Alignments for a candidate for acn in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Pseudomonas stutzeri RCH2

Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate GFF2473 Psest_2521 aconitate hydratase 1

Query= SwissProt::P37032
         (891 letters)



>FitnessBrowser__psRCH2:GFF2473
          Length = 891

 Score = 1246 bits (3224), Expect = 0.0
 Identities = 618/885 (69%), Positives = 717/885 (81%), Gaps = 2/885 (0%)

Query: 6   DSLSTKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTVTTKDI 65
           DSL  +  L V GKTY+YYSL +A  +    I+RLP SLKVLLENLLR+ED  TV   D+
Sbjct: 5   DSLKCRRSLEVAGKTYHYYSLPDAAAQ-LGDISRLPTSLKVLLENLLRWEDNQTVRADDL 63

Query: 66  KAIADWLHNKTSQHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISPLSPV 125
           K++  WL  ++S  EI +RP RVLMQDFTGVPAVVDLAAMR A+ K GG+  KI+PLSPV
Sbjct: 64  KSLVSWLDTRSSTMEIQYRPARVLMQDFTGVPAVVDLAAMRDAVAKAGGDPQKINPLSPV 123

Query: 126 DLVIDHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGICHQV 185
           DLVIDHSVMVD+F S  A E N +IE++RN ERYEFLRWGQ+AF NF VVPPGTGICHQV
Sbjct: 124 DLVIDHSVMVDRFGSDQAFEQNVEIEMQRNGERYEFLRWGQQAFDNFAVVPPGTGICHQV 183

Query: 186 NLEYLGKTVWNSENDGQLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVS 245
           NLEYLG+ VW  E +G+ +AYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVS
Sbjct: 184 NLEYLGQVVWTREENGETFAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVS 243

Query: 246 MLIPEVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLADRATI 305
           MLIPEVIGF+L+GKL EG+TATDLVLTVTQMLRK GVVGKFVEFYGPGL+ LPLADRATI
Sbjct: 244 MLIPEVIGFRLTGKLNEGVTATDLVLTVTQMLRKHGVVGKFVEFYGPGLDHLPLADRATI 303

Query: 306 SNMAPEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEEPVFTDS 365
            NMAPEYGATCGFFPVD+ TI YL LTGR++  IALVEAY+KAQGMW D ++  P FT +
Sbjct: 304 GNMAPEYGATCGFFPVDQVTIDYLRLTGRNEERIALVEAYSKAQGMWRDSNSPAPEFTAT 363

Query: 366 LHLDLGSVEPSLAGPKRPQDKVNLSSLPVEFNNFLIEVGKEKEKEKTFAVKNKDFQMKHG 425
           L LDL  V PS+AGPKRPQD+V L  +   F+  L   G++++ +  FAV  + FQ+KHG
Sbjct: 364 LELDLSQVRPSVAGPKRPQDRVTLGDIGANFDLLLETSGRQQQADTDFAVAAEQFQLKHG 423

Query: 426 HVVIAAITSCTNTSNPSVLMAAGLVAKKAIEKGLQRKPWVKSSLAPGSKVVTDYLRHAGL 485
            VVIAAITSCTNTSNP+VLMAAGLVAKKAIE+GLQRKPWVK+SLAPGSKVVTDYL  AGL
Sbjct: 424 AVVIAAITSCTNTSNPNVLMAAGLVAKKAIERGLQRKPWVKTSLAPGSKVVTDYLERAGL 483

Query: 486 QTYLDQLGFNLVGYGCTTCIGNSGPLPDDISHCVAEHDLVVSSVLSGNRNFEGRVHPQVR 545
             YLD+LGFNLVGYGCTTCIGNSGPLPD I   + ++DL+VSSVLSGNRNFEGRVHP V+
Sbjct: 484 TRYLDELGFNLVGYGCTTCIGNSGPLPDAIGQAITDNDLIVSSVLSGNRNFEGRVHPLVK 543

Query: 546 ANWLASPPLVVAYALCGTTCSDLSREPIGQDKEGNDVYLKDIWPSNEEIAAEVAKVSGTM 605
           ANWLASPPLVVA+AL GTT  D+ REP+G D +   VYLKDIWPS+ EIA  VA++ G M
Sbjct: 544 ANWLASPPLVVAFALAGTTRIDMDREPLGYDAQNQPVYLKDIWPSSAEIAEAVARIDGEM 603

Query: 606 FRKEYAEVFKGDAHWQAIQTSSGQTYEWNPDSTYIQHPPFFENLSLKPEPLKPIKQAYVL 665
           FR  YA+VF GD HWQ I  S+G TY WN +S+Y+Q+PP+FE++   P P   ++ A VL
Sbjct: 604 FRSRYADVFSGDEHWQKIPVSAGDTYAWNANSSYVQNPPYFEDIGQPPTPPADVENARVL 663

Query: 666 ALFGDSITTDHISPAGSIKASSPAGLYLKSKGVDEKDFNSYGSRRGNHEVMMRGTFANIR 725
           A+FGDSITTDHISPAG+IKASSPAGLYL+S GV  +DFNSYGSRRGNHEVMMRGTFANIR
Sbjct: 664 AVFGDSITTDHISPAGNIKASSPAGLYLQSLGVAPEDFNSYGSRRGNHEVMMRGTFANIR 723

Query: 726 IRNEMTPGQEGGVTRYVPTGETMSIYDAAMRYQENQQDLVIIAGKEYGTGSSRDWAAKGT 785
           IRNEM  G+EGG T Y P+GE +SIYDAAMRYQ     LV+IAGKEYGTGSSRDWAAKGT
Sbjct: 724 IRNEMLGGEEGGNTLYQPSGEKLSIYDAAMRYQAEGVPLVVIAGKEYGTGSSRDWAAKGT 783

Query: 786 NLLGVKAVITESFERIHRSNLIGMGILPLQFKEGTTRKTLKLDGSERISIE-ISDKLTPG 844
           NLLGVKAVI ESFERIHRSNLIGMG+L LQF    TR++L L+G E++SI  +   + P 
Sbjct: 784 NLLGVKAVIAESFERIHRSNLIGMGVLALQFVNDQTRQSLGLNGMEKLSIRGLDADIKPR 843

Query: 845 AMVPVTIERQDGDIEKIETLCRIDTADELEYYKNGGILQYVLRKI 889
            M+ V +ER DG  +  + L RIDT +E++Y+K GGIL YVLR++
Sbjct: 844 QMLTVDVERADGSRDSFQVLSRIDTLNEVQYFKAGGILHYVLRQL 888


Lambda     K      H
   0.316    0.134    0.393 

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: 2085
Number of extensions: 104
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: 891
Length of database: 891
Length adjustment: 43
Effective length of query: 848
Effective length of database: 848
Effective search space:   719104
Effective search space used:   719104
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 (21.6 bits)
S2: 56 (26.2 bits)

Align candidate GFF2473 Psest_2521 (aconitate hydratase 1)
to HMM TIGR01341 (acnA: aconitate hydratase 1 (EC 4.2.1.3))

# 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/TIGR01341.hmm
# target sequence database:        /tmp/gapView.22870.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01341  [M=876]
Accession:   TIGR01341
Description: aconitase_1: aconitate hydratase 1
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 1420.2   0.0          0 1420.0   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF2473  Psest_2521 aconitate hydratase 1


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF2473  Psest_2521 aconitate hydratase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1420.0   0.0         0         0       1     876 []      18     889 ..      18     889 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1420.0 bits;  conditional E-value: 0
                           TIGR01341   1 kkvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlqdft 75 
                                         k+++yysl+ ++ +l++is+lp sl++lle++lr+ d+++++ +d+++l++w  +  + +ei+++parv++qdft
  lcl|FitnessBrowser__psRCH2:GFF2473  18 KTYHYYSLPDAAAQLGDISRLPTSLKVLLENLLRWEDNQTVRADDLKSLVSWLDTRSSTMEIQYRPARVLMQDFT 92 
                                         689************************************************************************ PP

                           TIGR01341  76 Gvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwakkaf 150
                                         Gvpavvdlaa+r+av++ g+dp+kinpl+pvdlvidhsv vd++g+++a+e+nve+e++rn ery+fl+w+++af
  lcl|FitnessBrowser__psRCH2:GFF2473  93 GVPAVVDLAAMRDAVAKAGGDPQKINPLSPVDLVIDHSVMVDRFGSDQAFEQNVEIEMQRNGERYEFLRWGQQAF 167
                                         *************************************************************************** PP

                           TIGR01341 151 knlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaallGqpv 225
                                          n+ vvppgtGi+hqvnleyl++vv++ e++ge++aypd+lvGtdshttminGlGvlGwGvGGieaeaa+lGqpv
  lcl|FitnessBrowser__psRCH2:GFF2473 168 DNFAVVPPGTGICHQVNLEYLGQVVWTREENGETFAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPV 242
                                         *************************************************************************** PP

                           TIGR01341 226 slsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmapeyGataaff 300
                                         s+ +peviG++ltGkl+eGvtatdlvltvt++lrk+gvvgkfvef+G+gl++l+ladrati nmapeyGat++ff
  lcl|FitnessBrowser__psRCH2:GFF2473 243 SMLIPEVIGFRLTGKLNEGVTATDLVLTVTQMLRKHGVVGKFVEFYGPGLDHLPLADRATIGNMAPEYGATCGFF 317
                                         *************************************************************************** PP

                           TIGR01341 301 piddvtlqylrltgrdedkvelvekylkaqelfvd.dseepkytdvveldlsdveasvaGpkrpqdrvalkevka 374
                                         p+d+vt++ylrltgr+e+++ lve+y kaq++++d +s  p++t ++eldls+v++svaGpkrpqdrv+l ++ a
  lcl|FitnessBrowser__psRCH2:GFF2473 318 PVDQVTIDYLRLTGRNEERIALVEAYSKAQGMWRDsNSPAPEFTATLELDLSQVRPSVAGPKRPQDRVTLGDIGA 392
                                         **********************************977888*********************************** PP

                           TIGR01341 375 afksslesnagekglalrkeakekklegkeaelkdgavviaaitsctntsnpsvllgagllakkavelGlkvkpy 449
                                         +f   le+++ +++       ++ ++  ++ +lk+gavviaaitsctntsnp vl++agl+akka+e Gl++kp+
  lcl|FitnessBrowser__psRCH2:GFF2473 393 NFDLLLETSGRQQQ-----ADTDFAVAAEQFQLKHGAVVIAAITSCTNTSNPNVLMAAGLVAKKAIERGLQRKPW 462
                                         ***99998877766.....667788899*********************************************** PP

                           TIGR01341 450 vktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikendlevsavlsGnrnfegr 524
                                         vktslapGskvvtdyl ++gl++yl+elGfnlvGyGcttciGnsGpl++++++ai++ndl vs+vlsGnrnfegr
  lcl|FitnessBrowser__psRCH2:GFF2473 463 VKTSLAPGSKVVTDYLERAGLTRYLDELGFNLVGYGCTTCIGNSGPLPDAIGQAITDNDLIVSSVLSGNRNFEGR 537
                                         *************************************************************************** PP

                           TIGR01341 525 ihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeev 599
                                         +hplvkan+laspplvva+alaGt  id+++ep+g+d + ++vylkdiwps  eiae+v   +  e+f+ +y+ v
  lcl|FitnessBrowser__psRCH2:GFF2473 538 VHPLVKANWLASPPLVVAFALAGTTRIDMDREPLGYDAQNQPVYLKDIWPSSAEIAEAV-ARIDGEMFRSRYADV 611
                                         *********************************************************65.679************ PP

                           TIGR01341 600 tegnerwnelevtssdlyewdekstyireppffeelklepeevedikgarillllGdsittdhispaGsikkdsp 674
                                         ++g+e+w+++ v+ +d+y+w+ +s+y+++pp+fe++ + p+   d+++ar+l+++GdsittdhispaG+ik  sp
  lcl|FitnessBrowser__psRCH2:GFF2473 612 FSGDEHWQKIPVSAGDTYAWNANSSYVQNPPYFEDIGQPPTPPADVENARVLAVFGDSITTDHISPAGNIKASSP 686
                                         *************************************************************************** PP

                           TIGR01341 675 aakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvylpdsevvsvydaamkykkegvp 749
                                         a+ yl+  Gv ++dfnsyGsrrGnhevm+rGtfaniri+n+++ g+eGg t+y p +e++s+ydaam+y+ egvp
  lcl|FitnessBrowser__psRCH2:GFF2473 687 AGLYLQSLGVAPEDFNSYGSRRGNHEVMMRGTFANIRIRNEMLGGEEGGNTLYQPSGEKLSIYDAAMRYQAEGVP 761
                                         *************************************************************************** PP

                           TIGR01341 750 lvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltgeetidvddi 824
                                         lvv+aGkeyG+Gssrdwaakgt+llGvkaviaesferihrsnl+gmGvl l+f + +++++lgl+g e++ + ++
  lcl|FitnessBrowser__psRCH2:GFF2473 762 LVVIAGKEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLIGMGVLALQFVNDQTRQSLGLNGMEKLSIRGL 836
                                         **************************************************************************8 PP

                           TIGR01341 825 e.elkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkll 876
                                         + ++kp++ +tv + ++dg++ ++++  ridt  e++y+k gGil+yvlr+l+
  lcl|FitnessBrowser__psRCH2:GFF2473 837 DaDIKPRQMLTVDVERADGSRDSFQVLSRIDTLNEVQYFKAGGILHYVLRQLI 889
                                         548***********************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (891 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 0.03s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 8.69
//
[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