Alignments for a candidate for acn in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Pseudomonas stutzeri RCH2

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 GFF2274 Psest_2319 aconitate hydratase 1/2-methylisocitrate dehydratase, Fe/S-dependent

Query= SwissProt::Q937N8
         (869 letters)



>FitnessBrowser__psRCH2:GFF2274
          Length = 867

 Score = 1433 bits (3710), Expect = 0.0
 Identities = 712/866 (82%), Positives = 781/866 (90%), Gaps = 6/866 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+ +RKPLPGT LDYFD R A+EAIQPG+YDKLPYTSRVLAE LVRRC+P  LTDSL Q
Sbjct: 1   MNTEHRKPLPGTGLDYFDTREAIEAIQPGSYDKLPYTSRVLAEQLVRRCEPEALTDSLKQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           ++ RKRDLDFPW+PARVVCHDILGQTALVDLAGLRDAIA+QGGDPAKVNPVVP QLIVDH
Sbjct: 61  IIERKRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAEQGGDPAKVNPVVPTQLIVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVE  GFDPDAF KNRA+E+RRNEDRFHFI+WTK AFKNVDVIP GNGIMHQINLEKM
Sbjct: 121 SLAVEFAGFDPDAFEKNRAVEERRNEDRFHFIEWTKTAFKNVDVIPAGNGIMHQINLEKM 180

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPVI A  GVA+PDTCVGTDSHTPHVDALGVIAIGVGGLEAE VMLG  S MRLPDIVGV
Sbjct: 181 SPVIQARGGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAETVMLGLPSMMRLPDIVGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
            LTGKRQPGITATDIVLALTEFLRKE+VVGA++EF GEGA SLT+GDRATISNM PEYGA
Sbjct: 241 RLTGKRQPGITATDIVLALTEFLRKERVVGAWVEFFGEGADSLTIGDRATISNMCPEYGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TA+MF+ID+QTIDYL+LTGR  EQ+ LVE YA+  GLWA +L+ AEYERVL+FDLSSVVR
Sbjct: 301 TASMFYIDQQTIDYLKLTGREPEQVALVEQYAKETGLWATALEGAEYERVLEFDLSSVVR 360

Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDK---ASAQEAEGLMPDGAVIIAAITSCTNTSNP 417
           NMAGPSNPHKRLPTSAL ERGIA D DK   A A+EAEGL+PDGAVIIAAITSCTNTSNP
Sbjct: 361 NMAGPSNPHKRLPTSALHERGIA-DEDKLAAARAEEAEGLLPDGAVIIAAITSCTNTSNP 419

Query: 418 RNVIAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFAC 477
           RNV+AA LLA+ AN  GL RKPWVK+S APGSK  +LYLEEA LL +LEKLGFGIVA+AC
Sbjct: 420 RNVVAAGLLAKKANELGLVRKPWVKTSFAPGSKVAKLYLEEAGLLSELEKLGFGIVAYAC 479

Query: 478 TTCNGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIA 537
           TTCNGMSGALDP IQQEII+RDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIA
Sbjct: 480 TTCNGMSGALDPVIQQEIIERDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIA 539

Query: 538 GTIRFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAAS 597
           GT+RFDIE+DVLGTD++G P+ LKD+WPSDEEIDAIVA SVKPEQF+++Y PMF +    
Sbjct: 540 GTVRFDIEQDVLGTDKNGNPITLKDLWPSDEEIDAIVASSVKPEQFKQIYIPMFDLGTIE 599

Query: 598 GESVSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLN 657
            E+ SPLYDWRP STYIRRPPYWEGALAGERTLK +RPLA+L DNITTDHLSPSNAI+L+
Sbjct: 600 -EAKSPLYDWRPMSTYIRRPPYWEGALAGERTLKGMRPLAILPDNITTDHLSPSNAILLD 658

Query: 658 SAAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIE 717
           SAAGEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANP L+NEMAVVDG+ +KGSLAR+E
Sbjct: 659 SAAGEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPQLVNEMAVVDGKAQKGSLARVE 718

Query: 718 PEGKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIH 777
           PEGKV+RMWEAIETYM+RKQ LII+AGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIH
Sbjct: 719 PEGKVMRMWEAIETYMNRKQNLIIVAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIH 778

Query: 778 RTNLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVT 837
           RTNL+GMGVLP+EFKPG  RLTLGLDGTET+D+ GE  PR  LTLV++  +GE   VPVT
Sbjct: 779 RTNLVGMGVLPVEFKPGTTRLTLGLDGTETFDIEGELSPRCDLTLVIHHMSGEETRVPVT 838

Query: 838 CRLDSDEEVSIYEAGGVL-HFAQDFL 862
           CRLD+  EVS+Y+AGGVL  FA+DFL
Sbjct: 839 CRLDTAAEVSVYQAGGVLQRFAKDFL 864


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: 2244
Number of extensions: 74
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: 867
Length adjustment: 42
Effective length of query: 827
Effective length of database: 825
Effective search space:   682275
Effective search space used:   682275
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 GFF2274 Psest_2319 (aconitate hydratase 1/2-methylisocitrate dehydratase, Fe/S-dependent)
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.10034.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 1775.3   0.0          0 1775.1   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF2274  Psest_2319 aconitate hydratase 1


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF2274  Psest_2319 aconitate hydratase 1/2-methylisocitrate dehydratase, Fe/S-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1775.1   0.0         0         0       1     857 [.       2     864 ..       2     865 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1775.1 bits;  conditional E-value: 0
                           TIGR02333   1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwypar 75 
                                         nt++rk+lpgt ldyfd+r+a+eai+pg+ydklpytsrvlae+lvrr++pe l++slkq+ierkr+ldfpwypar
  lcl|FitnessBrowser__psRCH2:GFF2274   2 NTEHRKPLPGTGLDYFDTREAIEAIQPGSYDKLPYTSRVLAEQLVRRCEPEALTDSLKQIIERKRDLDFPWYPAR 76 
                                         7999*********************************************************************** PP

                           TIGR02333  76 vvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrnedrfhf 150
                                         vvchdilgqtalvdlaglrdaiae+ggdpa+vnpvv+tqlivdhslave++gfdpdafeknra+e+rrnedrfhf
  lcl|FitnessBrowser__psRCH2:GFF2274  77 VVCHDILGQTALVDLAGLRDAIAEQGGDPAKVNPVVPTQLIVDHSLAVEFAGFDPDAFEKNRAVEERRNEDRFHF 151
                                         *************************************************************************** PP

                           TIGR02333 151 inwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggleaetvml 225
                                         i+wtk+afknvdvipagngimhqinlekmspv+q++ gvafpdt+vgtdshtphvdalgviaigvggleaetvml
  lcl|FitnessBrowser__psRCH2:GFF2274 152 IEWTKTAFKNVDVIPAGNGIMHQINLEKMSPVIQARGGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAETVML 226
                                         *************************************************************************** PP

                           TIGR02333 226 graslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisnmtpeygat 300
                                         g +s+mrlpdivgv+ltgkrqpgitatdivlalteflrke+vv+a++effgega +lt+gdratisnm+peygat
  lcl|FitnessBrowser__psRCH2:GFF2274 227 GLPSMMRLPDIVGVRLTGKRQPGITATDIVLALTEFLRKERVVGAWVEFFGEGADSLTIGDRATISNMCPEYGAT 301
                                         *************************************************************************** PP

                           TIGR02333 301 aamfaideqtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsd 375
                                         a+mf+id+qtidylkltgre+eqv+lve yak +glwa +l+ a+yervl+fdlssvvrn+agpsnph+rl+ts 
  lcl|FitnessBrowser__psRCH2:GFF2274 302 ASMFYIDQQTIDYLKLTGREPEQVALVEQYAKETGLWATALEGAEYERVLEFDLSSVVRNMAGPSNPHKRLPTSA 376
                                         *************************************************************************** PP

                           TIGR02333 376 laakgiakevee......eaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgs 444
                                         l  +gia e +       eaegl+pdgaviiaaitsctntsnprnvvaaglla++an+lgl rkpwvk+s+apgs
  lcl|FitnessBrowser__psRCH2:GFF2274 377 LHERGIADEDKLaaaraeEAEGLLPDGAVIIAAITSCTNTSNPRNVVAAGLLAKKANELGLVRKPWVKTSFAPGS 451
                                         ******98754333444499******************************************************* PP

                           TIGR02333 445 kvvklyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaf 519
                                         kv+klyleeagll+eleklgfgiva+acttcngmsgaldpviqqeii+rdlyatavlsgnrnfdgrihpyakqaf
  lcl|FitnessBrowser__psRCH2:GFF2274 452 KVAKLYLEEAGLLSELEKLGFGIVAYACTTCNGMSGALDPVIQQEIIERDLYATAVLSGNRNFDGRIHPYAKQAF 526
                                         *************************************************************************** PP

                           TIGR02333 520 laspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdledaqkk 594
                                         laspplvvayaiagt+rfdie+dvlg+d++g++i lkd+wpsdeeida+va++vkpeqf+++yipmfdl++ +++
  lcl|FitnessBrowser__psRCH2:GFF2274 527 LASPPLVVAYAIAGTVRFDIEQDVLGTDKNGNPITLKDLWPSDEEIDAIVASSVKPEQFKQIYIPMFDLGTIEEA 601
                                         *************************************************************************** PP

                           TIGR02333 595 vsplydwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnailldsaageylakmglpeedfn 669
                                          splydwrpmstyirrppywegalagertlkgmrpla+l+dnittdhlspsnailldsaageylakmglpeedfn
  lcl|FitnessBrowser__psRCH2:GFF2274 602 KSPLYDWRPMSTYIRRPPYWEGALAGERTLKGMRPLAILPDNITTDHLSPSNAILLDSAAGEYLAKMGLPEEDFN 676
                                         *************************************************************************** PP

                           TIGR02333 670 syathrgdhltaqratfanpklfnemvkedgkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqg 744
                                         syathrgdhltaqratfanp+l+nem+ +dgk ++gslar+epegkv+rmweaietymnrkq lii+agadygqg
  lcl|FitnessBrowser__psRCH2:GFF2274 677 SYATHRGDHLTAQRATFANPQLVNEMAVVDGKAQKGSLARVEPEGKVMRMWEAIETYMNRKQNLIIVAGADYGQG 751
                                         *************************************************************************** PP

                           TIGR02333 745 ssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvt 819
                                         ssrdwaakgvrlagve ivaegferihrtnlvgmgvlp+efkpgt r tl+ldgte++d+ ge +pr+dltlv++
  lcl|FitnessBrowser__psRCH2:GFF2274 752 SSRDWAAKGVRLAGVEVIVAEGFERIHRTNLVGMGVLPVEFKPGTTRLTLGLDGTETFDIEGELSPRCDLTLVIH 826
                                         *************************************************************************** PP

                           TIGR02333 820 rkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfl 857
                                            ge+  vpvtcrldta evsvy+aggvlqrfa+dfl
  lcl|FitnessBrowser__psRCH2:GFF2274 827 HMSGEETRVPVTCRLDTAAEVSVYQAGGVLQRFAKDFL 864
                                         *************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (858 nodes)
Target sequences:                          1  (867 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 0.03s 00:00:00.10 Elapsed: 00:00:00.09
# Mc/sec: 8.22
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources