Alignments for a candidate for acn in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Pseudomonas benzenivorans DSM 8628

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_090439551.1 BLS63_RS00675 Fe/S-dependent 2-methylisocitrate dehydratase AcnD

Query= SwissProt::Q937N8
         (869 letters)



>NCBI__GCF_900100495.1:WP_090439551.1
          Length = 869

 Score = 1422 bits (3682), Expect = 0.0
 Identities = 710/870 (81%), Positives = 779/870 (89%), Gaps = 4/870 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MNS  RKPL GT LDYFD R AV+AI PGAY KLPYTSRVLAE LVRRC+P  LTDSL Q
Sbjct: 1   MNSQYRKPLAGTVLDYFDTREAVDAIAPGAYAKLPYTSRVLAEQLVRRCEPDALTDSLKQ 60

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

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVE  GFDPDAFAKNRAIEDRRNEDRFHFI+WTK AFKNVDVIP GNGIMHQINLEKM
Sbjct: 121 SLAVEAPGFDPDAFAKNRAIEDRRNEDRFHFIEWTKTAFKNVDVIPAGNGIMHQINLEKM 180

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

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           +LTGKRQPGITATDIVLA+TEFLRKE+VVGAY+EF GEGA SL++GDRATISNM PEYGA
Sbjct: 241 KLTGKRQPGITATDIVLAITEFLRKERVVGAYVEFFGEGADSLSIGDRATISNMCPEYGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TA+MF+ID+QTIDYL+LTGR  EQ+ LVE YA+  GLWAD+L  AEYERVL+FDLS+VVR
Sbjct: 301 TASMFYIDQQTIDYLKLTGREPEQVALVENYAKLTGLWADALVTAEYERVLEFDLSTVVR 360

Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKAS--AQEAEGLMPDGAVIIAAITSCTNTSNPR 418
           NMAGPSNPHKRLPTSAL ERGIA +   AS   +EAEGL+PDGAVIIAAITSCTNTSNPR
Sbjct: 361 NMAGPSNPHKRLPTSALHERGIADEAKLASGKVEEAEGLLPDGAVIIAAITSCTNTSNPR 420

Query: 419 NVIAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACT 478
           NV+AA LLA+ ANA GL RKPWVK+S APGSK  +LYLE+A LL +LE+LGFGIV +ACT
Sbjct: 421 NVVAAGLLAKKANALGLLRKPWVKTSFAPGSKVAKLYLEDAGLLSELEQLGFGIVGYACT 480

Query: 479 TCNGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG 538
           TCNGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG
Sbjct: 481 TCNGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG 540

Query: 539 TIRFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASG 598
           T+RFDIE+DVLGTD++G  + LKD+WPSDEEIDAIVA SVKPEQF+++Y PMF +     
Sbjct: 541 TVRFDIEQDVLGTDKNGNLITLKDLWPSDEEIDAIVAASVKPEQFKQIYIPMFDLGTIQ- 599

Query: 599 ESVSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNS 658
           E+ SPLYDWRP STYIRRPPYWEGALAGERTLK +RPLA+L DNITTDHLSPSNAI+L+S
Sbjct: 600 EAESPLYDWRPMSTYIRRPPYWEGALAGERTLKGMRPLAILPDNITTDHLSPSNAILLDS 659

Query: 659 AAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEP 718
           AAGEYL +MGLPEEDFNSYATHRGDHLTAQRATFANP L+NEMAVVDG VKKGSLAR+EP
Sbjct: 660 AAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPQLVNEMAVVDGVVKKGSLARVEP 719

Query: 719 EGKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHR 778
           EGKV+RMWEAIETYM+RKQ LII+AGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHR
Sbjct: 720 EGKVMRMWEAIETYMNRKQNLIIVAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHR 779

Query: 779 TNLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTC 838
           TNL+GMGVLP+EFKPG  RLTLGLDG+ETYD+ G+  PR  L LV++R+NGE  +VPVTC
Sbjct: 780 TNLVGMGVLPVEFKPGTTRLTLGLDGSETYDIEGDVSPRCELILVIHRRNGEVTQVPVTC 839

Query: 839 RLDSDEEVSIYEAGGVL-HFAQDFLESSRA 867
           RLD+  EV +Y+AGGVL  FAQDFLE + A
Sbjct: 840 RLDTAAEVHVYKAGGVLQRFAQDFLEGAIA 869


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: 2209
Number of extensions: 78
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: 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_090439551.1 BLS63_RS00675 (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.9707.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 1779.5   0.0          0 1779.3   0.0    1.0  1  lcl|NCBI__GCF_900100495.1:WP_090439551.1  BLS63_RS00675 Fe/S-dependent 2-m


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090439551.1  BLS63_RS00675 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1779.3   0.0         0         0       1     858 []       2     865 ..       2     865 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1779.3 bits;  conditional E-value: 0
                                 TIGR02333   1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldf 69 
                                               n++yrk+l+gt ldyfd+r+av+ai+pgay+klpytsrvlae+lvrr++p+ l++slkqlierkr+ldf
  lcl|NCBI__GCF_900100495.1:WP_090439551.1   2 NSQYRKPLAGTVLDYFDTREAVDAIAPGAYAKLPYTSRVLAEQLVRRCEPDALTDSLKQLIERKRDLDF 70 
                                               89******************************************************************* PP

                                 TIGR02333  70 pwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknra 138
                                               pwyparvvchdilgqtalvdlaglrdaiaekggdp++vnpvv+tqlivdhslave  gfdpdaf+knra
  lcl|NCBI__GCF_900100495.1:WP_090439551.1  71 PWYPARVVCHDILGQTALVDLAGLRDAIAEKGGDPSKVNPVVPTQLIVDHSLAVEAPGFDPDAFAKNRA 139
                                               ********************************************************************* PP

                                 TIGR02333 139 iedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvda 207
                                               iedrrnedrfhfi+wtk+afknvdvipagngimhqinlekmspv+q++ gvafpdt+vgtdshtphvda
  lcl|NCBI__GCF_900100495.1:WP_090439551.1 140 IEDRRNEDRFHFIEWTKTAFKNVDVIPAGNGIMHQINLEKMSPVIQARGGVAFPDTCVGTDSHTPHVDA 208
                                               ********************************************************************* PP

                                 TIGR02333 208 lgviaigvggleaetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffg 276
                                               lgviaigvggleaetvmlg +s+mrlpdivgv+ltgkrqpgitatdivla+teflrke+vv+ay+effg
  lcl|NCBI__GCF_900100495.1:WP_090439551.1 209 LGVIAIGVGGLEAETVMLGLPSMMRLPDIVGVKLTGKRQPGITATDIVLAITEFLRKERVVGAYVEFFG 277
                                               ********************************************************************* PP

                                 TIGR02333 277 egakaltlgdratisnmtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwadslkkav 345
                                               ega +l++gdratisnm+peygata+mf+id+qtidylkltgre+eqv+lve yak +glwad+l +a+
  lcl|NCBI__GCF_900100495.1:WP_090439551.1 278 EGADSLSIGDRATISNMCPEYGATASMFYIDQQTIDYLKLTGREPEQVALVENYAKLTGLWADALVTAE 346
                                               ********************************************************************* PP

                                 TIGR02333 346 yervlkfdlssvvrnlagpsnpharlatsdlaakgiakevee......eaeglmpdgaviiaaitsctn 408
                                               yervl+fdls+vvrn+agpsnph+rl+ts l  +gia e++       eaegl+pdgaviiaaitsctn
  lcl|NCBI__GCF_900100495.1:WP_090439551.1 347 YERVLEFDLSTVVRNMAGPSNPHKRLPTSALHERGIADEAKLasgkveEAEGLLPDGAVIIAAITSCTN 415
                                               *************************************9987555556599******************* PP

                                 TIGR02333 409 tsnprnvvaagllarnanklglkrkpwvksslapgskvvklyleeagllkeleklgfgivafacttcng 477
                                               tsnprnvvaaglla++an+lgl rkpwvk+s+apgskv+klyle+agll+ele+lgfgiv++acttcng
  lcl|NCBI__GCF_900100495.1:WP_090439551.1 416 TSNPRNVVAAGLLAKKANALGLLRKPWVKTSFAPGSKVAKLYLEDAGLLSELEQLGFGIVGYACTTCNG 484
                                               ********************************************************************* PP

                                 TIGR02333 478 msgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgv 546
                                               msgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagt+rfdie+dvlg+
  lcl|NCBI__GCF_900100495.1:WP_090439551.1 485 MSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTVRFDIEQDVLGT 553
                                               ********************************************************************* PP

                                 TIGR02333 547 dadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdledaqkkvsplydwrpmstyirrppywe 615
                                               d++g+ i lkd+wpsdeeida+vaa+vkpeqf+++yipmfdl++ q++ splydwrpmstyirrppywe
  lcl|NCBI__GCF_900100495.1:WP_090439551.1 554 DKNGNLITLKDLWPSDEEIDAIVAASVKPEQFKQIYIPMFDLGTIQEAESPLYDWRPMSTYIRRPPYWE 622
                                               ********************************************************************* PP

                                 TIGR02333 616 galagertlkgmrplavlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhltaqra 684
                                               galagertlkgmrpla+l+dnittdhlspsnailldsaageyl+kmglpeedfnsyathrgdhltaqra
  lcl|NCBI__GCF_900100495.1:WP_090439551.1 623 GALAGERTLKGMRPLAILPDNITTDHLSPSNAILLDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRA 691
                                               ********************************************************************* PP

                                 TIGR02333 685 tfanpklfnemvkedgkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdwaakg 753
                                               tfanp+l+nem+ +dg vk+gslar+epegkv+rmweaietymnrkq lii+agadygqgssrdwaakg
  lcl|NCBI__GCF_900100495.1:WP_090439551.1 692 TFANPQLVNEMAVVDGVVKKGSLARVEPEGKVMRMWEAIETYMNRKQNLIIVAGADYGQGSSRDWAAKG 760
                                               ********************************************************************* PP

                                 TIGR02333 754 vrlagveaivaegferihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkn 822
                                               vrlagve ivaegferihrtnlvgmgvlp+efkpgt r tl+ldg+e+yd+ g+++pr++l lv++r+n
  lcl|NCBI__GCF_900100495.1:WP_090439551.1 761 VRLAGVEVIVAEGFERIHRTNLVGMGVLPVEFKPGTTRLTLGLDGSETYDIEGDVSPRCELILVIHRRN 829
                                               ********************************************************************* PP

                                 TIGR02333 823 geklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
                                               ge  +vpvtcrldta ev+vy+aggvlqrfaqdfle
  lcl|NCBI__GCF_900100495.1:WP_090439551.1 830 GEVTQVPVTCRLDTAAEVHVYKAGGVLQRFAQDFLE 865
                                               **********************************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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.09
# Mc/sec: 7.55
//
[ok]

This GapMind analysis is from Sep 24 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