GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Burkholderia phytofirmans PsJN

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 BPHYT_RS30145 BPHYT_RS30145 aconitate hydratase

Query= SwissProt::Q937N8
         (869 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS30145 BPHYT_RS30145 aconitate
           hydratase
          Length = 865

 Score = 1460 bits (3780), Expect = 0.0
 Identities = 725/870 (83%), Positives = 790/870 (90%), Gaps = 6/870 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+ANRK LPGT+LD+FD RAAV+AIQPGAYDKLPYTSRVLAENLVRRCDP TLT SL Q
Sbjct: 1   MNTANRKRLPGTQLDFFDTRAAVDAIQPGAYDKLPYTSRVLAENLVRRCDPVTLTASLKQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           ++ RKR+LDFPWFPARVVCHDILGQTALVDLAGLRDAIA QGGDPA VNPVVP QL+VDH
Sbjct: 61  IIERKRELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAQGGDPALVNPVVPTQLVVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVECGGFDPDAFAKNRAIEDRRNEDRF FI+WTK+AF+NVDVIPPGNGI+HQINLE+M
Sbjct: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFDFINWTKRAFRNVDVIPPGNGILHQINLERM 180

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPV+   +GVA+PDT VGTDSHTP VDALGVIAIGVGGLEAE+VMLGRAS+MRLPDIVGV
Sbjct: 181 SPVVQVKDGVAFPDTLVGTDSHTPMVDALGVIAIGVGGLEAESVMLGRASYMRLPDIVGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           ELTGK   GITATD+VL+LTEFLRKEKVVGAYLEF G G + LTLGDRATI+NMAPE+GA
Sbjct: 241 ELTGKPAEGITATDVVLSLTEFLRKEKVVGAYLEFYGTGTAKLTLGDRATIANMAPEFGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TAAMF IDEQTI YL+LTGR DE +K VETYA+  GLWADSL NAEYERVLKFDLS+VVR
Sbjct: 301 TAAMFSIDEQTIKYLKLTGRDDELVKRVETYAKKTGLWADSLVNAEYERVLKFDLSTVVR 360

Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
            +AGPSNPH+RLP S LA RGI+        +   GLMPDGAVIIAAITSCTNT+NPRN+
Sbjct: 361 TLAGPSNPHRRLPVSELAARGIS-----GKVENEPGLMPDGAVIIAAITSCTNTNNPRNM 415

Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
           IAA LLARNAN RGL RKPW K+SLAPGSKAV LYLEEA LLP+LE+LGFG+VA+ACT+C
Sbjct: 416 IAAGLLARNANRRGLTRKPWAKTSLAPGSKAVTLYLEEAGLLPELEQLGFGVVAYACTSC 475

Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
           NGMSGALDP IQ+EI++RDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPVIQKEIVERDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535

Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
           RFDIEKDVLG D DG+ V LKDIWP+D EIDAIVA SVKPEQFRKVYEPMFA++  +GE 
Sbjct: 536 RFDIEKDVLGIDADGQAVTLKDIWPTDAEIDAIVASSVKPEQFRKVYEPMFAVSVDTGEK 595

Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
             PLY+WRP STYIRRPPYWEGALAGERTLK +RPLAVLGDNITTDHLSPSNAI+ +SA+
Sbjct: 596 ADPLYNWRPMSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAILADSAS 655

Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
           GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANPTL NEM + DG+VK GSLARIEPEG
Sbjct: 656 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPTLKNEMVLEDGKVKAGSLARIEPEG 715

Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
           KV RMWEAIETYM+RKQPLI+IAGADYGQGSSRDWAAKGVRLAG E IVAEGFERIHRTN
Sbjct: 716 KVTRMWEAIETYMERKQPLIVIAGADYGQGSSRDWAAKGVRLAGAEAIVAEGFERIHRTN 775

Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
           L+GMGVLPLEFKPGVNRLTL +DGTET+DVIGER+PRA LTLV++RKNGERVEVPVTCRL
Sbjct: 776 LVGMGVLPLEFKPGVNRLTLAIDGTETFDVIGERKPRADLTLVIHRKNGERVEVPVTCRL 835

Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESSRATA 869
           D+ EEVSIYEAGGVL  FAQDFLESS+  A
Sbjct: 836 DTAEEVSIYEAGGVLQRFAQDFLESSKKAA 865


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: 2239
Number of extensions: 85
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: 865
Length adjustment: 42
Effective length of query: 827
Effective length of database: 823
Effective search space:   680621
Effective search space used:   680621
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 BPHYT_RS30145 BPHYT_RS30145 (aconitate hydratase)
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.9464.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 1778.4   0.1          0 1778.2   0.1    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS30145  BPHYT_RS30145 aconitate hydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS30145  BPHYT_RS30145 aconitate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1778.2   0.1         0         0       1     858 []       2     859 ..       2     859 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1778.2 bits;  conditional E-value: 0
                                TIGR02333   1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfp 70 
                                              nt+ rk lpgt+ld+fd+raav+ai+pgaydklpytsrvlaenlvrr+dp tl+aslkq+ierkreldfp
  lcl|FitnessBrowser__BFirm:BPHYT_RS30145   2 NTANRKRLPGTQLDFFDTRAAVDAIQPGAYDKLPYTSRVLAENLVRRCDPVTLTASLKQIIERKRELDFP 71 
                                              7899****************************************************************** PP

                                TIGR02333  71 wyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraie 140
                                              w+parvvchdilgqtalvdlaglrdaia++ggdpa vnpvv+tql+vdhslave+ggfdpdaf+knraie
  lcl|FitnessBrowser__BFirm:BPHYT_RS30145  72 WFPARVVCHDILGQTALVDLAGLRDAIAAQGGDPALVNPVVPTQLVVDHSLAVECGGFDPDAFAKNRAIE 141
                                              ********************************************************************** PP

                                TIGR02333 141 drrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgv 210
                                              drrnedrf finwtk+af+nvdvip+gngi+hqinle+mspvvqvk+gvafpdtlvgtdshtp vdalgv
  lcl|FitnessBrowser__BFirm:BPHYT_RS30145 142 DRRNEDRFDFINWTKRAFRNVDVIPPGNGILHQINLERMSPVVQVKDGVAFPDTLVGTDSHTPMVDALGV 211
                                              ********************************************************************** PP

                                TIGR02333 211 iaigvggleaetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegak 280
                                              iaigvggleae+vmlgras+mrlpdivgveltgk + gitatd+vl+lteflrkekvv+aylef+g g+ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS30145 212 IAIGVGGLEAESVMLGRASYMRLPDIVGVELTGKPAEGITATDVVLSLTEFLRKEKVVGAYLEFYGTGTA 281
                                              ********************************************************************** PP

                                TIGR02333 281 altlgdratisnmtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwadslkkavyervl 350
                                               ltlgdrati+nm+pe+gataamf ideqti+ylkltgr++e vk vetyak +glwadsl +a+yervl
  lcl|FitnessBrowser__BFirm:BPHYT_RS30145 282 KLTLGDRATIANMAPEFGATAAMFSIDEQTIKYLKLTGRDDELVKRVETYAKKTGLWADSLVNAEYERVL 351
                                              ********************************************************************** PP

                                TIGR02333 351 kfdlssvvrnlagpsnpharlatsdlaakgiakeveeeaeglmpdgaviiaaitsctntsnprnvvaagl 420
                                              kfdls+vvr+lagpsnph+rl+ s+laa+gi+++ve+e+ glmpdgaviiaaitsctnt nprn++aagl
  lcl|FitnessBrowser__BFirm:BPHYT_RS30145 352 KFDLSTVVRTLAGPSNPHRRLPVSELAARGISGKVENEP-GLMPDGAVIIAAITSCTNTNNPRNMIAAGL 420
                                              ***************************************.****************************** PP

                                TIGR02333 421 larnanklglkrkpwvksslapgskvvklyleeagllkeleklgfgivafacttcngmsgaldpviqqei 490
                                              larnan++gl+rkpw k+slapgsk+v lyleeagll+ele+lgfg+va+act+cngmsgaldpviq+ei
  lcl|FitnessBrowser__BFirm:BPHYT_RS30145 421 LARNANRRGLTRKPWAKTSLAPGSKAVTLYLEEAGLLPELEQLGFGVVAYACTSCNGMSGALDPVIQKEI 490
                                              ********************************************************************** PP

                                TIGR02333 491 idrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwp 560
                                              ++rdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlg+dadg+ + lkdiwp
  lcl|FitnessBrowser__BFirm:BPHYT_RS30145 491 VERDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGIDADGQAVTLKDIWP 560
                                              ********************************************************************** PP

                                TIGR02333 561 sdeeidavvaaavkpeqfrkvyipmfdle.daqkkvsplydwrpmstyirrppywegalagertlkgmrp 629
                                              +d+eida+va++vkpeqfrkvy+pmf+++ d+++k+ ply+wrpmstyirrppywegalagertlkgmrp
  lcl|FitnessBrowser__BFirm:BPHYT_RS30145 561 TDAEIDAIVASSVKPEQFRKVYEPMFAVSvDTGEKADPLYNWRPMSTYIRRPPYWEGALAGERTLKGMRP 630
                                              ********************************************************************** PP

                                TIGR02333 630 lavlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemvked 699
                                              lavlgdnittdhlspsnail+dsa+geylakmglpeedfnsyathrgdhltaqratfanp l+nemv ed
  lcl|FitnessBrowser__BFirm:BPHYT_RS30145 631 LAVLGDNITTDHLSPSNAILADSASGEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPTLKNEMVLED 700
                                              ********************************************************************** PP

                                TIGR02333 700 gkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegfer 769
                                              gkvk gslariepegkvtrmweaietym+rkqpli+iagadygqgssrdwaakgvrlag eaivaegfer
  lcl|FitnessBrowser__BFirm:BPHYT_RS30145 701 GKVKAGSLARIEPEGKVTRMWEAIETYMERKQPLIVIAGADYGQGSSRDWAAKGVRLAGAEAIVAEGFER 770
                                              ********************************************************************** PP

                                TIGR02333 770 ihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkngeklevpvtcrldtaee 839
                                              ihrtnlvgmgvlplefkpg+nr tla+dgte++dv+ge++pradltlv++rknge++evpvtcrldtaee
  lcl|FitnessBrowser__BFirm:BPHYT_RS30145 771 IHRTNLVGMGVLPLEFKPGVNRLTLAIDGTETFDVIGERKPRADLTLVIHRKNGERVEVPVTCRLDTAEE 840
                                              ********************************************************************** PP

                                TIGR02333 840 vsvyeaggvlqrfaqdfle 858
                                              vs+yeaggvlqrfaqdfle
  lcl|FitnessBrowser__BFirm:BPHYT_RS30145 841 VSIYEAGGVLQRFAQDFLE 859
                                              *****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (858 nodes)
Target sequences:                          1  (865 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: 0.08u 0.03s 00:00:00.11 Elapsed: 00:00:00.10
# Mc/sec: 7.38
//
[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 preprint 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