target sequence database:        /tmp/gapView.12478.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02333  [M=858]
Accession:   TIGR02333
Description: 2met_isocit_dHY: 2-methylisocitrate dehydratase, Fe/S-dependent
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 1793.1   0.2          0 1792.9   0.2    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0029  N515DRAFT_0029 aconitase /2-meth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0029  N515DRAFT_0029 aconitase /2-methylcitrate dehydratase (trans-methylaconi
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1792.9   0.2         0         0       1     858 []       2     864 ..       2     864 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1792.9 bits;  conditional E-value: 0
                                    TIGR02333   1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkre 66 
                                                  nt yr++l gt+ldyfdaraaveai+pgayd+lpytsrvlaenlvrr+dp+ l +slkq+ierkre
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0029   2 NTVYRQSLLGTSLDYFDARAAVEAIQPGAYDTLPYTSRVLAENLVRRCDPAILAESLKQIIERKRE 67 
                                                  899*************************************************************** PP

                                    TIGR02333  67 ldfpwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpda 132
                                                   dfpw+parvvchdilgqtalvdlaglrdaia++ggdpa+vnpvv++qlivdhslave+ggfdp+a
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0029  68 RDFPWFPARVVCHDILGQTALVDLAGLRDAIADRGGDPAKVNPVVPVQLIVDHSLAVECGGFDPNA 133
                                                  ****************************************************************** PP

                                    TIGR02333 133 feknraiedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvk.....egvafpd 193
                                                  f++nraiedrrnedrfhfi+wt++af+nvdvip+gngimhqinlekmspv+qv+     +gva+pd
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 134 FARNRAIEDRRNEDRFHFIEWTRQAFENVDVIPPGNGIMHQINLEKMSPVIQVQhddqgKGVAYPD 199
                                                  ****************************************************974444469***** PP

                                    TIGR02333 194 tlvgtdshtphvdalgviaigvggleaetvmlgraslmrlpdivgveltgkrqpgitatdivlalt 259
                                                  t+vgtdshtphvdalgviaigvggleae+vmlgras+mrlpdi+gveltgkrqpgitatdivlalt
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 200 TCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIIGVELTGKRQPGITATDIVLALT 265
                                                  ****************************************************************** PP

                                    TIGR02333 260 eflrkekvvsayleffgegakaltlgdratisnmtpeygataamfaideqtidylkltgreeeqvk 325
                                                  eflr+ekvv+aylef gega +ltlgdratisnm+peygataamf+id+qt+dyl+ltgr +eqv+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 266 EFLRQEKVVGAYLEFRGEGAASLTLGDRATISNMAPEYGATAAMFFIDDQTLDYLRLTGRSDEQVR 331
                                                  ****************************************************************** PP

                                    TIGR02333 326 lvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiakeveeeaeg 391
                                                  lvetyakaaglwad+l  a+yer+l+fdlssvvrn+agpsnph+rl+t+dlaa+gia++++e++ g
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 332 LVETYAKAAGLWADTLAAAQYERTLSFDLSSVVRNMAGPSNPHKRLPTADLAARGIAGQWQEQP-G 396
                                                  ****************************************************************.* PP

                                    TIGR02333 392 lmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvklyleeagll 457
                                                  +mpdgaviiaaitsctntsnprnv+aa+llarnan++gl rkpwvksslapgsk+v+lyl+ea+ll
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 397 QMPDGAVIIAAITSCTNTSNPRNVIAAALLARNANARGLVRKPWVKSSLAPGSKAVELYLKEANLL 462
                                                  ****************************************************************** PP

                                    TIGR02333 458 keleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflasp 523
                                                  +eleklgfgivafacttcngmsgaldp+iqqei++rdlyatavlsgnrnfdgrihpyakqaflasp
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 463 PELEKLGFGIVAFACTTCNGMSGALDPAIQQEIVERDLYATAVLSGNRNFDGRIHPYAKQAFLASP 528
                                                  ****************************************************************** PP

                                    TIGR02333 524 plvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdle 589
                                                  plvvayaiagtirfdie+dvlg+da+g+++ lkdiwpsdeeid++vaa+vkpeqfrkvy+pmf+  
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 529 PLVVAYAIAGTIRFDIEQDVLGIDANGQPVTLKDIWPSDEEIDTIVAASVKPEQFRKVYEPMFART 594
                                                  ***************************************************************987 PP

                                    TIGR02333 590 .daqkkvsplydwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnailldsaa 654
                                                    ++++++plydwr +styirrppywegalagertlkgmr lavlgdnittdhlspsnai++dsaa
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 595 gRSGTRAAPLYDWRAQSTYIRRPPYWEGALAGERTLKGMRALAVLGDNITTDHLSPSNAIMADSAA 660
                                                  6999************************************************************** PP

                                    TIGR02333 655 geylakmglpeedfnsyathrgdhltaqratfanpklfnemvkedgkvkqgslariepegkvtrmw 720
                                                  geyla+mglpeedfnsyathrgdhltaqratfanp l nem+ +dg+vk+gslar+epegkv+rmw
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLLNEMAVVDGEVKKGSLARVEPEGKVMRMW 726
                                                  ****************************************************************** PP

                                    TIGR02333 721 eaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefk 786
                                                  eaietym+rkqpli+iagadygqgssrdwaakgvrlagveai aegferihrtnl+gmgvlplef+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 727 EAIETYMERKQPLIVIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTNLIGMGVLPLEFQ 792
                                                  ****************************************************************** PP

                                    TIGR02333 787 pgtnrktlaldgtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrf 852
                                                  pgt+rktl++dgte++dv g++tpra+ltlv++r+nge++evpvtcrldtaeevs+yeaggvlqrf
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 793 PGTDRKTLGIDGTETFDVTGARTPRAQLTLVIHRRNGERVEVPVTCRLDTAEEVSIYEAGGVLQRF 858
                                                  ****************************************************************** PP

                                    TIGR02333 853 aqdfle 858
                                                  aqdfle
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 859 AQDFLE 864
                                                  ****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (858 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 0.03s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 9.67
//
[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