Alignments for a candidate for acn in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Cupriavidus basilensis 4G11

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 RR42_RS11270 RR42_RS11270 aconitate hydratase

Query= SwissProt::Q937N8
         (869 letters)



>FitnessBrowser__Cup4G11:RR42_RS11270
          Length = 865

 Score = 1496 bits (3872), Expect = 0.0
 Identities = 740/870 (85%), Positives = 800/870 (91%), Gaps = 6/870 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+ANRKPLPGT+LD+FD RAAV+AIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSL Q
Sbjct: 1   MNTANRKPLPGTQLDFFDTRAAVDAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLKQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           ++ RK++LDFPWFPARVVCHDILGQTALVDLAGLRDAIA QGGDP  VNPVVP QL+VDH
Sbjct: 61  IIERKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAQGGDPVMVNPVVPTQLVVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVECGGFDPDAFAKNRAIEDRRNEDRF FI+WTK+AFKNVDVIPPGNGI+HQINLE+M
Sbjct: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFDFINWTKKAFKNVDVIPPGNGILHQINLERM 180

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPV+   +GVA+PDT VGTDSHTP VDALGVIAIGVGGLEAE+VMLGRASWMRLPDI+GV
Sbjct: 181 SPVVQVKDGVAFPDTLVGTDSHTPMVDALGVIAIGVGGLEAESVMLGRASWMRLPDIIGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           ELTGK QPGITATD VLALTEFLRKEKVV +YLEF GEG + LTLGDRATISNMAPE+G+
Sbjct: 241 ELTGKPQPGITATDTVLALTEFLRKEKVVSSYLEFFGEGTTHLTLGDRATISNMAPEFGS 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TAAMF+IDEQTI YL+LTGR D  +KLVETYA+ AGLWADSLKNAEY RVL+FDLS+VVR
Sbjct: 301 TAAMFYIDEQTIKYLKLTGRDDALVKLVETYAKEAGLWADSLKNAEYPRVLRFDLSTVVR 360

Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
           N+AGPSNPHKR+PTS LA RGI+        +   GLMPDGAVIIAA+TSCTNT+NPRN+
Sbjct: 361 NIAGPSNPHKRVPTSELAARGIS-----GKVENEPGLMPDGAVIIAAVTSCTNTNNPRNM 415

Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
           +AA LLARNAN  GL RKPWVKSSLAPGSKAV LYLEEANLLP+LE+LGFG+VA+ACT+C
Sbjct: 416 VAAGLLARNANKLGLTRKPWVKSSLAPGSKAVTLYLEEANLLPELEQLGFGVVAYACTSC 475

Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
           NGMSGALDP IQ+E++DRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPVIQKEVVDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535

Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
           RFDIEKDVLGTD DGKPV LKDIWPSDEEIDA+VA SVKP QFRKVYEPMFA+TA +GE 
Sbjct: 536 RFDIEKDVLGTDADGKPVTLKDIWPSDEEIDAVVAASVKPAQFRKVYEPMFAVTADTGEK 595

Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
            SPLYDWR  STYIRRPPYWEGALAGER L  +RPLAVLGDNITTDHLSPSNAIML+SAA
Sbjct: 596 ASPLYDWREMSTYIRRPPYWEGALAGERALTGMRPLAVLGDNITTDHLSPSNAIMLDSAA 655

Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
           GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANPTL NEM VVDG+VK GSLARIEPEG
Sbjct: 656 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPTLKNEMVVVDGKVKPGSLARIEPEG 715

Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
           KV RMWEAIETYM RKQPLI++AGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHRTN
Sbjct: 716 KVTRMWEAIETYMARKQPLIVVAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTN 775

Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
           L+GMGVLPLEFKPGVNR TLG+DGTETYDVIG+R PR  LTLV++RKNGERVEVPVTCRL
Sbjct: 776 LVGMGVLPLEFKPGVNRATLGIDGTETYDVIGDRTPRCDLTLVMHRKNGERVEVPVTCRL 835

Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESSRATA 869
           D+ EEVSIYEAGGVL  FAQDFLESS+A A
Sbjct: 836 DTAEEVSIYEAGGVLQRFAQDFLESSKAAA 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: 2304
Number of extensions: 93
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 RR42_RS11270 RR42_RS11270 (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.14717.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 1804.4   0.0          0 1804.3   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS11270  RR42_RS11270 aconitate hydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS11270  RR42_RS11270 aconitate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1804.3   0.0         0         0       1     858 []       2     859 ..       2     859 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1804.3 bits;  conditional E-value: 0
                                 TIGR02333   1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldf 69 
                                               nt+ rk+lpgt+ld+fd+raav+ai+pgaydklpytsrvlaenlvrr+dp+tl++slkq+ierk+eldf
  lcl|FitnessBrowser__Cup4G11:RR42_RS11270   2 NTANRKPLPGTQLDFFDTRAAVDAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLKQIIERKQELDF 70 
                                               7899***************************************************************** PP

                                 TIGR02333  70 pwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknra 138
                                               pw+parvvchdilgqtalvdlaglrdaia++ggdp  vnpvv+tql+vdhslave+ggfdpdaf+knra
  lcl|FitnessBrowser__Cup4G11:RR42_RS11270  71 PWFPARVVCHDILGQTALVDLAGLRDAIAAQGGDPVMVNPVVPTQLVVDHSLAVECGGFDPDAFAKNRA 139
                                               ********************************************************************* PP

                                 TIGR02333 139 iedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvda 207
                                               iedrrnedrf finwtkkafknvdvip+gngi+hqinle+mspvvqvk+gvafpdtlvgtdshtp vda
  lcl|FitnessBrowser__Cup4G11:RR42_RS11270 140 IEDRRNEDRFDFINWTKKAFKNVDVIPPGNGILHQINLERMSPVVQVKDGVAFPDTLVGTDSHTPMVDA 208
                                               ********************************************************************* PP

                                 TIGR02333 208 lgviaigvggleaetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffg 276
                                               lgviaigvggleae+vmlgras+mrlpdi+gveltgk qpgitatd vlalteflrkekvvs+yleffg
  lcl|FitnessBrowser__Cup4G11:RR42_RS11270 209 LGVIAIGVGGLEAESVMLGRASWMRLPDIIGVELTGKPQPGITATDTVLALTEFLRKEKVVSSYLEFFG 277
                                               ********************************************************************* PP

                                 TIGR02333 277 egakaltlgdratisnmtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwadslkkav 345
                                               eg+  ltlgdratisnm+pe+g+taamf+ideqti+ylkltgr+++ vklvetyak aglwadslk+a+
  lcl|FitnessBrowser__Cup4G11:RR42_RS11270 278 EGTTHLTLGDRATISNMAPEFGSTAAMFYIDEQTIKYLKLTGRDDALVKLVETYAKEAGLWADSLKNAE 346
                                               ********************************************************************* PP

                                 TIGR02333 346 yervlkfdlssvvrnlagpsnpharlatsdlaakgiakeveeeaeglmpdgaviiaaitsctntsnprn 414
                                               y+rvl+fdls+vvrn+agpsnph+r++ts+laa+gi+++ve+e+ glmpdgaviiaa+tsctnt nprn
  lcl|FitnessBrowser__Cup4G11:RR42_RS11270 347 YPRVLRFDLSTVVRNIAGPSNPHKRVPTSELAARGISGKVENEP-GLMPDGAVIIAAVTSCTNTNNPRN 414
                                               ********************************************.************************ PP

                                 TIGR02333 415 vvaagllarnanklglkrkpwvksslapgskvvklyleeagllkeleklgfgivafacttcngmsgald 483
                                               +vaagllarnanklgl+rkpwvksslapgsk+v lyleea+ll+ele+lgfg+va+act+cngmsgald
  lcl|FitnessBrowser__Cup4G11:RR42_RS11270 415 MVAAGLLARNANKLGLTRKPWVKSSLAPGSKAVTLYLEEANLLPELEQLGFGVVAYACTSCNGMSGALD 483
                                               ********************************************************************* PP

                                 TIGR02333 484 pviqqeiidrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgvdadgke 552
                                               pviq+e++drdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlg+dadgk+
  lcl|FitnessBrowser__Cup4G11:RR42_RS11270 484 PVIQKEVVDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGTDADGKP 552
                                               ********************************************************************* PP

                                 TIGR02333 553 irlkdiwpsdeeidavvaaavkpeqfrkvyipmfdle.daqkkvsplydwrpmstyirrppywegalag 620
                                               + lkdiwpsdeeidavvaa+vkp qfrkvy+pmf++  d+++k+splydwr mstyirrppywegalag
  lcl|FitnessBrowser__Cup4G11:RR42_RS11270 553 VTLKDIWPSDEEIDAVVAASVKPAQFRKVYEPMFAVTaDTGEKASPLYDWREMSTYIRRPPYWEGALAG 621
                                               ***********************************999******************************* PP

                                 TIGR02333 621 ertlkgmrplavlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhltaqratfanp 689
                                               er+l gmrplavlgdnittdhlspsnai+ldsaageylakmglpeedfnsyathrgdhltaqratfanp
  lcl|FitnessBrowser__Cup4G11:RR42_RS11270 622 ERALTGMRPLAVLGDNITTDHLSPSNAIMLDSAAGEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANP 690
                                               ********************************************************************* PP

                                 TIGR02333 690 klfnemvkedgkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdwaakgvrlag 758
                                                l+nemv +dgkvk gslariepegkvtrmweaietym rkqpli++agadygqgssrdwaakgvrlag
  lcl|FitnessBrowser__Cup4G11:RR42_RS11270 691 TLKNEMVVVDGKVKPGSLARIEPEGKVTRMWEAIETYMARKQPLIVVAGADYGQGSSRDWAAKGVRLAG 759
                                               ********************************************************************* PP

                                 TIGR02333 759 veaivaegferihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkngekle 827
                                               veaivaegferihrtnlvgmgvlplefkpg+nr+tl++dgte+ydv+g++tpr+dltlv++rknge++e
  lcl|FitnessBrowser__Cup4G11:RR42_RS11270 760 VEAIVAEGFERIHRTNLVGMGVLPLEFKPGVNRATLGIDGTETYDVIGDRTPRCDLTLVMHRKNGERVE 828
                                               ********************************************************************* PP

                                 TIGR02333 828 vpvtcrldtaeevsvyeaggvlqrfaqdfle 858
                                               vpvtcrldtaeevs+yeaggvlqrfaqdfle
  lcl|FitnessBrowser__Cup4G11:RR42_RS11270 829 VPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 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: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 13.23
//
[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