GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Shewanella loihica PV-4

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 5209348 Shew_1822 aconitate hydratase (RefSeq)

Query= SwissProt::Q937N8
         (869 letters)



>lcl|FitnessBrowser__PV4:5209348 Shew_1822 aconitate hydratase
           (RefSeq)
          Length = 862

 Score = 1422 bits (3680), Expect = 0.0
 Identities = 705/866 (81%), Positives = 776/866 (89%), Gaps = 6/866 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MNS +RKPLPG+ LDYFD RAAVEA+  GAYDKLPYT++VLAENLVRRC+P  L D+L Q
Sbjct: 1   MNSLHRKPLPGSALDYFDTRAAVEALSAGAYDKLPYTAKVLAENLVRRCEPELLNDALSQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           L+ RKRDLDFPW+PARVVCHDILGQTALVDLAGLRDAIA++GGDP+KVNPVVP QLIVDH
Sbjct: 61  LIDRKRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAEKGGDPSKVNPVVPTQLIVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVE  GF+ DAF KNRAIEDRRNEDRFHFI+WTK AFKNVDVI PGNGIMHQINLEKM
Sbjct: 121 SLAVEHAGFEKDAFEKNRAIEDRRNEDRFHFINWTKTAFKNVDVIQPGNGIMHQINLEKM 180

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPVI A +GVA+PDT VGTDSHTPHVDALGVIAIGVGGLEAENVMLGR S+MRLPDIVGV
Sbjct: 181 SPVIQARDGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRPSYMRLPDIVGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           ELTGKRQ GITATDIVLALTEFLR+EKVV AYLEF GEGA+ LTLGDRATISNM PE+GA
Sbjct: 241 ELTGKRQSGITATDIVLALTEFLRQEKVVSAYLEFFGEGAADLTLGDRATISNMTPEFGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           +A MF+ID+QTIDYL +TGR  EQ+KLVE YA+T GLWADSLK+AEYERVL FDLSSVVR
Sbjct: 301 SAGMFYIDQQTIDYLTITGRDSEQVKLVENYAKTTGLWADSLKDAEYERVLTFDLSSVVR 360

Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
           N+AGPSNPH+R+ TS LA +GIA        ++ + LMPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 NIAGPSNPHRRVATSELASQGIA-----GVVEQDDKLMPDGAVIIAAITSCTNTSNPRNV 415

Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
           IAA LLA+ AN  GL RKPWVK+S APGSK  ELYL++A LLP+LE+LGFGIV FACTTC
Sbjct: 416 IAAGLLAKKANELGLVRKPWVKTSFAPGSKVAELYLKDAGLLPELEQLGFGIVGFACTTC 475

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

Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
           RFDIEKD+LG D  G+P+ LKDIWPSDEEIDAIV  SVKP+QFR +Y PMF +    GE 
Sbjct: 536 RFDIEKDILGHDDKGEPIRLKDIWPSDEEIDAIVKASVKPQQFRDIYTPMFDLAVDYGED 595

Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
           V+PLYDWRPQSTYIRRPPYWEGALAGERTLK +RPLAVLGDNITTDHLSPSNAI+ +SAA
Sbjct: 596 VNPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAILASSAA 655

Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
           GEYLA+MGLPE DFNSYATHRGDHLTAQRATFANP LINEMA+VDG+VK+GSL R+EPEG
Sbjct: 656 GEYLAKMGLPEVDFNSYATHRGDHLTAQRATFANPKLINEMALVDGEVKQGSLTRLEPEG 715

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

Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
           L+GMGVLPLEFK G NR T G+DG+ET+DVIGE  PRA LT+V+ R+NGERVEVPV CRL
Sbjct: 776 LVGMGVLPLEFKAGENRHTYGIDGSETFDVIGEPTPRADLTVVITRQNGERVEVPVICRL 835

Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESS 865
           D+ +EV +Y+AGGVL  FAQDFLE++
Sbjct: 836 DTADEVLVYQAGGVLQRFAQDFLEAN 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: 2181
Number of extensions: 86
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: 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 5209348 Shew_1822 (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.6732.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 1801.5   0.0          0 1801.3   0.0    1.0  1  lcl|FitnessBrowser__PV4:5209348  Shew_1822 aconitate hydratase (R


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209348  Shew_1822 aconitate hydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1801.3   0.0         0         0       1     858 []       2     859 ..       2     859 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1801.3 bits;  conditional E-value: 0
                        TIGR02333   1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwyparvvc 78 
                                      n+ +rk+lpg++ldyfd+raavea+  gaydklpyt++vlaenlvrr++pe l+++l+qli+rkr+ldfpwyparvvc
  lcl|FitnessBrowser__PV4:5209348   2 NSLHRKPLPGSALDYFDTRAAVEALSAGAYDKLPYTAKVLAENLVRRCEPELLNDALSQLIDRKRDLDFPWYPARVVC 79 
                                      7889************************************************************************** PP

                        TIGR02333  79 hdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrnedrfhfinwtkk 156
                                      hdilgqtalvdlaglrdaiaekggdp++vnpvv+tqlivdhslave +gf++dafeknraiedrrnedrfhfinwtk+
  lcl|FitnessBrowser__PV4:5209348  80 HDILGQTALVDLAGLRDAIAEKGGDPSKVNPVVPTQLIVDHSLAVEHAGFEKDAFEKNRAIEDRRNEDRFHFINWTKT 157
                                      ****************************************************************************** PP

                        TIGR02333 157 afknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggleaetvmlgraslmrlp 234
                                      afknvdvi++gngimhqinlekmspv+q+++gvafpdtlvgtdshtphvdalgviaigvggleae+vmlgr+s+mrlp
  lcl|FitnessBrowser__PV4:5209348 158 AFKNVDVIQPGNGIMHQINLEKMSPVIQARDGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRPSYMRLP 235
                                      ****************************************************************************** PP

                        TIGR02333 235 divgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisnmtpeygataamfaideqtid 312
                                      divgveltgkrq+gitatdivlalteflr+ekvvsayleffgega  ltlgdratisnmtpe+ga+a+mf+id+qtid
  lcl|FitnessBrowser__PV4:5209348 236 DIVGVELTGKRQSGITATDIVLALTEFLRQEKVVSAYLEFFGEGAADLTLGDRATISNMTPEFGASAGMFYIDQQTID 313
                                      ****************************************************************************** PP

                        TIGR02333 313 ylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiakeveeeae 390
                                      yl++tgr++eqvklve yak++glwadslk+a+yervl+fdlssvvrn+agpsnph+r+ats+la++gia+ ve++  
  lcl|FitnessBrowser__PV4:5209348 314 YLTITGRDSEQVKLVENYAKTTGLWADSLKDAEYERVLTFDLSSVVRNIAGPSNPHRRVATSELASQGIAGVVEQDD- 390
                                      ***********************************************************************999876. PP

                        TIGR02333 391 glmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvklyleeagllkeleklgfgiv 468
                                       lmpdgaviiaaitsctntsnprnv+aaglla++an+lgl rkpwvk+s+apgskv++lyl++agll+ele+lgfgiv
  lcl|FitnessBrowser__PV4:5209348 391 KLMPDGAVIIAAITSCTNTSNPRNVIAAGLLAKKANELGLVRKPWVKTSFAPGSKVAELYLKDAGLLPELEQLGFGIV 468
                                      9***************************************************************************** PP

                        TIGR02333 469 afacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgv 546
                                      +facttcngmsgaldpviqqe+idrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekd+lg+
  lcl|FitnessBrowser__PV4:5209348 469 GFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDILGH 546
                                      ****************************************************************************** PP

                        TIGR02333 547 dadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdle.daqkkvsplydwrpmstyirrppywegalagert 623
                                      d +g +irlkdiwpsdeeida+v+a+vkp+qfr++y pmfdl  d+++ v plydwrp+styirrppywegalagert
  lcl|FitnessBrowser__PV4:5209348 547 DDKGEPIRLKDIWPSDEEIDAIVKASVKPQQFRDIYTPMFDLAvDYGEDVNPLYDWRPQSTYIRRPPYWEGALAGERT 624
                                      *******************************************9********************************** PP

                        TIGR02333 624 lkgmrplavlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemvkedgk 701
                                      lkgmrplavlgdnittdhlspsnail++saageylakmglpe dfnsyathrgdhltaqratfanpkl+nem+ +dg+
  lcl|FitnessBrowser__PV4:5209348 625 LKGMRPLAVLGDNITTDHLSPSNAILASSAAGEYLAKMGLPEVDFNSYATHRGDHLTAQRATFANPKLINEMALVDGE 702
                                      ****************************************************************************** PP

                        TIGR02333 702 vkqgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmg 779
                                      vkqgsl+r+epeg+v+rmweaietym+rkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmg
  lcl|FitnessBrowser__PV4:5209348 703 VKQGSLTRLEPEGEVMRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMG 780
                                      ****************************************************************************** PP

                        TIGR02333 780 vlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfl 857
                                      vlplefk+g+nr+t+++dg+e++dv+ge tpradlt+v+tr+nge++evpv crldta+ev vy+aggvlqrfaqdfl
  lcl|FitnessBrowser__PV4:5209348 781 VLPLEFKAGENRHTYGIDGSETFDVIGEPTPRADLTVVITRQNGERVEVPVICRLDTADEVLVYQAGGVLQRFAQDFL 858
                                      *****************************************************************************9 PP

                        TIGR02333 858 e 858
                                      e
  lcl|FitnessBrowser__PV4:5209348 859 E 859
                                      7 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: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.08
# Mc/sec: 8.56
//
[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 paper from 2022 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