Alignments for a candidate for acn in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_02981 H281DRAFT_02981 aconitase /2-methylcitrate dehydratase (trans-methylaconitate-forming)

Query= SwissProt::Q937N8
         (869 letters)



>FitnessBrowser__Burk376:H281DRAFT_02981
          Length = 865

 Score = 1449 bits (3752), Expect = 0.0
 Identities = 718/870 (82%), Positives = 790/870 (90%), Gaps = 6/870 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+A RK LPGT+LD+FDARAAV+AIQ GAYDKLPYTSRVLAENLVRRCDP TL  SL Q
Sbjct: 1   MNTAYRKRLPGTQLDFFDARAAVDAIQAGAYDKLPYTSRVLAENLVRRCDPVTLVASLKQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           +V RKR+LDFPWFPARVVCHDILGQTALVDLAGLRDAIA QGGDPA VNPVVP QL+VDH
Sbjct: 61  IVERKRELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAQGGDPAMVNPVVPTQLVVDH 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 SPVVQVNDGVAFPDTLVGTDSHTPMVDALGVIAIGVGGLEAESVMLGRASYMRLPDIVGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           +LTGK   GITATD+VL+LTEFLRKEKVVGAYLEF GEG + LTLGDRATI+NMAPE+GA
Sbjct: 241 KLTGKPAEGITATDVVLSLTEFLRKEKVVGAYLEFFGEGTAKLTLGDRATIANMAPEFGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TAAMF+IDEQTI YL+LTGR DE +KLVETYA+ AGLWADSL +AEYERVLKFDLS+VVR
Sbjct: 301 TAAMFYIDEQTIKYLKLTGRDDELVKLVETYAKEAGLWADSLTHAEYERVLKFDLSTVVR 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++RDLYATAVLSGNRNFDGRIHP+AKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPAIQKEIVERDLYATAVLSGNRNFDGRIHPFAKQAFLASPPLVVAYAIAGTI 535

Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
           RFDIEKDVLG D DG  V LKDIWPSDEEIDAIVA SVKPEQFRKVYEPMFA++  + E 
Sbjct: 536 RFDIEKDVLGVDADGNNVTLKDIWPSDEEIDAIVASSVKPEQFRKVYEPMFAVSVDTQEK 595

Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
            +PLYDWRP STYIRRPPYWEGALAGERTL+ +R LAVLGDNITTDHLSPSNAI+ +SAA
Sbjct: 596 ANPLYDWRPMSTYIRRPPYWEGALAGERTLQGMRALAVLGDNITTDHLSPSNAILPDSAA 655

Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
           GEYL +MGLPEEDFNSYATHRGDHLTAQRATFANPTL NEM + DG+VK GS ARIEPEG
Sbjct: 656 GEYLTKMGLPEEDFNSYATHRGDHLTAQRATFANPTLRNEMVIEDGKVKAGSFARIEPEG 715

Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
           K+ RMWEAIETYM+RKQPLI+IAGADYGQGSSRDWAAKGVRLAG E IVAEGFERIHRTN
Sbjct: 716 KITRMWEAIETYMERKQPLIVIAGADYGQGSSRDWAAKGVRLAGAEAIVAEGFERIHRTN 775

Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
           L+GMGVLPLEFKPGVNR+TL +DGTET+DVIGER+PR  LTLV++R++GERVEVPVTCRL
Sbjct: 776 LVGMGVLPLEFKPGVNRITLAIDGTETFDVIGERKPRTDLTLVIHRRSGERVEVPVTCRL 835

Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESSRATA 869
           D+ EE+SIYEAGGVL  FAQDFLESS+A A
Sbjct: 836 DTAEELSIYEAGGVLQRFAQDFLESSKAAA 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: 2221
Number of extensions: 82
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 H281DRAFT_02981 H281DRAFT_02981 (aconitase /2-methylcitrate dehydratase (trans-methylaconitate-forming))
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.10063.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 1777.8   0.1          0 1777.6   0.1    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_02981  H281DRAFT_02981 aconitase /2-met


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_02981  H281DRAFT_02981 aconitase /2-methylcitrate dehydratase (trans-methylacon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1777.6   0.1         0         0       1     858 []       2     859 ..       2     859 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1777.6 bits;  conditional E-value: 0
                                    TIGR02333   1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkre 66 
                                                  nt+yrk lpgt+ld+fdaraav+ai+ gaydklpytsrvlaenlvrr+dp tl aslkq++erkre
  lcl|FitnessBrowser__Burk376:H281DRAFT_02981   2 NTAYRKRLPGTQLDFFDARAAVDAIQAGAYDKLPYTSRVLAENLVRRCDPVTLVASLKQIVERKRE 67 
                                                  899*************************************************************** PP

                                    TIGR02333  67 ldfpwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpda 132
                                                  ldfpw+parvvchdilgqtalvdlaglrdaia++ggdpa vnpvv+tql+vdhslave+ggfdpda
  lcl|FitnessBrowser__Burk376:H281DRAFT_02981  68 LDFPWFPARVVCHDILGQTALVDLAGLRDAIAAQGGDPAMVNPVVPTQLVVDHSLAVECGGFDPDA 133
                                                  ****************************************************************** PP

                                    TIGR02333 133 feknraiedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgt 198
                                                  f+knraiedrrnedrf finwtk+af+nvdvip+gngi+hqinle+mspvvqv++gvafpdtlvgt
  lcl|FitnessBrowser__Burk376:H281DRAFT_02981 134 FAKNRAIEDRRNEDRFDFINWTKRAFRNVDVIPPGNGILHQINLERMSPVVQVNDGVAFPDTLVGT 199
                                                  ****************************************************************** PP

                                    TIGR02333 199 dshtphvdalgviaigvggleaetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrk 264
                                                  dshtp vdalgviaigvggleae+vmlgras+mrlpdivgv+ltgk + gitatd+vl+lteflrk
  lcl|FitnessBrowser__Burk376:H281DRAFT_02981 200 DSHTPMVDALGVIAIGVGGLEAESVMLGRASYMRLPDIVGVKLTGKPAEGITATDVVLSLTEFLRK 265
                                                  ****************************************************************** PP

                                    TIGR02333 265 ekvvsayleffgegakaltlgdratisnmtpeygataamfaideqtidylkltgreeeqvklvety 330
                                                  ekvv+ayleffgeg+  ltlgdrati+nm+pe+gataamf+ideqti+ylkltgr++e vklvety
  lcl|FitnessBrowser__Burk376:H281DRAFT_02981 266 EKVVGAYLEFFGEGTAKLTLGDRATIANMAPEFGATAAMFYIDEQTIKYLKLTGRDDELVKLVETY 331
                                                  ****************************************************************** PP

                                    TIGR02333 331 akaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiakeveeeaeglmpdg 396
                                                  ak aglwadsl +a+yervlkfdls+vvr+lagpsnph+rl+ s+laa+gi+++ve+e+ glmpdg
  lcl|FitnessBrowser__Burk376:H281DRAFT_02981 332 AKEAGLWADSLTHAEYERVLKFDLSTVVRTLAGPSNPHRRLPVSELAARGISGKVENEP-GLMPDG 396
                                                  ***********************************************************.****** PP

                                    TIGR02333 397 aviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvklyleeagllkelek 462
                                                  aviiaaitsctnt nprn++aagllarnan++gl+rkpw k+slapgsk+v lyleeagll+ele+
  lcl|FitnessBrowser__Burk376:H281DRAFT_02981 397 AVIIAAITSCTNTNNPRNMIAAGLLARNANRRGLTRKPWAKTSLAPGSKAVTLYLEEAGLLPELEQ 462
                                                  ****************************************************************** PP

                                    TIGR02333 463 lgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflaspplvva 528
                                                  lgfg+va+act+cngmsgaldp+iq+ei++rdlyatavlsgnrnfdgrihp+akqaflaspplvva
  lcl|FitnessBrowser__Burk376:H281DRAFT_02981 463 LGFGVVAYACTSCNGMSGALDPAIQKEIVERDLYATAVLSGNRNFDGRIHPFAKQAFLASPPLVVA 528
                                                  ****************************************************************** PP

                                    TIGR02333 529 yaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdle.daqk 593
                                                  yaiagtirfdiekdvlgvdadg+++ lkdiwpsdeeida+va++vkpeqfrkvy+pmf+++ d+q+
  lcl|FitnessBrowser__Burk376:H281DRAFT_02981 529 YAIAGTIRFDIEKDVLGVDADGNNVTLKDIWPSDEEIDAIVASSVKPEQFRKVYEPMFAVSvDTQE 594
                                                  ****************************************************************** PP

                                    TIGR02333 594 kvsplydwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnailldsaageyla 659
                                                  k+ plydwrpmstyirrppywegalagertl+gmr lavlgdnittdhlspsnail dsaageyl+
  lcl|FitnessBrowser__Burk376:H281DRAFT_02981 595 KANPLYDWRPMSTYIRRPPYWEGALAGERTLQGMRALAVLGDNITTDHLSPSNAILPDSAAGEYLT 660
                                                  ****************************************************************** PP

                                    TIGR02333 660 kmglpeedfnsyathrgdhltaqratfanpklfnemvkedgkvkqgslariepegkvtrmweaiet 725
                                                  kmglpeedfnsyathrgdhltaqratfanp l nemv+edgkvk gs+ariepegk+trmweaiet
  lcl|FitnessBrowser__Burk376:H281DRAFT_02981 661 KMGLPEEDFNSYATHRGDHLTAQRATFANPTLRNEMVIEDGKVKAGSFARIEPEGKITRMWEAIET 726
                                                  ****************************************************************** PP

                                    TIGR02333 726 ymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefkpgtnr 791
                                                  ym+rkqpli+iagadygqgssrdwaakgvrlag eaivaegferihrtnlvgmgvlplefkpg+nr
  lcl|FitnessBrowser__Burk376:H281DRAFT_02981 727 YMERKQPLIVIAGADYGQGSSRDWAAKGVRLAGAEAIVAEGFERIHRTNLVGMGVLPLEFKPGVNR 792
                                                  ****************************************************************** PP

                                    TIGR02333 792 ktlaldgtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfl 857
                                                   tla+dgte++dv+ge++pr+dltlv++r+ ge++evpvtcrldtaee+s+yeaggvlqrfaqdfl
  lcl|FitnessBrowser__Burk376:H281DRAFT_02981 793 ITLAIDGTETFDVIGERKPRTDLTLVIHRRSGERVEVPVTCRLDTAEELSIYEAGGVLQRFAQDFL 858
                                                  *****************************************************************9 PP

                                    TIGR02333 858 e 858
                                                  e
  lcl|FitnessBrowser__Burk376:H281DRAFT_02981 859 E 859
                                                  7 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: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.08
# Mc/sec: 9.16
//
[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