GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Pseudomonas fluorescens FW300-N2E3

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 AO353_00890 AO353_00890 Fe/S-dependent 2-methylisocitrate dehydratase AcnD

Query= SwissProt::Q937N8
         (869 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 AO353_00890
           Fe/S-dependent 2-methylisocitrate dehydratase AcnD
          Length = 864

 Score = 1449 bits (3752), Expect = 0.0
 Identities = 729/868 (83%), Positives = 782/868 (90%), Gaps = 6/868 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+  RK LPG+ LDYFD RAAVEAIQPGAYD LPYTSRVLAENLVRRCDPATLT+SL Q
Sbjct: 1   MNTDFRKSLPGSHLDYFDTRAAVEAIQPGAYDTLPYTSRVLAENLVRRCDPATLTESLKQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
            + RKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIA QGGDPA+VNPVVP QLIVDH
Sbjct: 61  FIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVE GGFDP+AF KNRAIEDRRNEDRFHFI+WTK+AFKNVDVIPPGNGIMHQINLEKM
Sbjct: 121 SLAVERGGFDPEAFEKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKM 180

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPVI   +GVA+PDTCVGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRASWMRLP+ VGV
Sbjct: 181 SPVIQVRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPESVGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           ELTGK QPGITATD+VLALTEFLRK+KVVGA+LEF GEGAS+LTLGDRATISNMAPEYGA
Sbjct: 241 ELTGKLQPGITATDMVLALTEFLRKQKVVGAWLEFFGEGASALTLGDRATISNMAPEYGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TAAMF+ID+QTIDYL+LTGR DEQ++LVE YA+T GLWADSLK A+YER L FDLSSVVR
Sbjct: 301 TAAMFYIDQQTIDYLKLTGREDEQVQLVENYAKTTGLWADSLKGAQYERGLTFDLSSVVR 360

Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
           NMAGPSNPH R+ TS LA +GI+   D     +  G MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 NMAGPSNPHARVATSDLAAQGISGQWD-----DVPGQMPDGAVIIAAITSCTNTSNPRNV 415

Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
           IAA LLARNAN  GL RKPWVKSSLAPGSK V LYL+EA L  +LE+LGFG+VAFACTTC
Sbjct: 416 IAAGLLARNANKLGLTRKPWVKSSLAPGSKTVALYLDEAGLTSELEQLGFGVVAFACTTC 475

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

Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
           RFDIEKDVLG   DGK + LKDIWPSDEEIDA+V  SVKPEQFR+VY PMFAI   +G  
Sbjct: 536 RFDIEKDVLGLSADGKEIRLKDIWPSDEEIDAVVKASVKPEQFRQVYIPMFAIHEDTGPK 595

Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
           V PLYDWR  STYIRRPPYWEGALAG R LK +RPLAVL DNITTDHLSPSNAIML+SAA
Sbjct: 596 VKPLYDWREMSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIMLDSAA 655

Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
           GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANP L NEM   +G+VK+GSLAR+EPEG
Sbjct: 656 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVQENGKVKQGSLARVEPEG 715

Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
           +V+RMWEAIETYM+RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE I AEGFERIHRTN
Sbjct: 716 QVMRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTN 775

Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
           L+GMGVLPLEFKPG +R TLG+DGTET+DVIGER PRATLTLV+ RKNGE+V VPVTCRL
Sbjct: 776 LVGMGVLPLEFKPGTDRKTLGIDGTETFDVIGERTPRATLTLVITRKNGEQVSVPVTCRL 835

Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESSRA 867
           D+ EEVSIYEAGGVL  FAQDFLES+ A
Sbjct: 836 DTAEEVSIYEAGGVLQRFAQDFLESAVA 863


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: 2203
Number of extensions: 79
Number of successful extensions: 3
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: 864
Length adjustment: 42
Effective length of query: 827
Effective length of database: 822
Effective search space:   679794
Effective search space used:   679794
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 AO353_00890 AO353_00890 (Fe/S-dependent 2-methylisocitrate dehydratase AcnD)
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.16890.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 1840.6   0.0          0 1840.4   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890  AO353_00890 Fe/S-dependent 2-met


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890  AO353_00890 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1840.4   0.0         0         0       1     858 []       2     859 ..       2     859 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1840.4 bits;  conditional E-value: 0
                                     TIGR02333   1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkr 65 
                                                   nt +rk+lpg++ldyfd+raaveai+pgayd+lpytsrvlaenlvrr+dp+tl++slkq+ierkr
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890   2 NTDFRKSLPGSHLDYFDTRAAVEAIQPGAYDTLPYTSRVLAENLVRRCDPATLTESLKQFIERKR 66 
                                                   799************************************************************** PP

                                     TIGR02333  66 eldfpwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdp 130
                                                   +ldfpw+parvvchdilgqtalvdlaglrdaia +ggdpaqvnpvv+tqlivdhslave ggfdp
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890  67 DLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDHSLAVERGGFDP 131
                                                   ***************************************************************** PP

                                     TIGR02333 131 dafeknraiedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtl 195
                                                   +afeknraiedrrnedrfhfinwtkkafknvdvip+gngimhqinlekmspv+qv++gvafpdt+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 132 EAFEKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKMSPVIQVRDGVAFPDTC 196
                                                   ***************************************************************** PP

                                     TIGR02333 196 vgtdshtphvdalgviaigvggleaetvmlgraslmrlpdivgveltgkrqpgitatdivlalte 260
                                                   vgtdshtphvdalgviaigvggleae+vmlgras+mrlp+ vgveltgk qpgitatd+vlalte
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 197 VGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPESVGVELTGKLQPGITATDMVLALTE 261
                                                   ***************************************************************** PP

                                     TIGR02333 261 flrkekvvsayleffgegakaltlgdratisnmtpeygataamfaideqtidylkltgreeeqvk 325
                                                   flrk+kvv+a+leffgega altlgdratisnm+peygataamf+id+qtidylkltgre+eqv+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 262 FLRKQKVVGAWLEFFGEGASALTLGDRATISNMAPEYGATAAMFYIDQQTIDYLKLTGREDEQVQ 326
                                                   ***************************************************************** PP

                                     TIGR02333 326 lvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiakeveeeae 390
                                                   lve yak++glwadslk a+yer l+fdlssvvrn+agpsnphar+atsdlaa+gi++++++++ 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 327 LVENYAKTTGLWADSLKGAQYERGLTFDLSSVVRNMAGPSNPHARVATSDLAAQGISGQWDDVP- 390
                                                   ****************************************************************. PP

                                     TIGR02333 391 glmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvklyleeag 455
                                                   g+mpdgaviiaaitsctntsnprnv+aagllarnanklgl+rkpwvksslapgsk+v lyl+eag
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 391 GQMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANKLGLTRKPWVKSSLAPGSKTVALYLDEAG 455
                                                   ***************************************************************** PP

                                     TIGR02333 456 llkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqafl 520
                                                   l +ele+lgfg+vafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqafl
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 456 LTSELEQLGFGVVAFACTTCNGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFL 520
                                                   ***************************************************************** PP

                                     TIGR02333 521 aspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipm 585
                                                   aspplvvayaiagtirfdiekdvlg+ adgkeirlkdiwpsdeeidavv+a+vkpeqfr+vyipm
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 521 ASPPLVVAYAIAGTIRFDIEKDVLGLSADGKEIRLKDIWPSDEEIDAVVKASVKPEQFRQVYIPM 585
                                                   ***************************************************************** PP

                                     TIGR02333 586 fdle.daqkkvsplydwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnail 649
                                                   f+++ d++ kv plydwr mstyirrppywegalag r lkgmrplavl+dnittdhlspsnai+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 586 FAIHeDTGPKVKPLYDWREMSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIM 650
                                                   ***989*********************************************************** PP

                                     TIGR02333 650 ldsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemvkedgkvkqgslariepeg 714
                                                   ldsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemv+e+gkvkqgslar+epeg
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 651 LDSAAGEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVQENGKVKQGSLARVEPEG 715
                                                   ***************************************************************** PP

                                     TIGR02333 715 kvtrmweaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmg 779
                                                   +v+rmweaietym+rkqpliiiagadygqgssrdwaakgvrlagveai aegferihrtnlvgmg
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 716 QVMRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTNLVGMG 780
                                                   ***************************************************************** PP

                                     TIGR02333 780 vlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvye 844
                                                   vlplefkpgt+rktl++dgte++dv+ge+tpra+ltlv+trknge++ vpvtcrldtaeevs+ye
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 781 VLPLEFKPGTDRKTLGIDGTETFDVIGERTPRATLTLVITRKNGEQVSVPVTCRLDTAEEVSIYE 845
                                                   ***************************************************************** PP

                                     TIGR02333 845 aggvlqrfaqdfle 858
                                                   aggvlqrfaqdfle
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 846 AGGVLQRFAQDFLE 859
                                                   ************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (858 nodes)
Target sequences:                          1  (864 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: 00:00:00.05
# 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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