Alignments for a candidate for acn in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Pseudomonas putida KT2440

Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate PP_2112 PP_2112 aconitate hydratase 1

Query= reanno::Marino:GFF3491
         (919 letters)



>FitnessBrowser__Putida:PP_2112
          Length = 913

 Score = 1308 bits (3386), Expect = 0.0
 Identities = 653/917 (71%), Positives = 748/917 (81%), Gaps = 15/917 (1%)

Query: 7   SKDSLNTLSSLDAGGKTFHYYSLPKAADTLGDLNRLPFSLKVLMENLLRNEDGTTVDRSH 66
           S DSLNTL  L  G KT+HY+SL +AA  LGDL RLP SLKVL+ENLLR EDG TV    
Sbjct: 3   SLDSLNTLKPLKVGDKTYHYFSLTEAARQLGDLQRLPMSLKVLLENLLRWEDGATVTGDD 62

Query: 67  IDAMVQWMKDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAMINPLSP 126
           + A+ QW+ +R SD EIQ+RPARVLMQDFTGVP VVDLAAMR A+  AG DP  INPLSP
Sbjct: 63  LRAIAQWLGERRSDREIQYRPARVLMQDFTGVPAVVDLAAMRAAMAKAGGDPQRINPLSP 122

Query: 127 VDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPGTGICHQ 186
           VDLVIDHSVMVD++G   +F +NV IEM+RN ERY FLRWGQ AFDNFRVVPPGTGICHQ
Sbjct: 123 VDLVIDHSVMVDRYGTPQAFAENVDIEMQRNGERYAFLRWGQSAFDNFRVVPPGTGICHQ 182

Query: 187 VNLEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAAMLGQPV 246
           VNLEYLG+TVW ++ DG+T A+PDTLVGTDSHTTMINGLG+LGWGVGGIEAEAAMLGQPV
Sbjct: 183 VNLEYLGRTVWTREADGRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPV 242

Query: 247 SMLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMPVADRAT 306
           SMLIPEV+GFK+TGKLREGITATDLVLTVT+MLRKKGVVGKFVEFYGDGL ++P+ADRAT
Sbjct: 243 SMLIPEVIGFKLTGKLREGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLAELPLADRAT 302

Query: 307 IANMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGHEPVYTDN 366
           IANMAPEYGATCGFFPVD+ T+ Y+RL+GR E  ++LVE Y KAQG+WR PG EP ++D 
Sbjct: 303 IANMAPEYGATCGFFPVDQVTLDYLRLSGRPEATVQLVEQYCKAQGMWRLPGQEPSFSDT 362

Query: 367 LELDMGEVEASLAGPKRPQDRVALKNMKSSFELLMETAEGPAENREANLESEGGQ-TAVG 425
           L LDM +VEASLAGPKRPQDRVAL  +  +F+  +E    P       LESEGG   AVG
Sbjct: 363 LALDMDDVEASLAGPKRPQDRVALGQVSQAFDHFIELQPKPLAKEVGRLESEGGGGVAVG 422

Query: 426 VDDS-----YKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAV 480
             D      Y H         G+   L  GAVVIAAITSCTNTSNPSVMMAAGL+A+KA+
Sbjct: 423 NADQTGAVDYSHQ--------GQTHTLRDGAVVIAAITSCTNTSNPSVMMAAGLVAKKAL 474

Query: 481 QKGLSTKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAV 540
           +KGL  KPWVK+SLAPGSKVVTDY K  G    LD+LGF+LVGYGCTTCIGNSGPL +A+
Sbjct: 475 EKGLQRKPWVKSSLAPGSKVVTDYFKAAGLTPYLDQLGFDLVGYGCTTCIGNSGPLDEAI 534

Query: 541 EKAISDGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGN 600
           EKAI   DLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAG+VRLDL++DPLG+
Sbjct: 535 EKAIGSADLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGSVRLDLTRDPLGS 594

Query: 601 DKDGNPVYLKDLWPSQQEIAEAVEKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSD 660
            KDG PVYL+D+WPSQQEIAEAV KV T MF KEYAEVF GDA W++I+VP++  Y W  
Sbjct: 595 GKDGQPVYLRDIWPSQQEIAEAVAKVDTAMFHKEYAEVFAGDAQWQAIEVPQAATYVWQA 654

Query: 661 KSTYIQHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQE 720
            STYIQHPPFF+G+   P  I +I  A +LALLGDSVTTDHISPAG+ K D+PAG+YL+E
Sbjct: 655 DSTYIQHPPFFDGIGGPPPQIANIHGARVLALLGDSVTTDHISPAGNIKTDSPAGRYLRE 714

Query: 721 HGVEPKDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAM 780
            GVEP+DFNSYGSRRGNHEVMMRGTFAN+RIRNEML G EGG T  VPTGE+++IYDAAM
Sbjct: 715 QGVEPRDFNSYGSRRGNHEVMMRGTFANIRIRNEMLAGEEGGNTLHVPTGEKLSIYDAAM 774

Query: 781 KYQEKGTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQ 840
           +YQ++GTPL+VIAG+EYGTGSSRDWAAKGT LLGVKAV+AES+ERIHRSNL+GMGV+PLQ
Sbjct: 775 RYQQEGTPLLVIAGQEYGTGSSRDWAAKGTNLLGVKAVLAESFERIHRSNLVGMGVLPLQ 834

Query: 841 FPEGTDRKSLKLTGEETISIEGLSG-EIKPGQTLKMTVKYKDGSTETCELKSRIDTANEA 899
           F  G +RK L LTG+E I + GL G  I PG +L + +  +DG  E  E+  RIDT NE 
Sbjct: 835 FKAGHNRKQLGLTGKEQIDVLGLDGAHIHPGMSLPLRITREDGQQEQIEVLCRIDTLNEV 894

Query: 900 VYFKHGGILHYVVREML 916
            YFK GGILHYV+R+M+
Sbjct: 895 EYFKAGGILHYVLRQMI 911


Lambda     K      H
   0.315    0.134    0.390 

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: 2361
Number of extensions: 105
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: 919
Length of database: 913
Length adjustment: 43
Effective length of query: 876
Effective length of database: 870
Effective search space:   762120
Effective search space used:   762120
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: 42 (22.0 bits)
S2: 57 (26.6 bits)

Align candidate PP_2112 PP_2112 (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.23846.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 1436.3   0.0          0 1436.1   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_2112  PP_2112 aconitate hydratase 1


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_2112  PP_2112 aconitate hydratase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1436.1   0.0         0         0       1     876 []      18     911 ..      18     911 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1436.1 bits;  conditional E-value: 0
                           TIGR01341   1 kkvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlqdft 75 
                                         k+++y+sl +++ +l+++++lp sl++lle++lr+ dg +++ +d+ a+++w  e  +d+ei+++parv++qdft
  lcl|FitnessBrowser__Putida:PP_2112  18 KTYHYFSLTEAARQLGDLQRLPMSLKVLLENLLRWEDGATVTGDDLRAIAQWLGERRSDREIQYRPARVLMQDFT 92 
                                         689************************************************************************ PP

                           TIGR01341  76 Gvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwakkaf 150
                                         Gvpavvdlaa+r a+++ g+dp++inpl+pvdlvidhsv vd++g+ +a+++nv++e++rn ery+fl+w++ af
  lcl|FitnessBrowser__Putida:PP_2112  93 GVPAVVDLAAMRAAMAKAGGDPQRINPLSPVDLVIDHSVMVDRYGTPQAFAENVDIEMQRNGERYAFLRWGQSAF 167
                                         *************************************************************************** PP

                           TIGR01341 151 knlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaallGqpv 225
                                          n++vvppgtGi+hqvnleyl++ v++ e dg+++a+pd+lvGtdshttminGlGvlGwGvGGieaeaa+lGqpv
  lcl|FitnessBrowser__Putida:PP_2112 168 DNFRVVPPGTGICHQVNLEYLGRTVWTREADGRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPV 242
                                         *************************************************************************** PP

                           TIGR01341 226 slsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmapeyGataaff 300
                                         s+ +peviG+kltGklreG+tatdlvltvt++lrkkgvvgkfvef+G+gl+el+ladratianmapeyGat++ff
  lcl|FitnessBrowser__Putida:PP_2112 243 SMLIPEVIGFKLTGKLREGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLAELPLADRATIANMAPEYGATCGFF 317
                                         *************************************************************************** PP

                           TIGR01341 301 piddvtlqylrltgrdedkvelvekylkaqelfvddseepkytdvveldlsdveasvaGpkrpqdrvalkevkaa 375
                                         p+d+vtl+ylrl+gr+e +v+lve+y+kaq++++  ++ep ++d++ ld++dveas+aGpkrpqdrval +v +a
  lcl|FitnessBrowser__Putida:PP_2112 318 PVDQVTLDYLRLSGRPEATVQLVEQYCKAQGMWRLPGQEPSFSDTLALDMDDVEASLAGPKRPQDRVALGQVSQA 392
                                         *************************************************************************** PP

                           TIGR01341 376 fkss..lesnagekglalr...............keakekklegkeaelkdgavviaaitsctntsnpsvllgag 433
                                         f +   l+ +   k+++                   a+++  +g++++l+dgavviaaitsctntsnpsv+++ag
  lcl|FitnessBrowser__Putida:PP_2112 393 FDHFieLQPKPLAKEVGRLeseggggvavgnadqTGAVDYSHQGQTHTLRDGAVVIAAITSCTNTSNPSVMMAAG 467
                                         *987333334444544432355666666665554445666667******************************** PP

                           TIGR01341 434 llakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikend 508
                                         l+akka+e Gl++kp+vk+slapGskvvtdy++ +gl+pyl++lGf+lvGyGcttciGnsGpl+e++e+ai   d
  lcl|FitnessBrowser__Putida:PP_2112 468 LVAKKALEKGLQRKPWVKSSLAPGSKVVTDYFKAAGLTPYLDQLGFDLVGYGCTTCIGNSGPLDEAIEKAIGSAD 542
                                         *************************************************************************** PP

                           TIGR01341 509 levsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiaelv 583
                                         l+v++vlsGnrnfegr+hplvk+n+laspplvvayalaG+v +dl+++p+g +kdG++vyl+diwps++eiae+v
  lcl|FitnessBrowser__Putida:PP_2112 543 LTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGSVRLDLTRDPLGSGKDGQPVYLRDIWPSQQEIAEAV 617
                                         *************************************************************************66 PP

                           TIGR01341 584 kkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeevedikgarillllGdsi 658
                                           +v + +f+key+ev+ g+++w+ +ev++ ++y w+ +styi++ppff+++   p ++ +i+gar+l+llGds+
  lcl|FitnessBrowser__Putida:PP_2112 618 -AKVDTAMFHKEYAEVFAGDAQWQAIEVPQAATYVWQADSTYIQHPPFFDGIGGPPPQIANIHGARVLALLGDSV 691
                                         .679*********************************************************************** PP

                           TIGR01341 659 ttdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvylpdsev 733
                                         ttdhispaG+ik dspa++yl+e+Gve+rdfnsyGsrrGnhevm+rGtfaniri+n+++ g+eGg t+++p++e+
  lcl|FitnessBrowser__Putida:PP_2112 692 TTDHISPAGNIKTDSPAGRYLREQGVEPRDFNSYGSRRGNHEVMMRGTFANIRIRNEMLAGEEGGNTLHVPTGEK 766
                                         *************************************************************************** PP

                           TIGR01341 734 vsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgeda 808
                                         +s+ydaam+y++eg+pl+v+aG+eyG+Gssrdwaakgt+llGvkav+aesferihrsnlvgmGvlpl+fk+g+++
  lcl|FitnessBrowser__Putida:PP_2112 767 LSIYDAAMRYQQEGTPLLVIAGQEYGTGSSRDWAAKGTNLLGVKAVLAESFERIHRSNLVGMGVLPLQFKAGHNR 841
                                         *************************************************************************** PP

                           TIGR01341 809 etlgltgeetidvddie..elkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkll 876
                                         + lgltg+e+idv +++  +++p+ ++++++++edg++e +e+ +ridt  e++y+k gGil+yvlr+++
  lcl|FitnessBrowser__Putida:PP_2112 842 KQLGLTGKEQIDVLGLDgaHIHPGMSLPLRITREDGQQEQIEVLCRIDTLNEVEYFKAGGILHYVLRQMI 911
                                         *************9975338***********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (913 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: 00:00:00.09
# Mc/sec: 8.59
//
[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