Alignments for a candidate for acn in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Pseudomonas simiae WCS417

Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate GFF1478 PS417_07515 aconitate hydratase

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



>FitnessBrowser__WCS417:GFF1478
          Length = 913

 Score = 1325 bits (3428), Expect = 0.0
 Identities = 657/912 (72%), Positives = 752/912 (82%), Gaps = 5/912 (0%)

Query: 7   SKDSLNTLSSLDAGGKTFHYYSLPKAADTLGDLNRLPFSLKVLMENLLRNEDGTTVDRSH 66
           S DSL TL +L+   KT+HY+SLP+AA +LGDL++LP SLKVL+ENLLR ED  TV  + 
Sbjct: 3   SLDSLRTLKTLEIDSKTYHYFSLPEAAKSLGDLDKLPMSLKVLLENLLRWEDNKTVTGAD 62

Query: 67  IDAMVQWMKDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAMINPLSP 126
           + A+  W+K+R SD EIQ+RPARVLMQDFTGVP VVDLAAMR AV  AG DP  INPLSP
Sbjct: 63  LKAIAAWLKERQSDREIQYRPARVLMQDFTGVPAVVDLAAMRAAVAKAGGDPQRINPLSP 122

Query: 127 VDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPGTGICHQ 186
           VDLVIDHSVMVDKFG   +F+ NV IEM+RN ERY FLRWGQ AFDNF VVPPGTGICHQ
Sbjct: 123 VDLVIDHSVMVDKFGTTGAFEQNVDIEMQRNGERYAFLRWGQSAFDNFSVVPPGTGICHQ 182

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

Query: 247 SMLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMPVADRAT 306
           SMLIPEV+GFK+TGKL+EGITATDLVLTVT+MLRKKGVVGKFVEFYGDGL D+P+ADRAT
Sbjct: 243 SMLIPEVIGFKLTGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLADLPLADRAT 302

Query: 307 IANMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGHEPVYTDN 366
           IANMAPEYGATCGFFPVDE T+ Y+RL+GR  E ++LVEAY KAQGLWR  G EPV+TD+
Sbjct: 303 IANMAPEYGATCGFFPVDEVTLDYLRLSGRPTETVKLVEAYTKAQGLWRNAGQEPVFTDS 362

Query: 367 LELDMGEVEASLAGPKRPQDRVALKNMKSSFELLMETAEGPAENREANLESEGGQ-TAVG 425
           L LDMG VEASLAGPKRPQDRVAL N+  +F   ++    P    E  LESEGG   AVG
Sbjct: 363 LALDMGSVEASLAGPKRPQDRVALPNVGQAFSDFLDLQFKPTNKEEGRLESEGGGGVAVG 422

Query: 426 VDDSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAVQKGLS 485
             D          E +G+  RL  GAVVIAAITSCTNTSNPSVMMAAGL+A+KAV+KGL+
Sbjct: 423 NADLV---GETDYEYDGQTYRLKNGAVVIAAITSCTNTSNPSVMMAAGLLAKKAVEKGLT 479

Query: 486 TKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAVEKAIS 545
            KPWVKTSLAPGSKVVTDY K  G    LDKLGF+LVGYGCTTCIGNSGPLP+ +EKAI 
Sbjct: 480 RKPWVKTSLAPGSKVVTDYYKAAGLTQYLDKLGFDLVGYGCTTCIGNSGPLPEPIEKAIQ 539

Query: 546 DGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGNDKDGN 605
             DL VASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAG VR+D+S +PLGND+ G+
Sbjct: 540 KADLAVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGTVRIDISSEPLGNDQHGH 599

Query: 606 PVYLKDLWPSQQEIAEAVEKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSDKSTYI 665
           PVYLKD+WP+ QEIA+AV +V T MF KEYAEVF GD  W++I+VP++  Y W   STYI
Sbjct: 600 PVYLKDIWPTSQEIADAVAQVTTGMFHKEYAEVFAGDEQWQAIEVPQAATYVWQKDSTYI 659

Query: 666 QHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQEHGVEP 725
           QHPPFF+ +      I D+K AN+LALLGDSVTTDHISPAG+ K D+PAG+YL+E GVEP
Sbjct: 660 QHPPFFDDIAGPLPVIKDVKGANVLALLGDSVTTDHISPAGNIKTDSPAGRYLREQGVEP 719

Query: 726 KDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAMKYQEK 785
           +DFNSYGSRRGNHEVMMRGTFAN+RIRNEML G EGG T ++PTGE+M IYDA+MKYQ  
Sbjct: 720 RDFNSYGSRRGNHEVMMRGTFANIRIRNEMLGGEEGGNTLYIPTGEKMPIYDASMKYQAS 779

Query: 786 GTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQFPEGT 845
           GTPLVV+AG+EYGTGSSRDWAAKGT LLGVKAV+AES+ERIHRSNL+GMGV+PLQF    
Sbjct: 780 GTPLVVVAGQEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQ 839

Query: 846 DRKSLKLTGEETISIEGLSG-EIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAVYFKH 904
           +RKSLKLTG+E I I GL+  EI P   L + +  +DGS+E  E+  RIDT NE  YFK 
Sbjct: 840 NRKSLKLTGKEKIDILGLTDVEIVPRMNLTLVITREDGSSEKVEVLCRIDTLNEVEYFKS 899

Query: 905 GGILHYVVREML 916
           GGILHYV+R+++
Sbjct: 900 GGILHYVLRQLI 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: 2370
Number of extensions: 100
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 GFF1478 PS417_07515 (aconitate hydratase)
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.4483.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 1427.8   0.0          0 1427.6   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF1478  PS417_07515 aconitate hydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF1478  PS417_07515 aconitate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1427.6   0.0         0         0       1     876 []      18     911 ..      18     911 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1427.6 bits;  conditional E-value: 0
                           TIGR01341   1 kkvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlqdft 75 
                                         k+++y+sl+++++sl++++klp sl++lle++lr+ d+++++  d++a++ w ke ++d+ei+++parv++qdft
  lcl|FitnessBrowser__WCS417:GFF1478  18 KTYHYFSLPEAAKSLGDLDKLPMSLKVLLENLLRWEDNKTVTGADLKAIAAWLKERQSDREIQYRPARVLMQDFT 92 
                                         689************************************************************************ PP

                           TIGR01341  76 Gvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwakkaf 150
                                         Gvpavvdlaa+r av++ g+dp++inpl+pvdlvidhsv vdk+g++ a+e+nv++e++rn ery+fl+w++ af
  lcl|FitnessBrowser__WCS417:GFF1478  93 GVPAVVDLAAMRAAVAKAGGDPQRINPLSPVDLVIDHSVMVDKFGTTGAFEQNVDIEMQRNGERYAFLRWGQSAF 167
                                         *************************************************************************** PP

                           TIGR01341 151 knlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaallGqpv 225
                                          n++vvppgtGi+hqvnleyl++ v+++++dg+++a+pd+lvGtdshttminGlGvlGwGvGGieaeaa+lGqpv
  lcl|FitnessBrowser__WCS417:GFF1478 168 DNFSVVPPGTGICHQVNLEYLGRTVWTKDEDGRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPV 242
                                         *************************************************************************** PP

                           TIGR01341 226 slsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmapeyGataaff 300
                                         s+ +peviG+kltGkl+eG+tatdlvltvt++lrkkgvvgkfvef+G+gl+ l+ladratianmapeyGat++ff
  lcl|FitnessBrowser__WCS417:GFF1478 243 SMLIPEVIGFKLTGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLADLPLADRATIANMAPEYGATCGFF 317
                                         *************************************************************************** PP

                           TIGR01341 301 piddvtlqylrltgrdedkvelvekylkaqelfvddseepkytdvveldlsdveasvaGpkrpqdrvalkevkaa 375
                                         p+d+vtl+ylrl+gr+ ++v+lve+y+kaq+l+++ ++ep++td + ld+ +veas+aGpkrpqdrval +v +a
  lcl|FitnessBrowser__WCS417:GFF1478 318 PVDEVTLDYLRLSGRPTETVKLVEAYTKAQGLWRNAGQEPVFTDSLALDMGSVEASLAGPKRPQDRVALPNVGQA 392
                                         *************************************************************************** PP

                           TIGR01341 376 fkssle..snagekglalr...............keakekklegkeaelkdgavviaaitsctntsnpsvllgag 433
                                         f   l+   + ++k+ +                    +++  +g++++lk+gavviaaitsctntsnpsv+++ag
  lcl|FitnessBrowser__WCS417:GFF1478 393 FSDFLDlqFKPTNKEEGRLeseggggvavgnadlVGETDYEYDGQTYRLKNGAVVIAAITSCTNTSNPSVMMAAG 467
                                         **99651145566654322367777777777665445667778******************************** PP

                           TIGR01341 434 llakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikend 508
                                         llakkave Gl +kp+vktslapGskvvtdy + +gl++yl++lGf+lvGyGcttciGnsGpl+e +e+ai++ d
  lcl|FitnessBrowser__WCS417:GFF1478 468 LLAKKAVEKGLTRKPWVKTSLAPGSKVVTDYYKAAGLTQYLDKLGFDLVGYGCTTCIGNSGPLPEPIEKAIQKAD 542
                                         *************************************************************************** PP

                           TIGR01341 509 levsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiaelv 583
                                         l v++vlsGnrnfegr+hplvk+n+laspplvvayalaGtv id+++ep+g d++G++vylkdiwp+ +eia++v
  lcl|FitnessBrowser__WCS417:GFF1478 543 LAVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGTVRIDISSEPLGNDQHGHPVYLKDIWPTSQEIADAV 617
                                         *************************************************************************65 PP

                           TIGR01341 584 kkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeevedikgarillllGdsi 658
                                           +v++ +f+key+ev+ g+e+w+ +ev++ ++y w+++styi++ppff+++      ++d+kga +l+llGds+
  lcl|FitnessBrowser__WCS417:GFF1478 618 -AQVTTGMFHKEYAEVFAGDEQWQAIEVPQAATYVWQKDSTYIQHPPFFDDIAGPLPVIKDVKGANVLALLGDSV 691
                                         .689*************************************************988999**************** PP

                           TIGR01341 659 ttdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvylpdsev 733
                                         ttdhispaG+ik dspa++yl+e+Gve+rdfnsyGsrrGnhevm+rGtfaniri+n+++ g+eGg t+y+p++e+
  lcl|FitnessBrowser__WCS417:GFF1478 692 TTDHISPAGNIKTDSPAGRYLREQGVEPRDFNSYGSRRGNHEVMMRGTFANIRIRNEMLGGEEGGNTLYIPTGEK 766
                                         *************************************************************************** PP

                           TIGR01341 734 vsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgeda 808
                                         + +yda+mky+ +g+plvv+aG+eyG+Gssrdwaakgt+llGvkaviaesferihrsnlvgmGvlpl+fk  +++
  lcl|FitnessBrowser__WCS417:GFF1478 767 MPIYDASMKYQASGTPLVVVAGQEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQNR 841
                                         *************************************************************************** PP

                           TIGR01341 809 etlgltgeetidvddieelk..pkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkll 876
                                         ++l ltg+e+id+ ++++++  p+ ++t+++++edg+ e ve+ +ridt  e++y+k+gGil+yvlr+l+
  lcl|FitnessBrowser__WCS417:GFF1478 842 KSLKLTGKEKIDILGLTDVEivPRMNLTLVITREDGSSEKVEVLCRIDTLNEVEYFKSGGILHYVLRQLI 911
                                         **************99865444*********************************************975 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: 00:00:00.08
# Mc/sec: 9.18
//
[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