GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Pontibacillus litoralis JSM 072002

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_036833329.1 N784_RS06120 aconitate hydratase AcnA

Query= BRENDA::P09339
         (909 letters)



>NCBI__GCF_000775615.1:WP_036833329.1
          Length = 904

 Score = 1409 bits (3648), Expect = 0.0
 Identities = 681/903 (75%), Positives = 788/903 (87%), Gaps = 1/903 (0%)

Query: 8   AAKDVFQARKTFTTNGKTYHYYSLKALEDSGIGKVSKLPYSIKVLLESVLRQVDGFVIKK 67
           A KD FQA K F  NGK Y+YY LK LE++G+GK+S+LPYSI+VLLESVLRQ DG VI+K
Sbjct: 2   AVKDTFQAHKQFELNGKKYNYYKLKTLEEAGLGKISRLPYSIRVLLESVLRQHDGEVIQK 61

Query: 68  EHVENLAKWGTAELKDIDVPFKPSRVILQDFTGVPAVVDLASLRKAMAAVGGDPDKINPE 127
           EH+E LAKWG+ E + +DVPFKPSRVILQDFTGVPAVVDLASLRKAM  +GG PDKINPE
Sbjct: 62  EHIEKLAKWGSKEAESVDVPFKPSRVILQDFTGVPAVVDLASLRKAMVDMGGSPDKINPE 121

Query: 128 IPVDLVIDHSVQVDKAGTEDALAVNMDLEFERNAERYKFLSWAKKAFNNYQAVPPATGIV 187
           +PVDLVIDHSVQVD+ GT  AL  NM+LEFERN ERY+FL+WAKKAF+NYQAVPPATGIV
Sbjct: 122 VPVDLVIDHSVQVDEYGTAKALDANMELEFERNKERYEFLNWAKKAFDNYQAVPPATGIV 181

Query: 188 HQVNLEFLASVVHAIE-EDGELVTYPDTLVGTDSHTTMINGIGVLGWGVGGIEAEAGMLG 246
           HQVNLE+LA+VVHAIE E GE   YPDTLVGTDSHTTMING+GVLGWGVGGIEAEAGMLG
Sbjct: 182 HQVNLEYLANVVHAIENEKGEYDAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAGMLG 241

Query: 247 QPSYFPVPEVIGAKLVGKLPNGTTATDLALKVTQVLREKGVVGKFVEFFGPGIAELPLAD 306
           QPSYFP PEVIG KL G LP GTTATDLALKVTQ LREK VVGKFVEFFGPG+ E+PLAD
Sbjct: 242 QPSYFPAPEVIGVKLTGTLPKGTTATDLALKVTQKLREKNVVGKFVEFFGPGLTEMPLAD 301

Query: 307 RATIANMAPEYGATCGFFPVDEEALNYLRLTGRDPEHIDVVEAYCRSNGLFYTPDAEDPQ 366
           RATI+NMAPEYGATCGFFPVD+E+L YLRLTGR  E I +VEAYC+ N LFYTPD EDP 
Sbjct: 302 RATISNMAPEYGATCGFFPVDQESLEYLRLTGRSEEQIQLVEAYCKENDLFYTPDQEDPT 361

Query: 367 FTDVVEIDLSQIEANLSGPKRPQDLIPLSAMQETFKKQLVSPAGNQGFGLNAEEENKEIK 426
           FTD+VEI L ++E NLSGPKRPQDLIPL+ M+E+F K L +P GNQGFGL+ +E++K++ 
Sbjct: 362 FTDLVEIKLDELEPNLSGPKRPQDLIPLTEMKESFNKALTAPEGNQGFGLDEKEKDKKVS 421

Query: 427 FKLLNGEETVMKTGAIAIAAITSCTNTSNPYVLIGAGLVAKKAVELGLKVPNYVKTSLAP 486
            +  +G+ + MKTGA+AIAAITSCTNTSNPYV++GAGL+AKKAVE GL+VP YVKTSLAP
Sbjct: 422 VQHPSGKSSTMKTGAVAIAAITSCTNTSNPYVMLGAGLLAKKAVEKGLEVPEYVKTSLAP 481

Query: 487 GSKVVTGYLVNSGLLPYMKELGFNLVGYGCTTCIGNSGPLSPEIEEAVAKNDLLITSVLS 546
           GSKVVT YL +SGL+ Y+++LGFN VGYGCTTCIGNSGPLSPE+E+A+A NDL ++SVLS
Sbjct: 482 GSKVVTRYLEDSGLMTYLEKLGFNTVGYGCTTCIGNSGPLSPEVEQAIADNDLTVSSVLS 541

Query: 547 GNRNFEGRIHPLVKGNYLASPPLVVAYALAGTVNINLKTDPIGVGKDGQNVYFNDIWPSM 606
           GNRNFEGRIHPLVK NYLASPPLVVAYALAGTV+I+L+ + +G   DG++V+F+DIWPSM
Sbjct: 542 GNRNFEGRIHPLVKANYLASPPLVVAYALAGTVDIDLRKESLGKDHDGKDVHFDDIWPSM 601

Query: 607 DEINALVKQTVTPELFRKEYETVFDDNKRWNEIETTDEALYKWDNDSTYIQNPPFFEEMS 666
           DEI A V + V PE+FRKEYE VFD N++WN+I+TTDE LY WD++STYIQNPPFF  +S
Sbjct: 602 DEIKAEVDKHVNPEIFRKEYEDVFDSNEKWNQIQTTDEPLYNWDDESTYIQNPPFFVGLS 661

Query: 667 VEPGKVEPLKGLRVVGKFGDSVTTDHISPAGAIGKDTPAGKYLQEKGVSPRDFNSYGSRR 726
            +P +V+ L GLRV+GKFGDSVTTDHISPAGAI KD PAGKYLQ+KGVSPR FNSYGSRR
Sbjct: 662 EDPSEVKDLDGLRVIGKFGDSVTTDHISPAGAIAKDMPAGKYLQDKGVSPRHFNSYGSRR 721

Query: 727 GNHEVMMRGTFANIRIKNQIAPGTEGGFTTYWPTGEVTSIYDACMKYKEDKTGLVVLAGK 786
           GNHEVMMRGTFANIRI+N+IAPGTEGG+TT+WPT EV  IYDA MKY+E  TGL+V+AG 
Sbjct: 722 GNHEVMMRGTFANIRIRNKIAPGTEGGYTTFWPTDEVMPIYDAAMKYQEQGTGLLVIAGN 781

Query: 787 DYGMGSSRDWAAKGTNLLGIRTVIAESFERIHRSNLVFMGVLPLQFKQGENADTLGLTGK 846
           DYGMGSSRDWAAKGTNLLGI+TVIAESFERIHRSNLV MGVLPLQFK G++AD+LGL+GK
Sbjct: 782 DYGMGSSRDWAAKGTNLLGIKTVIAESFERIHRSNLVMMGVLPLQFKDGDSADSLGLSGK 841

Query: 847 EVIEVDVDETVRPRDLVTVRAINEDGNVTTFEAVVRFDSEVEIDYYRHGGILQMVLREKM 906
           E  ++ +DETV+PRDLV V AI+E GN T F+ + RFDS VEIDYYRHGGILQ VLR+K+
Sbjct: 842 ETFDIKIDETVKPRDLVDVIAIDEAGNKTEFQVIARFDSGVEIDYYRHGGILQKVLRDKL 901

Query: 907 KQS 909
           + +
Sbjct: 902 QSN 904


Lambda     K      H
   0.316    0.135    0.394 

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: 2427
Number of extensions: 93
Number of successful extensions: 2
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: 909
Length of database: 904
Length adjustment: 43
Effective length of query: 866
Effective length of database: 861
Effective search space:   745626
Effective search space used:   745626
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 (21.5 bits)
S2: 56 (26.2 bits)

Align candidate WP_036833329.1 N784_RS06120 (aconitate hydratase AcnA)
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.3248502.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 1478.9   0.0          0 1478.7   0.0    1.0  1  NCBI__GCF_000775615.1:WP_036833329.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000775615.1:WP_036833329.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1478.7   0.0         0         0       1     876 []      18     901 ..      18     901 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1478.7 bits;  conditional E-value: 0
                             TIGR01341   1 kkvyyyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlq 72 
                                           kk++yy lk+lee+ l+kis+lp+s+r+llesvlr+ dg++i++e++e+l+kw ++e + ++++fkp+rv+lq
  NCBI__GCF_000775615.1:WP_036833329.1  18 KKYNYYKLKTLEEAgLGKISRLPYSIRVLLESVLRQHDGEVIQKEHIEKLAKWGSKEAESVDVPFKPSRVILQ 90 
                                           689*********99789******************************************************** PP

                             TIGR01341  73 dftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkw 145
                                           dftGvpavvdla+lr+a+ ++g+ p+kinp+vpvdlvidhsvqvd++g+ +al+an+elefernkery+fl+w
  NCBI__GCF_000775615.1:WP_036833329.1  91 DFTGVPAVVDLASLRKAMVDMGGSPDKINPEVPVDLVIDHSVQVDEYGTAKALDANMELEFERNKERYEFLNW 163
                                           ************************************************************************* PP

                             TIGR01341 146 akkafknlkvvppgtGivhqvnleylakvvfeae.kdgellaypdslvGtdshttminGlGvlGwGvGGieae 217
                                           akkaf n+++vpp+tGivhqvnleyla+vv+++e ++ge  aypd+lvGtdshttminGlGvlGwGvGGieae
  NCBI__GCF_000775615.1:WP_036833329.1 164 AKKAFDNYQAVPPATGIVHQVNLEYLANVVHAIEnEKGEYDAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAE 236
                                           *******************************975278************************************ PP

                             TIGR01341 218 aallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianma 290
                                           a++lGqp+++  peviGvkltG l +G+tatdl+l+vt+ lr+k+vvgkfveffG+gl+e++ladrati+nma
  NCBI__GCF_000775615.1:WP_036833329.1 237 AGMLGQPSYFPAPEVIGVKLTGTLPKGTTATDLALKVTQKLREKNVVGKFVEFFGPGLTEMPLADRATISNMA 309
                                           ************************************************************************* PP

                             TIGR01341 291 peyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd.dseepkytdvveldlsdveasvaGpkr 362
                                           peyGat++ffp+d+++l+ylrltgr+e++++lve+y+k ++lf++ d e+p++td+ve++l+++e++++Gpkr
  NCBI__GCF_000775615.1:WP_036833329.1 310 PEYGATCGFFPVDQESLEYLRLTGRSEEQIQLVEAYCKENDLFYTpDQEDPTFTDLVEIKLDELEPNLSGPKR 382
                                           *********************************************999************************* PP

                             TIGR01341 363 pqdrvalkevkaafksslesnagekglalrkeakekkle.....gkeaelkdgavviaaitsctntsnpsvll 430
                                           pqd ++l+e+k++f+++l  + g++g++l+ + k+kk+      gk+ ++k+gav+iaaitsctntsnp+v+l
  NCBI__GCF_000775615.1:WP_036833329.1 383 PQDLIPLTEMKESFNKALTAPEGNQGFGLDEKEKDKKVSvqhpsGKSSTMKTGAVAIAAITSCTNTSNPYVML 455
                                           ******************************9999999877788899*************************** PP

                             TIGR01341 431 gagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveea 503
                                           gagllakkave Gl+v++yvktslapGskvvt yl +sgl++yle+lGfn vGyGcttciGnsGpl+ eve+a
  NCBI__GCF_000775615.1:WP_036833329.1 456 GAGLLAKKAVEKGLEVPEYVKTSLAPGSKVVTRYLEDSGLMTYLEKLGFNTVGYGCTTCIGNSGPLSPEVEQA 528
                                           ************************************************************************* PP

                             TIGR01341 504 ikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsa 576
                                           i++ndl+vs+vlsGnrnfegrihplvkanylaspplvvayalaGtvdidl+ke +g d+dGk+v++ diwps+
  NCBI__GCF_000775615.1:WP_036833329.1 529 IADNDLTVSSVLSGNRNFEGRIHPLVKANYLASPPLVVAYALAGTVDIDLRKESLGKDHDGKDVHFDDIWPSM 601
                                           ************************************************************************* PP

                             TIGR01341 577 keiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeevedikgar 649
                                           +ei++ v+k+v++e+f+keye v+++ne+wn++++t+++ly+wd++styi++ppff +l+ +p+ev+d+ g+r
  NCBI__GCF_000775615.1:WP_036833329.1 602 DEIKAEVDKHVNPEIFRKEYEDVFDSNEKWNQIQTTDEPLYNWDDESTYIQNPPFFVGLSEDPSEVKDLDGLR 674
                                           ************************************************************************* PP

                             TIGR01341 650 illllGdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeG 722
                                           ++ ++Gds+ttdhispaG+i+kd pa+kyl++kGv++r fnsyGsrrGnhevm+rGtfaniri+nk+++g+eG
  NCBI__GCF_000775615.1:WP_036833329.1 675 VIGKFGDSVTTDHISPAGAIAKDMPAGKYLQDKGVSPRHFNSYGSRRGNHEVMMRGTFANIRIRNKIAPGTEG 747
                                           ************************************************************************* PP

                             TIGR01341 723 gltvylpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgm 795
                                           g+t+++p++ev+ +ydaamky+++g++l+v+aG++yG+Gssrdwaakgt+llG+k+viaesferihrsnlv+m
  NCBI__GCF_000775615.1:WP_036833329.1 748 GYTTFWPTDEVMPIYDAAMKYQEQGTGLLVIAGNDYGMGSSRDWAAKGTNLLGIKTVIAESFERIHRSNLVMM 820
                                           ************************************************************************* PP

                             TIGR01341 796 GvlplefkqgedaetlgltgeetidvddieelkpkkevtvelvkedgeketveavlridtevelayvkkgGil 868
                                           Gvlpl+fk+g++a++lgl+g+et d++  e++kp++ v v +++e g+k+ +++ +r+d+ ve++y+++gGil
  NCBI__GCF_000775615.1:WP_036833329.1 821 GVLPLQFKDGDSADSLGLSGKETFDIKIDETVKPRDLVDVIAIDEAGNKTEFQVIARFDSGVEIDYYRHGGIL 893
                                           ***********************99997799****************************************** PP

                             TIGR01341 869 qyvlrkll 876
                                           q vlr++l
  NCBI__GCF_000775615.1:WP_036833329.1 894 QKVLRDKL 901
                                           ****9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (904 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 25.69
//
[ok]

This GapMind analysis is from Sep 24 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