GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Lysobacter daejeonensis GH1-9

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 WP_036138977.1 N800_RS12170 Fe/S-dependent 2-methylisocitrate dehydratase AcnD

Query= SwissProt::Q937N8
         (869 letters)



>NCBI__GCF_000768355.1:WP_036138977.1
          Length = 869

 Score = 1476 bits (3820), Expect = 0.0
 Identities = 735/869 (84%), Positives = 797/869 (91%), Gaps = 3/869 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+A+RKPLPGTKLD+FDAR AVEA+QPGA+  LPYT+RV AEN+VR+ DPA     L Q
Sbjct: 1   MNNAHRKPLPGTKLDWFDAREAVEALQPGAWATLPYTARVHAENIVRKADPAMRDAYLRQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           LV R+RDLDFPWFPARVVCHDILGQTALVDLAGLRDAIAD+GGDPA+VNPVVPVQLIVDH
Sbjct: 61  LVERRRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADKGGDPAQVNPVVPVQLIVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAF+NVDVIPPGNGIMHQINLEKM
Sbjct: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFRNVDVIPPGNGIMHQINLEKM 180

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPVI+  +GVA+PDTCVGTDSHTPHVDALGVIA+GVGGLEAENVMLGRASWMRLPDIVGV
Sbjct: 181 SPVIYVQDGVAFPDTCVGTDSHTPHVDALGVIAVGVGGLEAENVMLGRASWMRLPDIVGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           ELTGK QPGITATDIVL+LTEFLRK+KVVGAYLEFRGEGA++LT+GDRATISNMAPEYGA
Sbjct: 241 ELTGKPQPGITATDIVLSLTEFLRKQKVVGAYLEFRGEGAAALTIGDRATISNMAPEYGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TAAMFFID+ T+DYLRLTGR+DEQ+ LVETYA+ AGLWAD L+ A+YER L FDLSSV R
Sbjct: 301 TAAMFFIDDNTLDYLRLTGRSDEQVALVETYAKAAGLWADDLRTAQYERTLHFDLSSVER 360

Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
            MAGPSNPH RLP + LAERGIA +L+ A AQEA+GL+PDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 TMAGPSNPHARLPVAQLAERGIAGNLEAARAQEAQGLLPDGAVIIAAITSCTNTSNPRNV 420

Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
           IAA LLARNA   GL RKPWVK+SLAPGSKAV LYL+EA L  DLE+LGFGIVAFACTTC
Sbjct: 421 IAAGLLARNAARLGLQRKPWVKTSLAPGSKAVALYLDEAGLTDDLEQLGFGIVAFACTTC 480

Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
           NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540

Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
           RFDIEKDVLG   DG+ + LKD+WP+D EIDA++  +VKPEQFRKVYEPMF +    G +
Sbjct: 541 RFDIEKDVLGV-VDGREIRLKDLWPTDAEIDAVMKAAVKPEQFRKVYEPMFNVRVEHGGA 599

Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
           VSPLYDWRPQSTYIRRPPYWEGALAGERTL+ +RPLAVLGDNITTDHLSPSNAI+L+SAA
Sbjct: 600 VSPLYDWRPQSTYIRRPPYWEGALAGERTLRGMRPLAVLGDNITTDHLSPSNAILLDSAA 659

Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMA-VVDGQVKKGSLARIEPE 719
           GEYL +MGLPEEDFNSYATHRGDHLTAQRATFANP L NEM    DG V++GSLARIEPE
Sbjct: 660 GEYLDKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVRKDDGSVRQGSLARIEPE 719

Query: 720 GKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRT 779
           G+V RMWEAIETYM+RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHRT
Sbjct: 720 GQVTRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRT 779

Query: 780 NLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCR 839
           NLIGMGVLPLEF+PG +R TL +DGTETYDVIGER PRATLTLV++R+NGERVEVPVTCR
Sbjct: 780 NLIGMGVLPLEFQPGADRTTLAIDGTETYDVIGERTPRATLTLVIHRRNGERVEVPVTCR 839

Query: 840 LDSDEEVSIYEAGGVL-HFAQDFLESSRA 867
           LD+ EEVSIYEAGGVL  FA DFLESS+A
Sbjct: 840 LDTAEEVSIYEAGGVLQRFANDFLESSKA 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: 2275
Number of extensions: 89
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 WP_036138977.1 N800_RS12170 (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.498688.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 1789.7   0.1          0 1789.5   0.1    1.0  1  NCBI__GCF_000768355.1:WP_036138977.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000768355.1:WP_036138977.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1789.5   0.1         0         0       1     858 []       2     864 ..       2     864 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1789.5 bits;  conditional E-value: 0
                             TIGR02333   1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwyp 73 
                                           n+++rk+lpgt+ld+fdar+avea++pga+++lpyt+rv aen+vr++dp++ +a+l+ql+er+r+ldfpw+p
  NCBI__GCF_000768355.1:WP_036138977.1   2 NNAHRKPLPGTKLDWFDAREAVEALQPGAWATLPYTARVHAENIVRKADPAMRDAYLRQLVERRRDLDFPWFP 74 
                                           7889********************************************************************* PP

                             TIGR02333  74 arvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrned 146
                                           arvvchdilgqtalvdlaglrdaia+kggdpaqvnpvv++qlivdhslave+ggfdpdaf+knraiedrrned
  NCBI__GCF_000768355.1:WP_036138977.1  75 ARVVCHDILGQTALVDLAGLRDAIADKGGDPAQVNPVVPVQLIVDHSLAVECGGFDPDAFAKNRAIEDRRNED 147
                                           ************************************************************************* PP

                             TIGR02333 147 rfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggle 219
                                           rfhfi+wtk+af+nvdvip+gngimhqinlekmspv+ v++gvafpdt+vgtdshtphvdalgvia+gvggle
  NCBI__GCF_000768355.1:WP_036138977.1 148 RFHFIDWTKQAFRNVDVIPPGNGIMHQINLEKMSPVIYVQDGVAFPDTCVGTDSHTPHVDALGVIAVGVGGLE 220
                                           ************************************************************************* PP

                             TIGR02333 220 aetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisn 292
                                           ae+vmlgras+mrlpdivgveltgk qpgitatdivl+lteflrk+kvv+aylef gega alt+gdratisn
  NCBI__GCF_000768355.1:WP_036138977.1 221 AENVMLGRASWMRLPDIVGVELTGKPQPGITATDIVLSLTEFLRKQKVVGAYLEFRGEGAAALTIGDRATISN 293
                                           ************************************************************************* PP

                             TIGR02333 293 mtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagps 365
                                           m+peygataamf+id++t+dyl+ltgr +eqv+lvetyakaaglwad+l++a+yer+l+fdlssv+r++agps
  NCBI__GCF_000768355.1:WP_036138977.1 294 MAPEYGATAAMFFIDDNTLDYLRLTGRSDEQVALVETYAKAAGLWADDLRTAQYERTLHFDLSSVERTMAGPS 366
                                           ************************************************************************* PP

                             TIGR02333 366 npharlatsdlaakgiakevee....eaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkp 434
                                           npharl+ ++la +gia+++e     ea+gl+pdgaviiaaitsctntsnprnv+aagllarna +lgl+rkp
  NCBI__GCF_000768355.1:WP_036138977.1 367 NPHARLPVAQLAERGIAGNLEAaraqEAQGLLPDGAVIIAAITSCTNTSNPRNVIAAGLLARNAARLGLQRKP 439
                                           ******************99866666899******************************************** PP

                             TIGR02333 435 wvksslapgskvvklyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnf 507
                                           wvk+slapgsk+v lyl+eagl ++le+lgfgivafacttcngmsgaldp+iqqeiidrdlyatavlsgnrnf
  NCBI__GCF_000768355.1:WP_036138977.1 440 WVKTSLAPGSKAVALYLDEAGLTDDLEQLGFGIVAFACTTCNGMSGALDPKIQQEIIDRDLYATAVLSGNRNF 512
                                           ************************************************************************* PP

                             TIGR02333 508 dgrihpyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrk 580
                                           dgrihpyakqaflaspplvvayaiagtirfdiekdvlgv +dg+eirlkd+wp+d+eidav++aavkpeqfrk
  NCBI__GCF_000768355.1:WP_036138977.1 513 DGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGV-VDGREIRLKDLWPTDAEIDAVMKAAVKPEQFRK 584
                                           ***************************************.********************************* PP

                             TIGR02333 581 vyipmfdle.daqkkvsplydwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnaillds 652
                                           vy+pmf++  +++ +vsplydwrp+styirrppywegalagertl+gmrplavlgdnittdhlspsnaillds
  NCBI__GCF_000768355.1:WP_036138977.1 585 VYEPMFNVRvEHGGAVSPLYDWRPQSTYIRRPPYWEGALAGERTLRGMRPLAVLGDNITTDHLSPSNAILLDS 657
                                           *********9*************************************************************** PP

                             TIGR02333 653 aageylakmglpeedfnsyathrgdhltaqratfanpklfnemvked.gkvkqgslariepegkvtrmweaie 724
                                           aageyl kmglpeedfnsyathrgdhltaqratfanpklfnemv++d g+v+qgslariepeg+vtrmweaie
  NCBI__GCF_000768355.1:WP_036138977.1 658 AAGEYLDKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVRKDdGSVRQGSLARIEPEGQVTRMWEAIE 730
                                           ********************************************9988************************* PP

                             TIGR02333 725 tymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefkpgtnrktlald 797
                                           tym+rkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnl+gmgvlplef+pg++r+tla+d
  NCBI__GCF_000768355.1:WP_036138977.1 731 TYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLIGMGVLPLEFQPGADRTTLAID 803
                                           ************************************************************************* PP

                             TIGR02333 798 gtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
                                           gte+ydv+ge+tpra+ltlv++r+nge++evpvtcrldtaeevs+yeaggvlqrfa+dfle
  NCBI__GCF_000768355.1:WP_036138977.1 804 GTETYDVIGERTPRATLTLVIHRRNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFANDFLE 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 45.42
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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