GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Shewanella sp. ANA-3

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 7026694 Shewana3_3827 aconitate hydratase (RefSeq)

Query= SwissProt::Q937N8
         (869 letters)



>FitnessBrowser__ANA3:7026694
          Length = 863

 Score = 1452 bits (3759), Expect = 0.0
 Identities = 721/866 (83%), Positives = 786/866 (90%), Gaps = 6/866 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+  RKPLPGT LDYFD R AVEAI PGAY KLPYTSRVLAENLVRRC+P  LT SL Q
Sbjct: 1   MNTLYRKPLPGTALDYFDTREAVEAISPGAYAKLPYTSRVLAENLVRRCEPEALTASLKQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           ++  K++LDFPWFPARVVCHDILGQTALVDLAGLRDAIA +GGDPA+VNPVVP QLIVDH
Sbjct: 61  IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVE GGFD DAFAKNRAIEDRRNEDRFHFI+WT++AFKN+DVIP GNGIMHQINLE+M
Sbjct: 121 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 180

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPV+HA +GVA+PDT VGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRAS+MRLPDI+GV
Sbjct: 181 SPVVHARDGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           ELTGK QPGITATDIVLALTEFLRKEKVV +YLEF GEGA +LTLGDRATISNM PE+GA
Sbjct: 241 ELTGKPQPGITATDIVLALTEFLRKEKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TAAMF+ID+QT+DYL LTGR+DEQ+KLVETYA+T GLW+D LK+AEY R L FDLSSVVR
Sbjct: 301 TAAMFYIDQQTLDYLTLTGRSDEQVKLVETYAKTTGLWSDDLKHAEYPRTLHFDLSSVVR 360

Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
            +AGPSNPH R+PT+ LA RGI+        +   GLMPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 TIAGPSNPHARVPTTELAARGIS-----GVVENEPGLMPDGAVIIAAITSCTNTSNPRNV 415

Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
           IAA LLARNANA+GL+RKPWVK+SLAPGSKAV+LYLEEANLLP+LE LGFGIV FACTTC
Sbjct: 416 IAAGLLARNANAKGLSRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTC 475

Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
           NGMSGALDP IQQE+IDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535

Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
           RFDIEKDVLG D+DG PV L DIWPSD EIDA++AKSVKPEQFR+VYEPMF ++   G+ 
Sbjct: 536 RFDIEKDVLGHDKDGNPVRLIDIWPSDAEIDAVIAKSVKPEQFRRVYEPMFDLSVDYGDK 595

Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
           V+PLYDWRPQSTYIRRPPYWEGALAGERTLK +RPLAVLGDNITTDHLSPSNAIM++SAA
Sbjct: 596 VTPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAA 655

Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
           GEYL +MGLPEEDFNSYATHRGDHLTAQRATFANP L NEMAVVDG+VK+GSLARIEPEG
Sbjct: 656 GEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAVVDGKVKQGSLARIEPEG 715

Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
           +V RMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHRTN
Sbjct: 716 QVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTN 775

Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
           L+GMGVLPLEFK G NR T G+DGTE +DV G+  PRA LT+++ RKNGERVEVPVTCRL
Sbjct: 776 LVGMGVLPLEFKAGENRATYGIDGTEVFDVYGDIAPRADLTVIITRKNGERVEVPVTCRL 835

Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESS 865
           D+ EEVSIY AGGVL  FAQDFLES+
Sbjct: 836 DTAEEVSIYSAGGVLQRFAQDFLESN 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: 2222
Number of extensions: 90
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: 863
Length adjustment: 42
Effective length of query: 827
Effective length of database: 821
Effective search space:   678967
Effective search space used:   678967
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 7026694 Shewana3_3827 (aconitate hydratase (RefSeq))
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.32588.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 1855.8   0.0          0 1855.6   0.0    1.0  1  lcl|FitnessBrowser__ANA3:7026694  Shewana3_3827 aconitate hydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026694  Shewana3_3827 aconitate hydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1855.6   0.0         0         0       1     858 []       2     859 ..       2     859 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1855.6 bits;  conditional E-value: 0
                         TIGR02333   1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwyparvv 77 
                                       nt yrk+lpgt+ldyfd+r+aveai pgay+klpytsrvlaenlvrr++pe l+aslkq+ie+k+eldfpw+parvv
  lcl|FitnessBrowser__ANA3:7026694   2 NTLYRKPLPGTALDYFDTREAVEAISPGAYAKLPYTSRVLAENLVRRCEPEALTASLKQIIESKQELDFPWFPARVV 78 
                                       899************************************************************************** PP

                         TIGR02333  78 chdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrnedrfhfinwt 154
                                       chdilgqtalvdlaglrdaia+kggdpaqvnpvv+tqlivdhslaveyggfd+daf+knraiedrrnedrfhfinwt
  lcl|FitnessBrowser__ANA3:7026694  79 CHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWT 155
                                       ***************************************************************************** PP

                         TIGR02333 155 kkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggleaetvmlgraslm 231
                                       +kafkn+dvip+gngimhqinle+mspvv++++gvafpdtlvgtdshtphvdalgviaigvggleae+vmlgras+m
  lcl|FitnessBrowser__ANA3:7026694 156 QKAFKNIDVIPQGNGIMHQINLERMSPVVHARDGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYM 232
                                       ***************************************************************************** PP

                         TIGR02333 232 rlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisnmtpeygataamfaide 308
                                       rlpdi+gveltgk qpgitatdivlalteflrkekvvs+yleffgega+altlgdratisnmtpe+gataamf+id+
  lcl|FitnessBrowser__ANA3:7026694 233 RLPDIIGVELTGKPQPGITATDIVLALTEFLRKEKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQ 309
                                       ***************************************************************************** PP

                         TIGR02333 309 qtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiakev 385
                                       qt+dyl+ltgr +eqvklvetyak++glw+d+lk+a+y+r+l+fdlssvvr++agpsnphar++t++laa+gi++ v
  lcl|FitnessBrowser__ANA3:7026694 310 QTLDYLTLTGRSDEQVKLVETYAKTTGLWSDDLKHAEYPRTLHFDLSSVVRTIAGPSNPHARVPTTELAARGISGVV 386
                                       ***************************************************************************** PP

                         TIGR02333 386 eeeaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvklyleeagllkelek 462
                                       e+e+ glmpdgaviiaaitsctntsnprnv+aagllarnan++gl rkpwvk+slapgsk+v+lyleea+ll+ele+
  lcl|FitnessBrowser__ANA3:7026694 387 ENEP-GLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLSRKPWVKTSLAPGSKAVQLYLEEANLLPELES 462
                                       ****.************************************************************************ PP

                         TIGR02333 463 lgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdi 539
                                       lgfgiv+facttcngmsgaldpviqqe+idrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdi
  lcl|FitnessBrowser__ANA3:7026694 463 LGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDI 539
                                       ***************************************************************************** PP

                         TIGR02333 540 ekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdle.daqkkvsplydwrpmstyirrppywe 615
                                       ekdvlg+d+dg+++rl+diwpsd+eidav+a++vkpeqfr+vy+pmfdl+ d+++kv+plydwrp+styirrppywe
  lcl|FitnessBrowser__ANA3:7026694 540 EKDVLGHDKDGNPVRLIDIWPSDAEIDAVIAKSVKPEQFRRVYEPMFDLSvDYGDKVTPLYDWRPQSTYIRRPPYWE 616
                                       ***************************************************************************** PP

                         TIGR02333 616 galagertlkgmrplavlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhltaqratfanpklf 692
                                       galagertlkgmrplavlgdnittdhlspsnai++dsaageyl+kmglpeedfnsyathrgdhltaqratfanpkl+
  lcl|FitnessBrowser__ANA3:7026694 617 GALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLK 693
                                       ***************************************************************************** PP

                         TIGR02333 693 nemvkedgkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegfer 769
                                       nem+ +dgkvkqgslariepeg+vtrmweaietym+rkqpliiiagadygqgssrdwaakgvrlagveaivaegfer
  lcl|FitnessBrowser__ANA3:7026694 694 NEMAVVDGKVKQGSLARIEPEGQVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFER 770
                                       ***************************************************************************** PP

                         TIGR02333 770 ihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeag 846
                                       ihrtnlvgmgvlplefk+g+nr+t+++dgtev+dv g+i+pradlt+++trknge++evpvtcrldtaeevs+y ag
  lcl|FitnessBrowser__ANA3:7026694 771 IHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVYGDIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYSAG 847
                                       ***************************************************************************** PP

                         TIGR02333 847 gvlqrfaqdfle 858
                                       gvlqrfaqdfle
  lcl|FitnessBrowser__ANA3:7026694 848 GVLQRFAQDFLE 859
                                       **********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (858 nodes)
Target sequences:                          1  (863 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: 0.07u 0.02s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 8.41
//
[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