GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Paraburkholderia bryophila 376MFSha3.1

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate H281DRAFT_06606 H281DRAFT_06606 aconitase

Query= BRENDA::A0A090AMG4
         (901 letters)



>FitnessBrowser__Burk376:H281DRAFT_06606
          Length = 905

 Score = 1429 bits (3700), Expect = 0.0
 Identities = 718/906 (79%), Positives = 790/906 (87%), 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 ++GK+PKSIEPL
Sbjct: 61  EHITQLANWKPTAPRVDEIPFVVSRVVLQDFTGVPLLADIAAMRGVAQRVGKNPKSIEPL 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
           PVYFLTPDVVGV LKG+LR GVTATDLVLTITE+LR+EKVVGKFVEF GEGT SLS+ +R
Sbjct: 241 PVYFLTPDVVGVNLKGKLREGVTATDLVLTITELLRKEKVVGKFVEFFGEGTRSLSLPDR 300

Query: 299 ATIGNMAPEYGATMGFFPVDERTIDYFRGTGRTEAEIAAFEAYFKAQKMFGVPKAADINF 358
           ATIGNMAPEYGATMGFFPVDE+TIDYF+GTGRT+AEI+AF+ YFKAQ +FG+PK  DI+F
Sbjct: 301 ATIGNMAPEYGATMGFFPVDEKTIDYFKGTGRTDAEISAFQNYFKAQNLFGIPKEGDIDF 360

Query: 359 TKLLTLDLSTVAPSLAGPKRPQDRIEIGNVKNTFIDLYSKPVAENGFNQPAEKLAQTFTT 418
           TK++TLDL TVAPSLAGPKRPQDRIEIGNVK+TF DL+SKPVAENGF +    L   +TT
Sbjct: 361 TKVVTLDLGTVAPSLAGPKRPQDRIEIGNVKSTFSDLFSKPVAENGFAKKEADLDAQYTT 420

Query: 419 SAGTQVKNGDILIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTVPKHIKTSLAPGSRVV 478
           S G  VKNGD+LIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTV  HIKTSLAPGSR+V
Sbjct: 421 SNGVNVKNGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTVAPHIKTSLAPGSRIV 480

Query: 479 TEYLTKTGLLPYLEKLGFDVAAYGCTTCIGNAGDLTPDLNEAIIGNDLICSAVLSGNRNF 538
           TEYLTKTGLLPYL+KLGF +AAYGCTTCIGNAGDLTP+LNEAI  ND++ +AVLSGNRNF
Sbjct: 481 TEYLTKTGLLPYLDKLGFTLAAYGCTTCIGNAGDLTPELNEAITKNDIVAAAVLSGNRNF 540

Query: 539 EARIHPNIKANFLASPPLVVAYALAGTVTRDLMTEPVGRGKNG-DVWLGDIWPTTEEIES 597
           EARIHPNI+ANFLASPPLVVAYA+AG +TRDLMTEPVG+GK G DV+LGDIWPT++E+  
Sbjct: 541 EARIHPNIRANFLASPPLVVAYAIAGNITRDLMTEPVGKGKGGKDVYLGDIWPTSDEVND 600

Query: 598 LLKYALDPKAFEANYGQVKSNPGKLWENTKGVTGDTYNWPDSTYIAEPPFF-EGFGMTPG 656
           LLK+ALD  AF  NY  + +  G LW   +G  G  Y+WP STYIAEPPFF   F MTP 
Sbjct: 601 LLKFALDADAFRKNYASL-TKKGDLWSKIEGEEGQVYDWPKSTYIAEPPFFGNDFSMTPA 659

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

Query: 716 EIMMRGTFANVRIKNLMIPALPDGSRFEGGETLFQPTGEQMSIYDAAMKYVSAGTPTVVF 775
           ++MMRGTFANVRIKNLMIPA  DGSR EGG T+ QP+GEQ+SIYDAAMKY+ AGTPT+VF
Sbjct: 720 DVMMRGTFANVRIKNLMIPAKADGSRVEGGLTIHQPSGEQLSIYDAAMKYIDAGTPTIVF 779

Query: 776 GGEEYGTGSSRDWAAKGTQLLGVKAVITRSFERIHRSNLVGMGVLPLQFKGADSVQSLGI 835
            GEEYGTGSSRDWAAKGTQLLGVKAV+ RSFERIHRSNLVGMGVLPLQFKG+DSVQSLGI
Sbjct: 780 AGEEYGTGSSRDWAAKGTQLLGVKAVVARSFERIHRSNLVGMGVLPLQFKGSDSVQSLGI 839

Query: 836 TGEETYDISGLEDGIKPMQDVTLTITRKDGSKQDVTVLLRIDTPIEVDYYQHGGILPFVL 895
           TGEETYDI GL    KP Q+VTL I  KDGS++ V VLLRIDTPIEVDYY+HGGILPFVL
Sbjct: 840 TGEETYDIEGLGADFKPQQEVTLVIRGKDGSEKRVPVLLRIDTPIEVDYYKHGGILPFVL 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: 2452
Number of extensions: 110
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 H281DRAFT_06606 H281DRAFT_06606 (aconitase)
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.13204.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 1314.4   0.0          0 1314.3   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_06606  H281DRAFT_06606 aconitase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_06606  H281DRAFT_06606 aconitase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1314.3   0.0         0         0       3     876 .]      19     903 ..      17     903 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1314.3 bits;  conditional E-value: 0
                                    TIGR01341   3 vyyyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkpa 67 
                                                   ++ysl++l ++ + ki++lp s+ri+lesvlrn dg+ki ee++ +l++wk ++ +  ei+f ++
  lcl|FitnessBrowser__Burk376:H281DRAFT_06606  19 GKFYSLPQLGKAlNIKIDRLPVSIRIVLESVLRNYDGKKIAEEHITQLANWKPTAPRVDEIPFVVS 84 
                                                  579******998788*************************************************** PP

                                    TIGR01341  68 rvvlqdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelef 133
                                                  rvvlqdftGvp++ d+aa+r   +++gk+p+ i+plvpvdlv+dhsvq+d+++e++al+ n++lef
  lcl|FitnessBrowser__Burk376:H281DRAFT_06606  85 RVVLQDFTGVPLLADIAAMRGVAQRVGKNPKSIEPLVPVDLVVDHSVQIDHFREKNALDLNMKLEF 150
                                                  ****************************************************************** PP

                                    TIGR01341 134 ernkerykflkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshtt 199
                                                  +rn+ery+f+kw+ +af  +kvvppg Givhqvnleyla+ v+++ +  +++ ypdslvGtdshtt
  lcl|FitnessBrowser__Burk376:H281DRAFT_06606 151 QRNNERYQFMKWGMQAFDTFKVVPPGVGIVHQVNLEYLARGVHKKAEGADTVYYPDSLVGTDSHTT 216
                                                  **********************************************99999*************** PP

                                    TIGR01341 200 minGlGvlGwGvGGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvg 265
                                                  minG+Gv+GwGvGGieaea++lGqpv++  p+v+Gv+l+GklreGvtatdlvlt+tellrk+ vvg
  lcl|FitnessBrowser__Burk376:H281DRAFT_06606 217 MINGIGVVGWGVGGIEAEAGMLGQPVYFLTPDVVGVNLKGKLREGVTATDLVLTITELLRKEKVVG 282
                                                  ****************************************************************** PP

                                    TIGR01341 266 kfveffGeglkelsladratianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaqe 331
                                                  kfveffGeg ++lsl+drati nmapeyGat++ffp+d++t++y++ tgr + +++  ++y kaq+
  lcl|FitnessBrowser__Burk376:H281DRAFT_06606 283 KFVEFFGEGTRSLSLPDRATIGNMAPEYGATMGFFPVDEKTIDYFKGTGRTDAEISAFQNYFKAQN 348
                                                  ****************************************************************** PP

                                    TIGR01341 332 lfvd.dseepkytdvveldlsdveasvaGpkrpqdrvalkevkaafksslesnagekglalrkeak 396
                                                  lf   +  ++ +t+vv ldl +v +s+aGpkrpqdr+++ +vk++f   ++++++e+g+a +    
  lcl|FitnessBrowser__Burk376:H281DRAFT_06606 349 LFGIpKEGDIDFTKVVTLDLGTVAPSLAGPKRPQDRIEIGNVKSTFSDLFSKPVAENGFAKKEADL 414
                                                  **9877789**************************************************9987776 PP

                                    TIGR01341 397 ekkle.gkeaelkdgavviaaitsctntsnpsvllgagllakkavelGlkvkpyvktslapGskvv 461
                                                  + +    +  ++k+g+v iaaitsctntsnpsvll+agllakkave+Gl v p++ktslapGs++v
  lcl|FitnessBrowser__Burk376:H281DRAFT_06606 415 DAQYTtSNGVNVKNGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTVAPHIKTSLAPGSRIV 480
                                                  66544278899******************************************************* PP

                                    TIGR01341 462 tdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikendlevsavlsGnrnfegrihp 527
                                                  t+yl+++gllpyl++lGf+l  yGcttciGn+G+l+ e++eai++nd++++avlsGnrnfe+rihp
  lcl|FitnessBrowser__Burk376:H281DRAFT_06606 481 TEYLTKTGLLPYLDKLGFTLAAYGCTTCIGNAGDLTPELNEAITKNDIVAAAVLSGNRNFEARIHP 546
                                                  ****************************************************************** PP

                                    TIGR01341 528 lvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiaelvkkavkkelfk 593
                                                   ++an+laspplvvaya+aG+++ dl +ep+g +k Gk+vyl diwp+ +e+++l k a+  + f+
  lcl|FitnessBrowser__Burk376:H281DRAFT_06606 547 NIRANFLASPPLVVAYAIAGNITRDLMTEPVGKGKGGKDVYLGDIWPTSDEVNDLLKFALDADAFR 612
                                                  ****************************************************************** PP

                                    TIGR01341 594 keyeevtegnerwnelevtssdlyewdekstyireppff.eelklepee.vedikgarillllGds 657
                                                  k+y+++t++ + w ++e  ++++y+w +kstyi eppff ++++++p++ +  +k+ar l  +Gds
  lcl|FitnessBrowser__Burk376:H281DRAFT_06606 613 KNYASLTKKGDLWSKIEGEEGQVYDW-PKSTYIAEPPFFgNDFSMTPADsIAAVKNARALGIFGDS 677
                                                  **************************.79**********55689999762678************* PP

                                    TIGR01341 658 ittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgk... 720
                                                  +ttdhispaGsik+dspa+k+lke+Gv++ dfnsyGsrrGnh+vm+rGtfan+rikn ++++k   
  lcl|FitnessBrowser__Burk376:H281DRAFT_06606 678 VTTDHISPAGSIKEDSPAGKWLKENGVQKADFNSYGSRRGNHDVMMRGTFANVRIKNLMIPAKadg 743
                                                  ***********************************************************9864333 PP

                                    TIGR01341 721 ...eGgltvylpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaes 783
                                                     eGglt++ p +e++s+ydaamky + g+p++v aG+eyG+Gssrdwaakgt+llGvkav+a+s
  lcl|FitnessBrowser__Burk376:H281DRAFT_06606 744 srvEGGLTIHQPSGEQLSIYDAAMKYIDAGTPTIVFAGEEYGTGSSRDWAAKGTQLLGVKAVVARS 809
                                                  3448************************************************************** PP

                                    TIGR01341 784 ferihrsnlvgmGvlplefkqgedaetlgltgeetidvddi.eelkpkkevtvelvkedgeketve 848
                                                  ferihrsnlvgmGvlpl+fk  ++ ++lg+tgeet d++++  + kp++evt+++  +dg+++ v 
  lcl|FitnessBrowser__Burk376:H281DRAFT_06606 810 FERIHRSNLVGMGVLPLQFKGSDSVQSLGITGEETYDIEGLgADFKPQQEVTLVIRGKDGSEKRVP 875
                                                  ****************************************7369********************** PP

                                    TIGR01341 849 avlridtevelayvkkgGilqyvlrkll 876
                                                  + lridt++e++y+k+gGil +vlr ll
  lcl|FitnessBrowser__Burk376:H281DRAFT_06606 876 VLLRIDTPIEVDYYKHGGILPFVLRSLL 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: 0.08u 0.03s 00:00:00.11 Elapsed: 00:00:00.09
# Mc/sec: 8.06
//
[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