GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Magnetospirillum magneticum AMB-1

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_011386009.1 AMB_RS18485 aconitate hydratase AcnA

Query= BRENDA::A0A090AMG4
         (901 letters)



>lcl|NCBI__GCF_000009985.1:WP_011386009.1 AMB_RS18485 aconitate
           hydratase AcnA
          Length = 903

 Score = 1139 bits (2945), Expect = 0.0
 Identities = 571/898 (63%), Positives = 691/898 (76%), Gaps = 9/898 (1%)

Query: 9   LKNFKIGNKSC-QYYSLPALGKSLGIDVQRLPVSIRIVLESVLRNCDGKKVTEEHVKQLA 67
           L++  +G++   +YY+L AL       V RLPVSIRIVLESVLRNCDGK++TEEHV+QLA
Sbjct: 9   LRDLSLGHERLSRYYALAALDAVTDGPVSRLPVSIRIVLESVLRNCDGKRITEEHVRQLA 68

Query: 68  NWQANARREDEIPFVVARVVLQDFTGVPLLADIAAMRSVADKMGKSPKSIEPLVPVDLVV 127
           NW+ +A R  EIPFVVAR+VLQDFTGVPLL D+AAMR VA   GK+PK IEPLVPVDLVV
Sbjct: 69  NWRPDAPRTQEIPFVVARIVLQDFTGVPLLCDLAAMRGVAQAFGKNPKIIEPLVPVDLVV 128

Query: 128 DHSVMIDYFGTKNALDLNMKLEFKRNQERYQFMKWGMQAFDTFGVVPPGFGIVHQVNLEY 187
           DHSV +D++G  ++LDLNM+ EF+RN ERY+F+KWGMQAFDTF VVPPG GIVHQVNLE+
Sbjct: 129 DHSVQVDHYGEADSLDLNMRREFQRNAERYRFIKWGMQAFDTFRVVPPGIGIVHQVNLEF 188

Query: 188 LARGVHLDKKNNVYYPDSLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQPVYFLTPDV 247
           LARGV   +K+ + YPD+LVGTDSHTTMIN +GV GWGVGGIEAEAGMLGQP+ FLTPDV
Sbjct: 189 LARGVL--EKDGITYPDTLVGTDSHTTMINALGVAGWGVGGIEAEAGMLGQPLVFLTPDV 246

Query: 248 VGVELKGQLRGGVTATDLVLTITEMLRREKVVGKFVEFCGEGTASLSVAERATIGNMAPE 307
           VGV L G+L  G TATDLVL +TE LRR KVVGKFVEF GEGT SL+V +RATI NMAPE
Sbjct: 247 VGVHLHGRLPEGATATDLVLFLTERLRRAKVVGKFVEFFGEGTRSLAVPDRATIANMAPE 306

Query: 308 YGATMGFFPVDERTIDYFRGTGRTEAEIAAFEAYFKAQKMFGVPKAADINFTKLLTLDLS 367
           YGATMGFFPVD+ T+ Y   TGRT++EI  F AY+ AQ +FG+P   DI++++++  DL 
Sbjct: 307 YGATMGFFPVDKETVRYLEATGRTDSEIEVFRAYYSAQGLFGMPMPGDIDYSEVIEFDLG 366

Query: 368 TVAPSLAGPKRPQDRIEIGNVKNTFIDLYSKPVAENGFNQPAEKLAQTFT--TSAGTQVK 425
           +V PS+AGPKRPQDR+ + +++  F  L+S P  ++G+ +PAE L +     T+A   + 
Sbjct: 367 SVQPSIAGPKRPQDRLNLSDMRRAFTSLFSAPAKDDGYGRPAEALGRRHRVETTAAADIG 426

Query: 426 NGDILIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTVPKHIKTSLAPGSRVVTEYLTKT 485
           +GD+LIAAITSCTNTSNP V+LAAGLLA+KAV  GL V   +KTSLAPGSRVVTEYL K 
Sbjct: 427 HGDVLIAAITSCTNTSNPGVMLAAGLLARKAVALGLKVGPRVKTSLAPGSRVVTEYLAKA 486

Query: 486 GLLPYLEKLGFDVAAYGCTTCIGNAGDLTPDLNEAIIGNDLICSAVLSGNRNFEARIHPN 545
           GLL  LE LGF V AYGCTTCIGN+G L PDL +AI  +DL+C+AVLSGNRNFEARIHP 
Sbjct: 487 GLLGDLESLGFGVVAYGCTTCIGNSGPLMPDLEQAIAADDLVCAAVLSGNRNFEARIHPA 546

Query: 546 IKANFLASPPLVVAYALAGTVTRDLMTEPVGRGKNGD-VWLGDIWPTTEEIESLLKYALD 604
           IKANFL SPPLVVA+A+AG +  D+  EP+G GK+G  V L DIWP+  E+   L  A D
Sbjct: 547 IKANFLMSPPLVVAFAIAGRIAIDMTQEPLGTGKDGKPVMLKDIWPSGREVADALLVATD 606

Query: 605 PKAFEANYGQ-VKSNPGKLWENTKGVTGDTYNWPDSTYIAEPPFFEGFGMTPGAMPAVKG 663
           P+ +   Y   V  NP  LW +    TG  Y W  STYIAEPPFFE F   P  +  + G
Sbjct: 607 PELYRRLYSDFVHGNP--LWNDIPTQTGPAYAWETSTYIAEPPFFERFSPQPAGVGDIIG 664

Query: 664 ARALGVFGDSVTTDHISPAGSIKETSPAGKWLKENGVMKADFNSYGSRRGNHEIMMRGTF 723
           ARAL +FGDSVTTDHISPAGSI  +SPAG++L  +GV   DFNSYG+RRGNHE+MMRGTF
Sbjct: 665 ARALAIFGDSVTTDHISPAGSIAVSSPAGQYLLAHGVAAGDFNSYGARRGNHEVMMRGTF 724

Query: 724 ANVRIKNLMIPALPDGSRFEGGETLFQPTGEQMSIYDAAMKYVSAGTPTVVFGGEEYGTG 783
           ANVRI+NLM+PA  DGSR EGG TL QP G +M I+DAA +Y  AG P++VF G EYGTG
Sbjct: 725 ANVRIRNLMLPAKVDGSRVEGGLTLHQPEGSEMPIFDAASRYQEAGIPSIVFAGTEYGTG 784

Query: 784 SSRDWAAKGTQLLGVKAVITRSFERIHRSNLVGMGVLPLQFKGADSVQSLGITGEETYDI 843
           SSRDWAAKG +LLGV+AV+ +SFERIHRSNLVGMGVLPLQF+  +S  SLGI G+E + +
Sbjct: 785 SSRDWAAKGPKLLGVRAVVAQSFERIHRSNLVGMGVLPLQFRDGESAASLGIAGDEEFHV 844

Query: 844 SGLEDGIKPMQDVTLTITRKDGSKQDVTVLLRIDTPIEVDYYQHGGILPFVLRQLLAA 901
            GL   ++P Q+V L I  + G  + +++ LR+DT IE+DY  HGGILP+VLR LLAA
Sbjct: 845 RGLSGVLRPRQEVVLEIVNRQGRSRAISLQLRVDTAIELDYLSHGGILPYVLRDLLAA 902


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: 2151
Number of extensions: 86
Number of successful extensions: 6
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: 903
Length adjustment: 43
Effective length of query: 858
Effective length of database: 860
Effective search space:   737880
Effective search space used:   737880
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 WP_011386009.1 AMB_RS18485 (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.32593.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 1260.9   0.0          0 1260.7   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011386009.1  AMB_RS18485 aconitate hydratase 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011386009.1  AMB_RS18485 aconitate hydratase AcnA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1260.7   0.0         0         0       4     876 .]      21     900 ..      18     900 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1260.7 bits;  conditional E-value: 0
                                 TIGR01341   4 yyyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvl 71 
                                                yy+l al+   ++ +s+lp s+ri+lesvlrn+dg++i+ee+v +l++w+ ++ + +ei+f +ar+vl
  lcl|NCBI__GCF_000009985.1:WP_011386009.1  21 RYYALAALDAVtDGPVSRLPVSIRIVLESVLRNCDGKRITEEHVRQLANWRPDAPRTQEIPFVVARIVL 89 
                                               7******99765899****************************************************** PP

                                 TIGR01341  72 qdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkery 140
                                               qdftGvp++ dlaa+r   +++gk+p+ i+plvpvdlv+dhsvqvd++ge ++l+ n+++ef+rn+ery
  lcl|NCBI__GCF_000009985.1:WP_011386009.1  90 QDFTGVPLLCDLAAMRGVAQAFGKNPKIIEPLVPVDLVVDHSVQVDHYGEADSLDLNMRREFQRNAERY 158
                                               ********************************************************************* PP

                                 TIGR01341 141 kflkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGw 209
                                               +f+kw+ +af  ++vvppg Givhqvnle+la+ v e++     ++ypd+lvGtdshttmin lGv+Gw
  lcl|NCBI__GCF_000009985.1:WP_011386009.1 159 RFIKWGMQAFDTFRVVPPGIGIVHQVNLEFLARGVLEKD----GITYPDTLVGTDSHTTMINALGVAGW 223
                                               ***********************************9877....79************************ PP

                                 TIGR01341 210 GvGGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkel 278
                                               GvGGieaea++lGqp+ +  p+v+Gv+l G+l eG tatdlvl +te lr+  vvgkfveffGeg ++l
  lcl|NCBI__GCF_000009985.1:WP_011386009.1 224 GVGGIEAEAGMLGQPLVFLTPDVVGVHLHGRLPEGATATDLVLFLTERLRRAKVVGKFVEFFGEGTRSL 292
                                               ********************************************************************* PP

                                 TIGR01341 279 sladratianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd.dseepkytdvv 346
                                               +++dratianmapeyGat++ffp+d++t+ yl+ tgr + ++e+ ++y  aq+lf      ++ y++v+
  lcl|NCBI__GCF_000009985.1:WP_011386009.1 293 AVPDRATIANMAPEYGATMGFFPVDKETVRYLEATGRTDSEIEVFRAYYSAQGLFGMpMPGDIDYSEVI 361
                                               *******************************************************9978899******* PP

                                 TIGR01341 347 eldlsdveasvaGpkrpqdrvalkevkaafksslesnagekglalrkeak..ekkle.gkeaelkdgav 412
                                               e dl +v++s+aGpkrpqdr++l+++++af+s ++ +a + g++ + ea   ++ +e    a + +g+v
  lcl|NCBI__GCF_000009985.1:WP_011386009.1 362 EFDLGSVQPSIAGPKRPQDRLNLSDMRRAFTSLFSAPAKDDGYGRPAEALgrRHRVEtTAAADIGHGDV 430
                                               *******************************************998766511444553566789***** PP

                                 TIGR01341 413 viaaitsctntsnpsvllgagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnl 481
                                                iaaitsctntsnp v+l+aglla+kav lGlkv p vktslapGs+vvt+yla++gll  le lGf +
  lcl|NCBI__GCF_000009985.1:WP_011386009.1 431 LIAAITSCTNTSNPGVMLAAGLLARKAVALGLKVGPRVKTSLAPGSRVVTEYLAKAGLLGDLESLGFGV 499
                                               ********************************************************************* PP

                                 TIGR01341 482 vGyGcttciGnsGpleeeveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvd 550
                                               v yGcttciGnsGpl  ++e+ai+ +dl+ +avlsGnrnfe+rihp +kan+l+spplvva+a+aG++ 
  lcl|NCBI__GCF_000009985.1:WP_011386009.1 500 VAYGCTTCIGNSGPLMPDLEQAIAADDLVCAAVLSGNRNFEARIHPAIKANFLMSPPLVVAFAIAGRIA 568
                                               ********************************************************************* PP

                                 TIGR01341 551 idlekepigtdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyew 619
                                               id+++ep+gt+kdGk+v lkdiwps +e+a++   a  +el+++ y+ +++gn  wn++ + +++ y+w
  lcl|NCBI__GCF_000009985.1:WP_011386009.1 569 IDMTQEPLGTGKDGKPVMLKDIWPSGREVADALLVATDPELYRRLYSDFVHGNPLWNDIPTQTGPAYAW 637
                                               ********************************************************************* PP

                                 TIGR01341 620 dekstyireppffeelklepeevedikgarillllGdsittdhispaGsikkdspaakylkekGverrd 688
                                               +  styi eppffe ++ +p+ v di gar l+ +Gds+ttdhispaGsi+  spa++yl  +Gv   d
  lcl|NCBI__GCF_000009985.1:WP_011386009.1 638 E-TSTYIAEPPFFERFSPQPAGVGDIIGARALAIFGDSVTTDHISPAGSIAVSSPAGQYLLAHGVAAGD 705
                                               6.79***************************************************************** PP

                                 TIGR01341 689 fnsyGsrrGnhevmlrGtfaniriknklvkgk......eGgltvylpdsevvsvydaamkykkegvplv 751
                                               fnsyG+rrGnhevm+rGtfan+ri+n ++++k      eGglt++ p++ ++ ++daa +y++ g+p +
  lcl|NCBI__GCF_000009985.1:WP_011386009.1 706 FNSYGARRGNHEVMMRGTFANVRIRNLMLPAKvdgsrvEGGLTLHQPEGSEMPIFDAASRYQEAGIPSI 774
                                               ****************************87643333448****************************** PP

                                 TIGR01341 752 vlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltgeetid 820
                                               v aG eyG+Gssrdwaakg+kllGv+av+a+sferihrsnlvgmGvlpl+f++ge+a +lg+ g+e+ +
  lcl|NCBI__GCF_000009985.1:WP_011386009.1 775 VFAGTEYGTGSSRDWAAKGPKLLGVRAVVAQSFERIHRSNLVGMGVLPLQFRDGESAASLGIAGDEEFH 843
                                               ********************************************************************* PP

                                 TIGR01341 821 vddiee.lkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkll 876
                                               v +++  l+p++ev +e+v+++g  ++++ +lr+dt++el+y+++gGil yvlr+ll
  lcl|NCBI__GCF_000009985.1:WP_011386009.1 844 VRGLSGvLRPRQEVVLEIVNRQGRSRAISLQLRVDTAIELDYLSHGGILPYVLRDLL 900
                                               ***875279*********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (903 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: 8.61
//
[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