GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Marino:GFF3491
          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.6293.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: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.09
# Mc/sec: 8.60
//
[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:

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