GapMind for catabolism of small carbon sources

 

Alignments 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)



>NCBI__GCF_000009985.1:WP_011386009.1
          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.15242.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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.07
# Mc/sec: 10.21
//
[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