GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Marinobacter adhaerens HP15

Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate GFF3491 HP15_3433 aconitate hydratase 1

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



>lcl|FitnessBrowser__Marino:GFF3491 HP15_3433 aconitate hydratase 1
          Length = 919

 Score = 1845 bits (4780), Expect = 0.0
 Identities = 919/919 (100%), Positives = 919/919 (100%)

Query: 1   MSNESLSKDSLNTLSSLDAGGKTFHYYSLPKAADTLGDLNRLPFSLKVLMENLLRNEDGT 60
           MSNESLSKDSLNTLSSLDAGGKTFHYYSLPKAADTLGDLNRLPFSLKVLMENLLRNEDGT
Sbjct: 1   MSNESLSKDSLNTLSSLDAGGKTFHYYSLPKAADTLGDLNRLPFSLKVLMENLLRNEDGT 60

Query: 61  TVDRSHIDAMVQWMKDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAM 120
           TVDRSHIDAMVQWMKDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAM
Sbjct: 61  TVDRSHIDAMVQWMKDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAM 120

Query: 121 INPLSPVDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPG 180
           INPLSPVDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPG
Sbjct: 121 INPLSPVDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPG 180

Query: 181 TGICHQVNLEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAA 240
           TGICHQVNLEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAA
Sbjct: 181 TGICHQVNLEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAA 240

Query: 241 MLGQPVSMLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMP 300
           MLGQPVSMLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMP
Sbjct: 241 MLGQPVSMLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMP 300

Query: 301 VADRATIANMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGHE 360
           VADRATIANMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGHE
Sbjct: 301 VADRATIANMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGHE 360

Query: 361 PVYTDNLELDMGEVEASLAGPKRPQDRVALKNMKSSFELLMETAEGPAENREANLESEGG 420
           PVYTDNLELDMGEVEASLAGPKRPQDRVALKNMKSSFELLMETAEGPAENREANLESEGG
Sbjct: 361 PVYTDNLELDMGEVEASLAGPKRPQDRVALKNMKSSFELLMETAEGPAENREANLESEGG 420

Query: 421 QTAVGVDDSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAV 480
           QTAVGVDDSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAV
Sbjct: 421 QTAVGVDDSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAV 480

Query: 481 QKGLSTKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAV 540
           QKGLSTKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAV
Sbjct: 481 QKGLSTKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAV 540

Query: 541 EKAISDGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGN 600
           EKAISDGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGN
Sbjct: 541 EKAISDGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGN 600

Query: 601 DKDGNPVYLKDLWPSQQEIAEAVEKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSD 660
           DKDGNPVYLKDLWPSQQEIAEAVEKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSD
Sbjct: 601 DKDGNPVYLKDLWPSQQEIAEAVEKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSD 660

Query: 661 KSTYIQHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQE 720
           KSTYIQHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQE
Sbjct: 661 KSTYIQHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQE 720

Query: 721 HGVEPKDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAM 780
           HGVEPKDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAM
Sbjct: 721 HGVEPKDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAM 780

Query: 781 KYQEKGTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQ 840
           KYQEKGTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQ
Sbjct: 781 KYQEKGTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQ 840

Query: 841 FPEGTDRKSLKLTGEETISIEGLSGEIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAV 900
           FPEGTDRKSLKLTGEETISIEGLSGEIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAV
Sbjct: 841 FPEGTDRKSLKLTGEETISIEGLSGEIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAV 900

Query: 901 YFKHGGILHYVVREMLRTA 919
           YFKHGGILHYVVREMLRTA
Sbjct: 901 YFKHGGILHYVVREMLRTA 919


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: 2757
Number of extensions: 100
Number of successful extensions: 1
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: 919
Length adjustment: 43
Effective length of query: 876
Effective length of database: 876
Effective search space:   767376
Effective search space used:   767376
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 GFF3491 HP15_3433 (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.23751.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 1461.1   0.0          0 1460.9   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF3491  HP15_3433 aconitate hydratase 1


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3491  HP15_3433 aconitate hydratase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1460.9   0.0         0         0       1     876 []      22     916 ..      22     916 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1460.9 bits;  conditional E-value: 0
                           TIGR01341   1 kkvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlqdft 75 
                                         k+ +yysl++++++l+++++lp sl++l+e++lrn dg+++  ++++a+++w k+ ++d+ei+f+parv++qdft
  lcl|FitnessBrowser__Marino:GFF3491  22 KTFHYYSLPKAADTLGDLNRLPFSLKVLMENLLRNEDGTTVDRSHIDAMVQWMKDRHSDTEIQFRPARVLMQDFT 96 
                                         689************************************************************************ PP

                           TIGR01341  76 Gvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwakkaf 150
                                         Gvp vvdlaa+reav++ gkdp++inpl+pvdlvidhsv vdk+g+ ++++ nv +e+ern+ery+fl+w+++af
  lcl|FitnessBrowser__Marino:GFF3491  97 GVPGVVDLAAMREAVQAAGKDPAMINPLSPVDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAF 171
                                         *************************************************************************** PP

                           TIGR01341 151 knlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaallGqpv 225
                                          n++vvppgtGi+hqvnleyl+k v+++++dg+++aypd+lvGtdshttminGlG+lGwGvGGieaeaa+lGqpv
  lcl|FitnessBrowser__Marino:GFF3491 172 DNFRVVPPGTGICHQVNLEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAAMLGQPV 246
                                         *************************************************************************** PP

                           TIGR01341 226 slsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmapeyGataaff 300
                                         s+ +pev+G+k+tGklreG+tatdlvltvte+lrkkgvvgkfvef+G+glk +++adratianmapeyGat++ff
  lcl|FitnessBrowser__Marino:GFF3491 247 SMLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMPVADRATIANMAPEYGATCGFF 321
                                         *************************************************************************** PP

                           TIGR01341 301 piddvtlqylrltgrdedkvelvekylkaqelfvddseepkytdvveldlsdveasvaGpkrpqdrvalkevkaa 375
                                         p+d++t++y+rltgr+e+++elve+y+kaq+l+++ ++ep+ytd +eld+ +veas+aGpkrpqdrvalk++k++
  lcl|FitnessBrowser__Marino:GFF3491 322 PVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGHEPVYTDNLELDMGEVEASLAGPKRPQDRVALKNMKSS 396
                                         *************************************************************************** PP

                           TIGR01341 376 fkssles...nagekglalr................keakekklegkeaelkdgavviaaitsctntsnpsvllg 431
                                         f+  +e+   +a +++ +l+                + ++   ++g++ +l+ gavviaaitsctntsnpsv+++
  lcl|FitnessBrowser__Marino:GFF3491 397 FELLMETaegPAENREANLEseggqtavgvddsykhHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMA 471
                                         *86544311144556656656666666666688865556667889****************************** PP

                           TIGR01341 432 agllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaike 506
                                         agl+a+kav+ Gl  kp+vktslapGskvvtdyl+  g+++ l++lGfnlvGyGcttciGnsGpl+++ve+ai +
  lcl|FitnessBrowser__Marino:GFF3491 472 AGLIAQKAVQKGLSTKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAVEKAISD 546
                                         *************************************************************************** PP

                           TIGR01341 507 ndlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiae 581
                                         +dl+v++vlsGnrnfegr+hplvk+n+laspplvvayalaG+v +dl+++p+g dkdG++vylkd+wps++eiae
  lcl|FitnessBrowser__Marino:GFF3491 547 GDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGNDKDGNPVYLKDLWPSQQEIAE 621
                                         *************************************************************************** PP

                           TIGR01341 582 lvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeevedikgarillllGd 656
                                         +v ++vk+++f+key+ev++g+++w++++v++s++yew +kstyi++ppffe+lk ep+ ++dik+a il+llGd
  lcl|FitnessBrowser__Marino:GFF3491 622 AV-EKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSDKSTYIQHPPFFEGLKEEPDAIDDIKDANILALLGD 695
                                         65.68********************************************************************** PP

                           TIGR01341 657 sittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvylpds 731
                                         s+ttdhispaGs k+d+pa+kyl+e+Gve++dfnsyGsrrGnhevm+rGtfan+ri+n++++g eGg+t+++p++
  lcl|FitnessBrowser__Marino:GFF3491 696 SVTTDHISPAGSFKPDTPAGKYLQEHGVEPKDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTG 770
                                         *************************************************************************** PP

                           TIGR01341 732 evvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqge 806
                                         e++++ydaamky+++g+plvv+aGkeyG+Gssrdwaakgt+llGvkav+aes+erihrsnl+gmGv+pl+f++g+
  lcl|FitnessBrowser__Marino:GFF3491 771 EQMAIYDAAMKYQEKGTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQFPEGT 845
                                         *************************************************************************** PP

                           TIGR01341 807 daetlgltgeetidvddi.eelkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkll 876
                                         d+++l ltgeeti ++++  e+kp++++++++  +dg+ et e + ridt+ e  y+k+gGil+yv+r++l
  lcl|FitnessBrowser__Marino:GFF3491 846 DRKSLKLTGEETISIEGLsGEIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAVYFKHGGILHYVVREML 916
                                         *****************6269***********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (919 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: 00:00:00.07
# Mc/sec: 10.67
//
[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:

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:

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:

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, or view the source code.

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