GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Azospirillum thiophilum BV-S

Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_045580974.1 AL072_RS06770 aconitate hydratase AcnA

Query= SwissProt::P37032
         (891 letters)



>NCBI__GCF_001305595.1:WP_045580974.1
          Length = 896

 Score = 1190 bits (3079), Expect = 0.0
 Identities = 590/890 (66%), Positives = 704/890 (79%), Gaps = 3/890 (0%)

Query: 4   GQDSLSTKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTVTTK 63
           GQDSL T+  L+  GK+Y+Y+SLK AE      ++RLP+S+KVLLENLLRFEDG TV+  
Sbjct: 6   GQDSLKTRRSLSAGGKSYDYFSLKAAEQAGLGDLSRLPFSMKVLLENLLRFEDGRTVSVD 65

Query: 64  DIKAIADWLHNKTSQHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISPLS 123
           D+KA+A WL +K S  EIA+RP RVLMQDFTGVPAV DLAAMR A+  +GG+  KI+PL 
Sbjct: 66  DVKAVAQWLVDKRSDREIAYRPARVLMQDFTGVPAVCDLAAMREAMAALGGDPAKINPLV 125

Query: 124 PVDLVIDHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGICH 183
           PVDLVIDHSVMVD F  AD+ + N  +E ERN ERYEFLRWGQKAF NF+VVPPGTGICH
Sbjct: 126 PVDLVIDHSVMVDYFGGADSFQRNVDLEFERNLERYEFLRWGQKAFDNFRVVPPGTGICH 185

Query: 184 QVNLEYLGKTVW-NSENDGQLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 242
           QVN EYL + VW +++  G+  AYPDTLVGTDSHTTM+NGL VLGWGVGGIEAEAAMLGQ
Sbjct: 186 QVNTEYLSQVVWTDADPSGRPVAYPDTLVGTDSHTTMVNGLSVLGWGVGGIEAEAAMLGQ 245

Query: 243 PVSMLIPEVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLADR 302
           P+SMLIPEVIGFKL+G++KEG+TATDLVLTVTQMLR+KGVVGKFVEF+GPGL+ + L DR
Sbjct: 246 PISMLIPEVIGFKLTGRMKEGMTATDLVLTVTQMLRRKGVVGKFVEFFGPGLDSMTLPDR 305

Query: 303 ATISNMAPEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEEPVF 362
           ATI NMAPEYGATCG FP+D ETI+YL  TGRD   +ALVEAYAKAQGMW + D+ +PVF
Sbjct: 306 ATIGNMAPEYGATCGIFPIDAETIRYLTFTGRDPGRVALVEAYAKAQGMWREPDSPDPVF 365

Query: 363 TDSLHLDLGSVEPSLAGPKRPQDKVNLSSLPVEFNNFLIEVGKEKEKEKTFAVKNKDFQM 422
           +D L LD+G+VEPSLAGPKRPQD+V LS+L   F   + E  K  + +K   VK+  + +
Sbjct: 366 SDVLELDMGTVEPSLAGPKRPQDRVALSALAQGFARDMAEAYKADDPKKAVPVKDAGYSL 425

Query: 423 KHGHVVIAAITSCTNTSNPSVLMAAGLVAKKAIEKGLQRKPWVKSSLAPGSKVVTDYLRH 482
           + G VVIAAITSCTNTSNP+VL+AAGL+AKKA+EKGL +KPWVK+SLAPGS+VVTDYL  
Sbjct: 426 EQGAVVIAAITSCTNTSNPAVLVAAGLLAKKAVEKGLAQKPWVKTSLAPGSQVVTDYLAK 485

Query: 483 AGLQTYLDQLGFNLVGYGCTTCIGNSGPLPDDISHCVAEHDLVVSSVLSGNRNFEGRVHP 542
           AGLQ YLD+LGFN+VGYGCTTCIGNSGPLP+ I+  V + +LVV +VLSGNRNFEGRV+P
Sbjct: 486 AGLQPYLDRLGFNIVGYGCTTCIGNSGPLPEPIAAAVEDGNLVVGAVLSGNRNFEGRVNP 545

Query: 543 QVRANWLASPPLVVAYALCGTTCSDLSREPIGQDKEGNDVYLKDIWPSNEEIAAEV-AKV 601
             RAN+LASPPL VAYAL G    DL+ EP+G   +G  VYLKDIWP+N E+   + A +
Sbjct: 546 HTRANYLASPPLCVAYALAGNLNIDLTTEPLGTGTDGQPVYLKDIWPTNREVQDAIDASL 605

Query: 602 SGTMFRKEYAEVFKGDAHWQAIQTSSGQTYEWNPDSTYIQHPPFFENLSLKPEPLKPIKQ 661
           +  MFR  Y++VFKG   WQAI T+ GQTY+W   STY++ PPFF  L+   +P+  ++ 
Sbjct: 606 TADMFRSRYSDVFKGPEQWQAIATAEGQTYQWQDASTYVKLPPFFSGLTRTLDPVSDVRG 665

Query: 662 AYVLALFGDSITTDHISPAGSIKASSPAGLYLKSKGVDEKDFNSYGSRRGNHEVMMRGTF 721
           A  LA+ GDSITTDHISPAGSIK +SPAG YL S  V  +DFNSYG+RRGNHEVMMRGTF
Sbjct: 666 ARALAVLGDSITTDHISPAGSIKRTSPAGEYLLSHQVRLQDFNSYGARRGNHEVMMRGTF 725

Query: 722 ANIRIRNEMTPGQEGGVTRYVPTGETMSIYDAAMRYQENQQDLVIIAGKEYGTGSSRDWA 781
           ANIRIRNE+ PG EGG T++ P+GE + IY AAMRY +    LV++AGKEYGTGSSRDWA
Sbjct: 726 ANIRIRNELLPGVEGGETKHYPSGERLPIYTAAMRYADEGVPLVVVAGKEYGTGSSRDWA 785

Query: 782 AKGTNLLGVKAVITESFERIHRSNLIGMGILPLQFKEGTTRKTLKLDGSERISIE-ISDK 840
           AKGT LLG+KAVI ESFERIHRSNL+GMGILPLQFK+G TR  LKLDGSE   I  I   
Sbjct: 786 AKGTRLLGIKAVIAESFERIHRSNLVGMGILPLQFKDGLTRADLKLDGSETFDIAGIEQD 845

Query: 841 LTPGAMVPVTIERQDGDIEKIETLCRIDTADELEYYKNGGILQYVLRKIS 890
           L P   V +T+ R DG +E    L RIDT DE+EYY+NGG+L +VLR ++
Sbjct: 846 LRPRKDVALTLTRADGTVEHHTLLLRIDTLDEVEYYRNGGVLNFVLRNLA 895


Lambda     K      H
   0.316    0.134    0.393 

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: 2095
Number of extensions: 86
Number of successful extensions: 4
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: 891
Length of database: 896
Length adjustment: 43
Effective length of query: 848
Effective length of database: 853
Effective search space:   723344
Effective search space used:   723344
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 (21.6 bits)
S2: 56 (26.2 bits)

Align candidate WP_045580974.1 AL072_RS06770 (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.1465066.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 1377.4   0.0          0 1377.2   0.0    1.0  1  NCBI__GCF_001305595.1:WP_045580974.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001305595.1:WP_045580974.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1377.2   0.0         0         0       1     875 [.      21     894 ..      21     895 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1377.2 bits;  conditional E-value: 0
                             TIGR01341   1 kkvyyyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlq 72 
                                           k++ y+slka+e++ l+++s+lp s+++lle++lr  dg++++ +dv+a+++w  ++ +d+eia++parv++q
  NCBI__GCF_001305595.1:WP_045580974.1  21 KSYDYFSLKAAEQAgLGDLSRLPFSMKVLLENLLRFEDGRTVSVDDVKAVAQWLVDKRSDREIAYRPARVLMQ 93 
                                           5789********98789******************************************************** PP

                             TIGR01341  73 dftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkw 145
                                           dftGvpav dlaa+rea+++lg+dp+kinplvpvdlvidhsv vd++g  ++++ nv+lefern ery+fl+w
  NCBI__GCF_001305595.1:WP_045580974.1  94 DFTGVPAVCDLAAMREAMAALGGDPAKINPLVPVDLVIDHSVMVDYFGGADSFQRNVDLEFERNLERYEFLRW 166
                                           ************************************************************************* PP

                             TIGR01341 146 akkafknlkvvppgtGivhqvnleylakvvfea.ekdgellaypdslvGtdshttminGlGvlGwGvGGieae 217
                                           ++kaf n++vvppgtGi+hqvn eyl++vv++  +  g+ +aypd+lvGtdshttm+nGl vlGwGvGGieae
  NCBI__GCF_001305595.1:WP_045580974.1 167 GQKAFDNFRVVPPGTGICHQVNTEYLSQVVWTDaDPSGRPVAYPDTLVGTDSHTTMVNGLSVLGWGVGGIEAE 239
                                           ******************************9751568************************************ PP

                             TIGR01341 218 aallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianma 290
                                           aa+lGqp+s+ +peviG+kltG+++eG+tatdlvltvt++lr+kgvvgkfveffG+gl++++l+drati nma
  NCBI__GCF_001305595.1:WP_045580974.1 240 AAMLGQPISMLIPEVIGFKLTGRMKEGMTATDLVLTVTQMLRRKGVVGKFVEFFGPGLDSMTLPDRATIGNMA 312
                                           ************************************************************************* PP

                             TIGR01341 291 peyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd.dseepkytdvveldlsdveasvaGpkr 362
                                           peyGat+++fpid++t+ yl  tgrd  +v lve+y+kaq+++++ ds +p+++dv+eld+ +ve+s+aGpkr
  NCBI__GCF_001305595.1:WP_045580974.1 313 PEYGATCGIFPIDAETIRYLTFTGRDPGRVALVEAYAKAQGMWREpDSPDPVFSDVLELDMGTVEPSLAGPKR 385
                                           *********************************************9*************************** PP

                             TIGR01341 363 pqdrvalkevkaafksslesnagekglalrkeakekklegkeaelkdgavviaaitsctntsnpsvllgagll 435
                                           pqdrval+++ + f++ + +     +   +k+a+  k  +  ++l++gavviaaitsctntsnp+vl++agll
  NCBI__GCF_001305595.1:WP_045580974.1 386 PQDRVALSALAQGFARDMAEAYKADD---PKKAVPVK--DAGYSLEQGAVVIAAITSCTNTSNPAVLVAAGLL 453
                                           **************999887666655...55555544..899******************************* PP

                             TIGR01341 436 akkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikend 508
                                           akkave Gl  kp+vktslapGs+vvtdyla++gl+pyl++lGfn+vGyGcttciGnsGpl+e ++ a+ +++
  NCBI__GCF_001305595.1:WP_045580974.1 454 AKKAVEKGLAQKPWVKTSLAPGSQVVTDYLAKAGLQPYLDRLGFNIVGYGCTTCIGNSGPLPEPIAAAVEDGN 526
                                           ************************************************************************* PP

                             TIGR01341 509 levsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiae 581
                                           l+v avlsGnrnfegr++p ++anylasppl vayalaG+++idl++ep+gt++dG++vylkdiwp+++e+++
  NCBI__GCF_001305595.1:WP_045580974.1 527 LVVGAVLSGNRNFEGRVNPHTRANYLASPPLCVAYALAGNLNIDLTTEPLGTGTDGQPVYLKDIWPTNREVQD 599
                                           ************************************************************************* PP

                             TIGR01341 582 lvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeevedikgarillll 654
                                           +++ +++ ++f+ +y+ v++g e+w+ + ++++++y+w++ sty+++ppff++l+ + + v+d++gar l++l
  NCBI__GCF_001305595.1:WP_045580974.1 600 AIDASLTADMFRSRYSDVFKGPEQWQAIATAEGQTYQWQDASTYVKLPPFFSGLTRTLDPVSDVRGARALAVL 672
                                           ************************************************************************* PP

                             TIGR01341 655 GdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvy 727
                                           GdsittdhispaGsik+ spa++yl  + v  +dfnsyG+rrGnhevm+rGtfaniri+n+l++g eGg t++
  NCBI__GCF_001305595.1:WP_045580974.1 673 GDSITTDHISPAGSIKRTSPAGEYLLSHQVRLQDFNSYGARRGNHEVMMRGTFANIRIRNELLPGVEGGETKH 745
                                           ************************************************************************* PP

                             TIGR01341 728 lpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlpl 800
                                           +p +e + +y aam+y +egvplvv+aGkeyG+Gssrdwaakgt+llG+kaviaesferihrsnlvgmG+lpl
  NCBI__GCF_001305595.1:WP_045580974.1 746 YPSGERLPIYTAAMRYADEGVPLVVVAGKEYGTGSSRDWAAKGTRLLGIKAVIAESFERIHRSNLVGMGILPL 818
                                           ************************************************************************* PP

                             TIGR01341 801 efkqgedaetlgltgeetidvddi.eelkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvl 872
                                           +fk+g ++  l l+g+et d+ +i ++l+p+k+v ++l+++dg +e  +  lridt  e++y+++gG+l++vl
  NCBI__GCF_001305595.1:WP_045580974.1 819 QFKDGLTRADLKLDGSETFDIAGIeQDLRPRKDVALTLTRADGTVEHHTLLLRIDTLDEVEYYRNGGVLNFVL 891
                                           ***********************8358********************************************** PP

                             TIGR01341 873 rkl 875
                                           r+l
  NCBI__GCF_001305595.1:WP_045580974.1 892 RNL 894
                                           *96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (896 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 32.22
//
[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