GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Pseudomonas taeanensis MS-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 WP_025165804.1 TMS3_RS13490 Fe/S-dependent 2-methylisocitrate dehydratase AcnD

Query= SwissProt::Q937N8
         (869 letters)



>NCBI__GCF_000498575.2:WP_025165804.1
          Length = 869

 Score = 1424 bits (3687), Expect = 0.0
 Identities = 710/870 (81%), Positives = 775/870 (89%), Gaps = 4/870 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MNS  RKPLPGT+LD+FD RAAV+AI P AY KLPYTSRVLAE LVRRC+P  LTDSL Q
Sbjct: 1   MNSQFRKPLPGTRLDFFDTRAAVDAIAPDAYAKLPYTSRVLAEQLVRRCEPDALTDSLKQ 60

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

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVE  GFDPDAF KNRAIEDRRNEDRFHFI+WTK AFKNVDVIP GNGIMHQINLEKM
Sbjct: 121 SLAVEAPGFDPDAFTKNRAIEDRRNEDRFHFIEWTKTAFKNVDVIPAGNGIMHQINLEKM 180

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

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
            L GKRQPGITATDIVLA+TEFLRKE+VVGA++EF GEGA SLT+GDRATISNM PEYGA
Sbjct: 241 RLVGKRQPGITATDIVLAITEFLRKERVVGAWVEFFGEGADSLTIGDRATISNMCPEYGA 300

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

Query: 361 NMAGPSNPHKRLPTSALAERGIAVD--LDKASAQEAEGLMPDGAVIIAAITSCTNTSNPR 418
           NMAGPSNPH+RLPTSAL ERGIA +  L     +E+EGLMPDGAVIIAAITSCTNTSNPR
Sbjct: 361 NMAGPSNPHRRLPTSALHERGIADEGKLAAGKIEESEGLMPDGAVIIAAITSCTNTSNPR 420

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

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

Query: 539 TIRFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASG 598
           T+RFDIE+DVLG D+ G PV LKD+WPSDEEIDAIVA SVKPEQF+++Y PMF +     
Sbjct: 541 TVRFDIEQDVLGIDKAGNPVTLKDLWPSDEEIDAIVAASVKPEQFKQIYIPMFDLGTIQ- 599

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

Query: 659 AAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEP 718
           AAGEYL +MGLPEEDFNSYATHRGDHLTAQRATFANP L+NEMAVVDGQVKKGSLAR+EP
Sbjct: 660 AAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPQLVNEMAVVDGQVKKGSLARVEP 719

Query: 719 EGKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHR 778
           EGKV+RMWEAIE YM+RKQ LII+AGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHR
Sbjct: 720 EGKVMRMWEAIEAYMNRKQSLIIVAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHR 779

Query: 779 TNLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTC 838
           TNL+GMGVLP+EFKPG  RLTLGLDGTETYD+ GE  PR  LTLV+ RKNGE   VPV C
Sbjct: 780 TNLVGMGVLPVEFKPGTTRLTLGLDGTETYDIQGELSPRGELTLVIQRKNGEVTRVPVIC 839

Query: 839 RLDSDEEVSIYEAGGVL-HFAQDFLESSRA 867
           RLD+  EV++Y AGGVL  FAQDFLE + A
Sbjct: 840 RLDTAAEVNVYNAGGVLQRFAQDFLEGAVA 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: 2229
Number of extensions: 87
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_025165804.1 TMS3_RS13490 (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.2966739.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 1773.1   0.0          0 1772.9   0.0    1.0  1  NCBI__GCF_000498575.2:WP_025165804.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000498575.2:WP_025165804.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1772.9   0.0         0         0       1     858 []       2     865 ..       2     865 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1772.9 bits;  conditional E-value: 0
                             TIGR02333   1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwyp 73 
                                           n+++rk+lpgt ld+fd+raav+ai+p ay+klpytsrvlae+lvrr++p+ l++slkqlierkr+ldfpwyp
  NCBI__GCF_000498575.2:WP_025165804.1   2 NSQFRKPLPGTRLDFFDTRAAVDAIAPDAYAKLPYTSRVLAEQLVRRCEPDALTDSLKQLIERKRDLDFPWYP 74 
                                           899********************************************************************** PP

                             TIGR02333  74 arvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrned 146
                                           arvvchdilgqtalvdlaglrdaiaekggdp++vnpvv+tqlivdhslave  gfdpdaf+knraiedrrned
  NCBI__GCF_000498575.2:WP_025165804.1  75 ARVVCHDILGQTALVDLAGLRDAIAEKGGDPSKVNPVVPTQLIVDHSLAVEAPGFDPDAFTKNRAIEDRRNED 147
                                           ************************************************************************* PP

                             TIGR02333 147 rfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggle 219
                                           rfhfi+wtk+afknvdvipagngimhqinlekmspv+q++ gvafpdt+vgtdshtphvdalgviaigvggle
  NCBI__GCF_000498575.2:WP_025165804.1 148 RFHFIEWTKTAFKNVDVIPAGNGIMHQINLEKMSPVIQARGGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLE 220
                                           ************************************************************************* PP

                             TIGR02333 220 aetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisn 292
                                           aetvmlg +s+mrlpdivgv+l gkrqpgitatdivla+teflrke+vv+a++effgega +lt+gdratisn
  NCBI__GCF_000498575.2:WP_025165804.1 221 AETVMLGLPSMMRLPDIVGVRLVGKRQPGITATDIVLAITEFLRKERVVGAWVEFFGEGADSLTIGDRATISN 293
                                           ************************************************************************* PP

                             TIGR02333 293 mtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagps 365
                                           m+peygata+mf+id+qtidylkltgre+eqv+lve yak++glwad+l +a+yervl+fdls+vvrn+agps
  NCBI__GCF_000498575.2:WP_025165804.1 294 MCPEYGATASMFYIDQQTIDYLKLTGREPEQVALVENYAKTTGLWADALVTAEYERVLEFDLSTVVRNMAGPS 366
                                           ************************************************************************* PP

                             TIGR02333 366 npharlatsdlaakgiakevee......eaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkr 432
                                           nph+rl+ts l  +gia e +       e+eglmpdgaviiaaitsctntsnprnvvaagl+a++an+lgl r
  NCBI__GCF_000498575.2:WP_025165804.1 367 NPHRRLPTSALHERGIADEGKLaagkieESEGLMPDGAVIIAAITSCTNTSNPRNVVAAGLVAKKANALGLVR 439
                                           ****************987654444555999****************************************** PP

                             TIGR02333 433 kpwvksslapgskvvklyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnr 505
                                           kpwvk+s+apgskv+klyle+agll+ele+lgfgiv++acttcngmsgaldpviqqeiidrdlyatavlsgnr
  NCBI__GCF_000498575.2:WP_025165804.1 440 KPWVKTSFAPGSKVAKLYLEDAGLLSELEQLGFGIVGYACTTCNGMSGALDPVIQQEIIDRDLYATAVLSGNR 512
                                           ************************************************************************* PP

                             TIGR02333 506 nfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqf 578
                                           nfdgrihpyakqaflaspplvvayaiagt+rfdie+dvlg+d+ g+++ lkd+wpsdeeida+vaa+vkpeqf
  NCBI__GCF_000498575.2:WP_025165804.1 513 NFDGRIHPYAKQAFLASPPLVVAYAIAGTVRFDIEQDVLGIDKAGNPVTLKDLWPSDEEIDAIVAASVKPEQF 585
                                           ************************************************************************* PP

                             TIGR02333 579 rkvyipmfdledaqkkvsplydwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnailld 651
                                           +++yipmfdl++ q++ splydwrpmstyirrppywegalagertlkgmrpla+l+dnittdhlspsnailld
  NCBI__GCF_000498575.2:WP_025165804.1 586 KQIYIPMFDLGTIQEAESPLYDWRPMSTYIRRPPYWEGALAGERTLKGMRPLAILPDNITTDHLSPSNAILLD 658
                                           ************************************************************************* PP

                             TIGR02333 652 saageylakmglpeedfnsyathrgdhltaqratfanpklfnemvkedgkvkqgslariepegkvtrmweaie 724
                                           saageyl+kmglpeedfnsyathrgdhltaqratfanp+l+nem+ +dg+vk+gslar+epegkv+rmweaie
  NCBI__GCF_000498575.2:WP_025165804.1 659 SAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPQLVNEMAVVDGQVKKGSLARVEPEGKVMRMWEAIE 731
                                           ************************************************************************* PP

                             TIGR02333 725 tymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefkpgtnrktlald 797
                                           +ymnrkq lii+agadygqgssrdwaakgvrlagve ivaegferihrtnlvgmgvlp+efkpgt r tl+ld
  NCBI__GCF_000498575.2:WP_025165804.1 732 AYMNRKQSLIIVAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTNLVGMGVLPVEFKPGTTRLTLGLD 804
                                           ************************************************************************* PP

                             TIGR02333 798 gtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
                                           gte+yd+ ge +pr +ltlv++rknge   vpv crldta ev+vy+aggvlqrfaqdfle
  NCBI__GCF_000498575.2:WP_025165804.1 805 GTETYDIQGELSPRGELTLVIQRKNGEVTRVPVICRLDTAAEVNVYNAGGVLQRFAQDFLE 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 27.75
//
[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:

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