GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS30145
          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.17327.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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 12.42
//
[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:

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