GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Burkholderia phytofirmans PsJN

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate BPHYT_RS33980 BPHYT_RS33980 aconitate hydratase

Query= BRENDA::A0A090AMG4
         (901 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS33980 BPHYT_RS33980 aconitate
           hydratase
          Length = 905

 Score = 1413 bits (3658), Expect = 0.0
 Identities = 710/906 (78%), Positives = 786/906 (86%), Gaps = 6/906 (0%)

Query: 1   MPHNTLDTLKNFKIGNKSCQYYSLPALGKSLGIDVQRLPVSIRIVLESVLRNCDGKKVTE 60
           M HN   TLK F  G+   ++YSLP LGK+L I + RLPVSIRIVLESVLRN DGKK+ E
Sbjct: 1   MAHNLHKTLKEFDSGSGKGKFYSLPQLGKALNIKIDRLPVSIRIVLESVLRNYDGKKIAE 60

Query: 61  EHVKQLANWQANARREDEIPFVVARVVLQDFTGVPLLADIAAMRSVADKMGKSPKSIEPL 120
           EH++QLANW+  A R DEIPFVV+RVVLQDFTGVPLLADIAAMR VA  MGK PKSIEPL
Sbjct: 61  EHIEQLANWKPTAARVDEIPFVVSRVVLQDFTGVPLLADIAAMRGVAKHMGKDPKSIEPL 120

Query: 121 VPVDLVVDHSVMIDYFGTKNALDLNMKLEFKRNQERYQFMKWGMQAFDTFGVVPPGFGIV 180
           VPVDLVVDHSV ID+F  KNALDLNMKLEF+RN ERYQFMKWGMQAFDTF VVPPG GIV
Sbjct: 121 VPVDLVVDHSVQIDHFREKNALDLNMKLEFQRNNERYQFMKWGMQAFDTFKVVPPGVGIV 180

Query: 181 HQVNLEYLARGVH--LDKKNNVYYPDSLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQ 238
           HQVNLEYLARGVH   +  + VYYPDSLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQ
Sbjct: 181 HQVNLEYLARGVHKKAEGADTVYYPDSLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQ 240

Query: 239 PVYFLTPDVVGVELKGQLRGGVTATDLVLTITEMLRREKVVGKFVEFCGEGTASLSVAER 298
           PVYFLTPDVVGVELKG+LR G+TATDLVLT+TE+LR+EKVVGKFVEF GEGT SLS+ +R
Sbjct: 241 PVYFLTPDVVGVELKGKLREGLTATDLVLTVTELLRKEKVVGKFVEFFGEGTKSLSLPDR 300

Query: 299 ATIGNMAPEYGATMGFFPVDERTIDYFRGTGRTEAEIAAFEAYFKAQKMFGVPKAADINF 358
           ATIGNMAPEYGATMGFFPVDE+TI+YF+GTGRT+AEI+AFE YFKAQ +FG+PKA  I++
Sbjct: 301 ATIGNMAPEYGATMGFFPVDEKTIEYFKGTGRTDAEISAFENYFKAQGLFGIPKAGQIDY 360

Query: 359 TKLLTLDLSTVAPSLAGPKRPQDRIEIGNVKNTFIDLYSKPVAENGFNQPAEKLAQTFTT 418
           TK++TLDL TV PSLAGPKRPQDRIEIG+VK+TF DL+SKPVAENGF + A  L   +TT
Sbjct: 361 TKVVTLDLGTVTPSLAGPKRPQDRIEIGHVKSTFSDLFSKPVAENGFAKKAADLEAQYTT 420

Query: 419 SAGTQVKNGDILIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTVPKHIKTSLAPGSRVV 478
           S G  VKNGDILIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTV  HIKTSLAPGSR+V
Sbjct: 421 SNGVDVKNGDILIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTVAPHIKTSLAPGSRIV 480

Query: 479 TEYLTKTGLLPYLEKLGFDVAAYGCTTCIGNAGDLTPDLNEAIIGNDLICSAVLSGNRNF 538
           TEYLTKT L+ YL+KLGF +AAYGCTTCIGNAGDLTP+LNEAI  ND++ +AVLSGNRNF
Sbjct: 481 TEYLTKTDLMKYLDKLGFTLAAYGCTTCIGNAGDLTPELNEAITKNDIVAAAVLSGNRNF 540

Query: 539 EARIHPNIKANFLASPPLVVAYALAGTVTRDLMTEPVGRGKNG-DVWLGDIWPTTEEIES 597
           EARIHPNI+ANFLASPPLVVAYA+AG +TRDLMTEPVG+GK G D++LGDIWPT+EE+  
Sbjct: 541 EARIHPNIRANFLASPPLVVAYAIAGNITRDLMTEPVGKGKGGKDIYLGDIWPTSEEVNE 600

Query: 598 LLKYALDPKAFEANYGQVKSNPGKLWENTKGVTGDTYNWPDSTYIAEPPFF-EGFGMTPG 656
           LLK+ALD  AF  NY  + +  G LW   +G  G  Y+WP STYIAEPPFF + F M P 
Sbjct: 601 LLKFALDADAFRKNYSAL-TKKGDLWSKIEGEEGQVYDWPKSTYIAEPPFFGKDFSMQPA 659

Query: 657 -AMPAVKGARALGVFGDSVTTDHISPAGSIKETSPAGKWLKENGVMKADFNSYGSRRGNH 715
            ++ AVK ARALG+FGDSVTTDHISPAGSIKE SPAGKWLKENGV KADFNSYGSRRGNH
Sbjct: 660 DSIAAVKDARALGIFGDSVTTDHISPAGSIKEDSPAGKWLKENGVQKADFNSYGSRRGNH 719

Query: 716 EIMMRGTFANVRIKNLMIPALPDGSRFEGGETLFQPTGEQMSIYDAAMKYVSAGTPTVVF 775
           ++MMRGTFANVRIKNLMIPA  DG+R EGG T+ QP+GEQ+SIYDAAMKY+ AGTPTVVF
Sbjct: 720 DVMMRGTFANVRIKNLMIPAKADGTRVEGGLTIHQPSGEQLSIYDAAMKYIDAGTPTVVF 779

Query: 776 GGEEYGTGSSRDWAAKGTQLLGVKAVITRSFERIHRSNLVGMGVLPLQFKGADSVQSLGI 835
            GEEYGTGSSRDWAAKGTQLLGVK V+ RSFERIHRSNLVGMGVLPLQFKG+DSVQSLGI
Sbjct: 780 AGEEYGTGSSRDWAAKGTQLLGVKVVVARSFERIHRSNLVGMGVLPLQFKGSDSVQSLGI 839

Query: 836 TGEETYDISGLEDGIKPMQDVTLTITRKDGSKQDVTVLLRIDTPIEVDYYQHGGILPFVL 895
           TGEETYDI GL    KP Q+VTL I  K+G ++ V VLLRIDTPIEVDYY+HGGILPFVL
Sbjct: 840 TGEETYDIEGLGADFKPQQEVTLVIRDKEGKEKRVQVLLRIDTPIEVDYYKHGGILPFVL 899

Query: 896 RQLLAA 901
           R LLAA
Sbjct: 900 RSLLAA 905


Lambda     K      H
   0.317    0.136    0.400 

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: 2397
Number of extensions: 102
Number of successful extensions: 5
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: 901
Length of database: 905
Length adjustment: 43
Effective length of query: 858
Effective length of database: 862
Effective search space:   739596
Effective search space used:   739596
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 (21.7 bits)
S2: 56 (26.2 bits)

Align candidate BPHYT_RS33980 BPHYT_RS33980 (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.19777.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 1319.3   0.0          0 1319.1   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS33980  BPHYT_RS33980 aconitate hydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS33980  BPHYT_RS33980 aconitate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1319.1   0.0         0         0       3     876 .]      19     903 ..      17     903 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1319.1 bits;  conditional E-value: 0
                                TIGR01341   3 vyyyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvl 71 
                                               ++ysl++l ++ + ki++lp s+ri+lesvlrn dg+ki ee++e+l++wk ++ +  ei+f ++rvvl
  lcl|FitnessBrowser__BFirm:BPHYT_RS33980  19 GKFYSLPQLGKAlNIKIDRLPVSIRIVLESVLRNYDGKKIAEEHIEQLANWKPTAARVDEIPFVVSRVVL 88 
                                              579******998788******************************************************* PP

                                TIGR01341  72 qdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkeryk 141
                                              qdftGvp++ d+aa+r   k++gkdp+ i+plvpvdlv+dhsvq+d+++e++al+ n++lef+rn+ery+
  lcl|FitnessBrowser__BFirm:BPHYT_RS33980  89 QDFTGVPLLADIAAMRGVAKHMGKDPKSIEPLVPVDLVVDHSVQIDHFREKNALDLNMKLEFQRNNERYQ 158
                                              ********************************************************************** PP

                                TIGR01341 142 flkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGv 211
                                              f+kw+ +af  +kvvppg Givhqvnleyla+ v+++ +  +++ ypdslvGtdshttminG+Gv+GwGv
  lcl|FitnessBrowser__BFirm:BPHYT_RS33980 159 FMKWGMQAFDTFKVVPPGVGIVHQVNLEYLARGVHKKAEGADTVYYPDSLVGTDSHTTMINGIGVVGWGV 228
                                              **************************************99999*************************** PP

                                TIGR01341 212 GGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsla 281
                                              GGieaea++lGqpv++  p+v+Gv l+GklreG+tatdlvltvtellrk+ vvgkfveffGeg k+lsl+
  lcl|FitnessBrowser__BFirm:BPHYT_RS33980 229 GGIEAEAGMLGQPVYFLTPDVVGVELKGKLREGLTATDLVLTVTELLRKEKVVGKFVEFFGEGTKSLSLP 298
                                              ********************************************************************** PP

                                TIGR01341 282 dratianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd.dseepkytdvveldl 350
                                              drati nmapeyGat++ffp+d++t++y++ tgr + +++  e+y kaq+lf   ++ ++ yt+vv ldl
  lcl|FitnessBrowser__BFirm:BPHYT_RS33980 299 DRATIGNMAPEYGATMGFFPVDEKTIEYFKGTGRTDAEISAFENYFKAQGLFGIpKAGQIDYTKVVTLDL 368
                                              ****************************************************988999************ PP

                                TIGR01341 351 sdveasvaGpkrpqdrvalkevkaafksslesnagekglalrkeakekkle.gkeaelkdgavviaaits 419
                                               +v +s+aGpkrpqdr+++ +vk++f   ++++++e+g+a +    e +    +   +k+g++ iaaits
  lcl|FitnessBrowser__BFirm:BPHYT_RS33980 369 GTVTPSLAGPKRPQDRIEIGHVKSTFSDLFSKPVAENGFAKKAADLEAQYTtSNGVDVKNGDILIAAITS 438
                                              **************************************9988666555443278899************* PP

                                TIGR01341 420 ctntsnpsvllgagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttc 489
                                              ctntsnpsvll+agllakkave+Gl v p++ktslapGs++vt+yl++++l++yl++lGf+l  yGcttc
  lcl|FitnessBrowser__BFirm:BPHYT_RS33980 439 CTNTSNPSVLLAAGLLAKKAVEAGLTVAPHIKTSLAPGSRIVTEYLTKTDLMKYLDKLGFTLAAYGCTTC 508
                                              ********************************************************************** PP

                                TIGR01341 490 iGnsGpleeeveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepig 559
                                              iGn+G+l+ e++eai++nd++++avlsGnrnfe+rihp ++an+laspplvvaya+aG+++ dl +ep+g
  lcl|FitnessBrowser__BFirm:BPHYT_RS33980 509 IGNAGDLTPELNEAITKNDIVAAAVLSGNRNFEARIHPNIRANFLASPPLVVAYAIAGNITRDLMTEPVG 578
                                              ********************************************************************** PP

                                TIGR01341 560 tdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyirep 629
                                               +k Gk++yl diwp+ +e++el k a+  + f+k+y+++t++ + w ++e  ++++y+w +kstyi ep
  lcl|FitnessBrowser__BFirm:BPHYT_RS33980 579 KGKGGKDIYLGDIWPTSEEVNELLKFALDADAFRKNYSALTKKGDLWSKIEGEEGQVYDW-PKSTYIAEP 647
                                              ************************************************************.79******* PP

                                TIGR01341 630 pff.eelklepee.vedikgarillllGdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrG 697
                                              pff ++++++p++ +  +k+ar l  +Gds+ttdhispaGsik+dspa+k+lke+Gv++ dfnsyGsrrG
  lcl|FitnessBrowser__BFirm:BPHYT_RS33980 648 PFFgKDFSMQPADsIAAVKDARALGIFGDSVTTDHISPAGSIKEDSPAGKWLKENGVQKADFNSYGSRRG 717
                                              ***66899999762678***************************************************** PP

                                TIGR01341 698 nhevmlrGtfaniriknklvkgk......eGgltvylpdsevvsvydaamkykkegvplvvlaGkeyGsG 761
                                              nh+vm+rGtfan+rikn ++++k      eGglt++ p +e++s+ydaamky + g+p+vv aG+eyG+G
  lcl|FitnessBrowser__BFirm:BPHYT_RS33980 718 NHDVMMRGTFANVRIKNLMIPAKadgtrvEGGLTIHQPSGEQLSIYDAAMKYIDAGTPTVVFAGEEYGTG 787
                                              *******************98643333448**************************************** PP

                                TIGR01341 762 ssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltgeetidvddi.eelkpk 830
                                              ssrdwaakgt+llGvk+v+a+sferihrsnlvgmGvlpl+fk  ++ ++lg+tgeet d++++  + kp+
  lcl|FitnessBrowser__BFirm:BPHYT_RS33980 788 SSRDWAAKGTQLLGVKVVVARSFERIHRSNLVGMGVLPLQFKGSDSVQSLGITGEETYDIEGLgADFKPQ 857
                                              **************************************************************7369**** PP

                                TIGR01341 831 kevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkll 876
                                              +evt+++ +++g+++ v++ lridt++e++y+k+gGil +vlr ll
  lcl|FitnessBrowser__BFirm:BPHYT_RS33980 858 QEVTLVIRDKEGKEKRVQVLLRIDTPIEVDYYKHGGILPFVLRSLL 903
                                              ******************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (905 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 12.98
//
[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 preprint 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