GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Pseudomonas putida KT2440

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 PP_2336 PP_2336 aconitate hydratase 1

Query= SwissProt::Q937N8
         (869 letters)



>FitnessBrowser__Putida:PP_2336
          Length = 862

 Score = 1459 bits (3777), Expect = 0.0
 Identities = 739/867 (85%), Positives = 782/867 (90%), Gaps = 8/867 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+A RK LPGT LDYFDARAAVEAI+PGAYD LPYTSRVLAENLVRRCDPATL  SL Q
Sbjct: 1   MNTAYRKHLPGTDLDYFDARAAVEAIKPGAYDGLPYTSRVLAENLVRRCDPATLDASLSQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           L+ RKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIAD+GGDPA+VNPVVPVQLIVDH
Sbjct: 61  LIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADKGGDPAQVNPVVPVQLIVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVECGGFDP AF KNRAIEDRRNEDRFHFI+WTK+AFKNVDVI PGNGIMHQINLEKM
Sbjct: 121 SLAVECGGFDPQAFEKNRAIEDRRNEDRFHFINWTKKAFKNVDVIQPGNGIMHQINLEKM 180

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPV+H+D GVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLP+IVGV
Sbjct: 181 SPVVHSDRGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPEIVGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           ELTGK  P ITATD+VLALTEFLRK+KVVGAYLEF GEGA +LTLGDRATISNMAPEYGA
Sbjct: 241 ELTGKLAPNITATDLVLALTEFLRKQKVVGAYLEFHGEGARALTLGDRATISNMAPEYGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TAAMF ID+QTIDYLRLTGR ++Q+KLVETYA+  GLWADSL  A YER L FDLSSVVR
Sbjct: 301 TAAMFAIDQQTIDYLRLTGREEQQVKLVETYAKATGLWADSLGGAVYERTLSFDLSSVVR 360

Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
           NMAGPSNPH R+ TS LA +GIA      S +E  G MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 NMAGPSNPHARVATSDLAAKGIA-----GSWEEVPGQMPDGAVIIAAITSCTNTSNPRNV 415

Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
           IAA L+ARNAN  GL RKPWVKSSLAPGSKAV+LYLEEA L  +LE+LGFGIVAFACTTC
Sbjct: 416 IAAGLIARNANKLGLTRKPWVKSSLAPGSKAVQLYLEEAGLEKELEQLGFGIVAFACTTC 475

Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
           NGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535

Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
           RFDIEKDVLG   DGK + LKDIWPSDEEIDA+V  +VKPEQFRKVY PMFAI    G  
Sbjct: 536 RFDIEKDVLGV-VDGKEIRLKDIWPSDEEIDAVVRAAVKPEQFRKVYIPMFAIEEDRGPK 594

Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
           V+PLYDWRP STYIRRPPYWEGALAGERTL+ +RPLAVL DNITTDHLSPSNAIML+SAA
Sbjct: 595 VAPLYDWRPMSTYIRRPPYWEGALAGERTLRGMRPLAVLPDNITTDHLSPSNAIMLDSAA 654

Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMA-VVDGQVKKGSLARIEPE 719
           GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANP L NEM    DG VK+GSLARIEPE
Sbjct: 655 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVRNDDGSVKQGSLARIEPE 714

Query: 720 GKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRT 779
           GKV RMWEAIETYM RKQPLII+AGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHRT
Sbjct: 715 GKVTRMWEAIETYMQRKQPLIIVAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRT 774

Query: 780 NLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCR 839
           NL+GMGVLPLEFKPG +R TLGLDG+ETYDV+G R PRATLTLVV R NGE +EVPVTCR
Sbjct: 775 NLVGMGVLPLEFKPGTDRKTLGLDGSETYDVLGARTPRATLTLVVTRANGECLEVPVTCR 834

Query: 840 LDSDEEVSIYEAGGVL-HFAQDFLESS 865
           LD+ EEVSIYEAGGVL  FAQDFLE++
Sbjct: 835 LDTAEEVSIYEAGGVLQRFAQDFLEAT 861


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: 2240
Number of extensions: 88
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: 862
Length adjustment: 42
Effective length of query: 827
Effective length of database: 820
Effective search space:   678140
Effective search space used:   678140
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_2336 PP_2336 (aconitate hydratase 1)
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.1387951.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 1883.2   0.0          0 1883.1   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_2336  PP_2336 aconitate hydratase 1


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_2336  PP_2336 aconitate hydratase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1883.1   0.0         0         0       1     858 []       2     859 ..       2     859 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1883.1 bits;  conditional E-value: 0
                           TIGR02333   1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwypar 75 
                                         nt+yrk+lpgtdldyfdaraaveaikpgayd lpytsrvlaenlvrr+dp+tl+asl+qlierkr+ldfpw+par
  lcl|FitnessBrowser__Putida:PP_2336   2 NTAYRKHLPGTDLDYFDARAAVEAIKPGAYDGLPYTSRVLAENLVRRCDPATLDASLSQLIERKRDLDFPWFPAR 76 
                                         899************************************************************************ PP

                           TIGR02333  76 vvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrnedrfhf 150
                                         vvchdilgqtalvdlaglrdaia+kggdpaqvnpvv++qlivdhslave+ggfdp+afeknraiedrrnedrfhf
  lcl|FitnessBrowser__Putida:PP_2336  77 VVCHDILGQTALVDLAGLRDAIADKGGDPAQVNPVVPVQLIVDHSLAVECGGFDPQAFEKNRAIEDRRNEDRFHF 151
                                         *************************************************************************** PP

                           TIGR02333 151 inwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggleaetvml 225
                                         inwtkkafknvdvi++gngimhqinlekmspvv++++gva+pdt+vgtdshtphvdalgviaigvggleae+vml
  lcl|FitnessBrowser__Putida:PP_2336 152 INWTKKAFKNVDVIQPGNGIMHQINLEKMSPVVHSDRGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVML 226
                                         *************************************************************************** PP

                           TIGR02333 226 graslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisnmtpeygat 300
                                         gras+mrlp+ivgveltgk +p+itatd+vlalteflrk+kvv+aylef+gega+altlgdratisnm+peygat
  lcl|FitnessBrowser__Putida:PP_2336 227 GRASWMRLPEIVGVELTGKLAPNITATDLVLALTEFLRKQKVVGAYLEFHGEGARALTLGDRATISNMAPEYGAT 301
                                         *************************************************************************** PP

                           TIGR02333 301 aamfaideqtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsd 375
                                         aamfaid+qtidyl+ltgree+qvklvetyaka+glwadsl  avyer+l+fdlssvvrn+agpsnphar+atsd
  lcl|FitnessBrowser__Putida:PP_2336 302 AAMFAIDQQTIDYLRLTGREEQQVKLVETYAKATGLWADSLGGAVYERTLSFDLSSVVRNMAGPSNPHARVATSD 376
                                         *************************************************************************** PP

                           TIGR02333 376 laakgiakeveeeaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvkly 450
                                         laakgia+++ee++ g+mpdgaviiaaitsctntsnprnv+aagl+arnanklgl+rkpwvksslapgsk+v+ly
  lcl|FitnessBrowser__Putida:PP_2336 377 LAAKGIAGSWEEVP-GQMPDGAVIIAAITSCTNTSNPRNVIAAGLIARNANKLGLTRKPWVKSSLAPGSKAVQLY 450
                                         **************.************************************************************ PP

                           TIGR02333 451 leeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflasppl 525
                                         leeagl+kele+lgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflasppl
  lcl|FitnessBrowser__Putida:PP_2336 451 LEEAGLEKELEQLGFGIVAFACTTCNGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPL 525
                                         *************************************************************************** PP

                           TIGR02333 526 vvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdle.daqkkvsply 599
                                         vvayaiagtirfdiekdvlgv +dgkeirlkdiwpsdeeidavv+aavkpeqfrkvyipmf++e d++ kv+ply
  lcl|FitnessBrowser__Putida:PP_2336 526 VVAYAIAGTIRFDIEKDVLGV-VDGKEIRLKDIWPSDEEIDAVVRAAVKPEQFRKVYIPMFAIEeDRGPKVAPLY 599
                                         *********************.*****************************************989********* PP

                           TIGR02333 600 dwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnailldsaageylakmglpeedfnsyath 674
                                         dwrpmstyirrppywegalagertl+gmrplavl+dnittdhlspsnai+ldsaageylakmglpeedfnsyath
  lcl|FitnessBrowser__Putida:PP_2336 600 DWRPMSTYIRRPPYWEGALAGERTLRGMRPLAVLPDNITTDHLSPSNAIMLDSAAGEYLAKMGLPEEDFNSYATH 674
                                         *************************************************************************** PP

                           TIGR02333 675 rgdhltaqratfanpklfnemvked.gkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqgssrd 748
                                         rgdhltaqratfanpklfnemv++d g+vkqgslariepegkvtrmweaietym+rkqplii+agadygqgssrd
  lcl|FitnessBrowser__Putida:PP_2336 675 RGDHLTAQRATFANPKLFNEMVRNDdGSVKQGSLARIEPEGKVTRMWEAIETYMQRKQPLIIVAGADYGQGSSRD 749
                                         ************************99************************************************* PP

                           TIGR02333 749 waakgvrlagveaivaegferihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkng 823
                                         waakgvrlagveaivaegferihrtnlvgmgvlplefkpgt+rktl+ldg+e+ydv+g++tpra+ltlvvtr+ng
  lcl|FitnessBrowser__Putida:PP_2336 750 WAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKPGTDRKTLGLDGSETYDVLGARTPRATLTLVVTRANG 824
                                         *************************************************************************** PP

                           TIGR02333 824 eklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
                                         e+levpvtcrldtaeevs+yeaggvlqrfaqdfle
  lcl|FitnessBrowser__Putida:PP_2336 825 ECLEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 859
                                         *********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (858 nodes)
Target sequences:                          1  (862 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 36.96
//
[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