Alignments for a candidate for acn in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Echinicola vietnamensis KMM 6221, DSM 17526

Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate Echvi_4039 Echvi_4039 aconitate hydratase 1

Query= SwissProt::Q5SMF6
         (902 letters)



>FitnessBrowser__Cola:Echvi_4039
          Length = 925

 Score = 1047 bits (2707), Expect = 0.0
 Identities = 539/923 (58%), Positives = 682/923 (73%), Gaps = 42/923 (4%)

Query: 9   KTLTTKSGTYGYYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTREDIEALARW 68
           K L T  G+  Y+ L  L+ +G  +++ LPFSIR++LE+ LRN D + +T+E  E L  W
Sbjct: 10  KQLDTAKGSLNYWSLAALQEQG-HKINELPFSIRILLENALRNYDDFAITKEHTETLLNW 68

Query: 69  RPDPGEINVPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVVPADLVIDHS 128
           +P+  + +VP K ARV++QDFTGVPAVVD+A++R     KG DP++INP++P DLV+DHS
Sbjct: 69  KPEASDKDVPYKPARVLMQDFTGVPAVVDIASLRAEAVRKGKDPQKINPLIPVDLVVDHS 128

Query: 129 VQVDAFGTAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVHQVNIEYLTK 188
           VQVD FGT Y++  NV+ EYERN ERY  LKWAQ + +NF VVPPG GI HQVN+EYL K
Sbjct: 129 VQVDYFGTNYSYKKNVDVEYERNGERYEFLKWAQKSFDNFSVVPPGMGICHQVNLEYLAK 188

Query: 189 VVMTGKRDGLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQPYYMLAPRVV 248
            V+  +RDG    FPD+LVGTDSHT MVNG+GV+GWGVGGIEAEA +LGQP Y + P+VV
Sbjct: 189 GVI--ERDGNV--FPDTLVGTDSHTPMVNGIGVVGWGVGGIEAEAALLGQPIYFIMPQVV 244

Query: 249 GFKLYGELPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRATIANMAPEY 308
           G KL GELP G TATD+VLT+TE+LRKHGVVGKFVE +GPG+  L+ PDRATI+NM+PE+
Sbjct: 245 GLKLTGELPLGTTATDMVLTITELLRKHGVVGKFVEVFGPGLDTLTVPDRATISNMSPEF 304

Query: 309 GATMGFFPVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQYSEYLELDLS 368
           G T+ +FP+D+ TL+Y+ +T R ++ ++LVE Y KA  L+R  E EE V+YS  +ELDL 
Sbjct: 305 GCTVTYFPIDDRTLDYMSKTNRSKDQIKLVEDYAKANMLWR--EDEESVKYSSLVELDLG 362

Query: 369 AVEPSLAGPKRPQDRVPLKEVKKSF-----------LAHLTKPVKERGFG---------- 407
            VEP+++GPKRPQD++ ++  K+ F              + K  K R F           
Sbjct: 363 TVEPTVSGPKRPQDKILVRNFKEKFGELLEEVHGREYIPIDKRDKSRWFSEGGGQPVDKP 422

Query: 408 --LSED-QLQRK-------VLVKRRDEEFELTHGSVVIAAITSCTNTSNPSVMLGAGLLA 457
             L ED ++  K       V VK  +EEF L+ GS+VIAAITSCTNTSNPSVM+GAGL+A
Sbjct: 423 GDLPEDVEIATKTKNGLKTVEVKINNEEFALSDGSIVIAAITSCTNTSNPSVMIGAGLVA 482

Query: 458 KKAVEAGLDRKPWVKTSLAPGSKVVTDYLEMSGLMPFLEALGFHLVGYGCTTCIGNSGPL 517
           +KA E GLD KPWVKTSLAPGSKVVTDYLE SGL+  LEAL FH+VGYGCT+CIGNSGPL
Sbjct: 483 QKARERGLDVKPWVKTSLAPGSKVVTDYLEASGLLDDLEALRFHVVGYGCTSCIGNSGPL 542

Query: 518 PEDIAKAVEEGNLVVAAVLSGNRNFEGRINPHVKANYLASPMLVVAYALAGRMDIDFTTE 577
           P+ IA AVEE +LVVA+VLSGNRNFE R++P VK NYL SPMLVVAYALAGR+D+D   E
Sbjct: 543 PKHIAHAVEENDLVVASVLSGNRNFEARVHPQVKMNYLMSPMLVVAYALAGRVDVDLNEE 602

Query: 578 PLGFDPNGKPIYLKDIWPSMEEIREAIRKTLDPELFKKEYSKVFEGDERWQALPAPTGEL 637
           PLGFDPN +P+YLKDIWPS +EI E + K L P  F K Y ++FEG+E+W+ L AP+ ++
Sbjct: 603 PLGFDPNLEPVYLKDIWPSNDEIFEVMGKVLSPGDFDKNYGEIFEGNEQWKNLQAPSDKV 662

Query: 638 YQWDPESTYIQNPPFFEDLGER--KVEDIRGARVLLVLGDSVTTDHISPAGAIPVKSPAG 695
           Y W  +STYI+  PFF+ L     + ++I+GARVLL LGDS+TTDHISPAGA    SPAG
Sbjct: 663 YNWSEKSTYIKEAPFFQGLSNEVPEPQNIQGARVLLKLGDSITTDHISPAGAFAESSPAG 722

Query: 696 QYLISKGVKPEDFNSYGSRRGNHEVMMRGTFANIRIKNLMLDGIEGGYAKKLPEGDVDFV 755
           QYL+ +GV+ +DFNSYGSRRGN EVM+RGTFAN+RIKN  L   EGGY   +P G+   V
Sbjct: 723 QYLVGRGVEKKDFNSYGSRRGNDEVMVRGTFANVRIKN-QLASREGGYTTHIPSGEEMTV 781

Query: 756 YNVAMRYKAEGTPLLVIAGKEYGTGSSRDWAAKGTYLLGIRAVLAESFERIHRSNLVGMG 815
           +  + +Y+ + TPL+V+AGKEYG+GSSRDWAAKGT LLGI AV+AES+ERIHRSNLVGMG
Sbjct: 782 FEASEKYQKDDTPLVVLAGKEYGSGSSRDWAAKGTTLLGIHAVIAESYERIHRSNLVGMG 841

Query: 816 VLPLEFLPGENRETLGLTGYEVYDILGL-EDLKPRKLVDIVARREDGSEVRFQAIARLDT 874
           VLPL+F  G++  +LGL G E   I G+ E L P K +   A+++ G+ V F  + RLD+
Sbjct: 842 VLPLQFAEGQSASSLGLDGKEEITIEGITEGLTPLKNLKATAKKDGGAVVNFDVVCRLDS 901

Query: 875 PVEVDYYKNGGILQTVLLNMLKE 897
            VE+ YYKNGGIL  VL   LK+
Sbjct: 902 EVEIAYYKNGGILHYVLREFLKQ 924


Lambda     K      H
   0.317    0.137    0.399 

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: 2285
Number of extensions: 107
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 902
Length of database: 925
Length adjustment: 43
Effective length of query: 859
Effective length of database: 882
Effective search space:   757638
Effective search space used:   757638
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 Echvi_4039 Echvi_4039 (aconitate hydratase 1)
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.8809.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 1333.3   0.0          0 1327.8   0.0    2.0  1  lcl|FitnessBrowser__Cola:Echvi_4039  Echvi_4039 aconitate hydratase 1


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_4039  Echvi_4039 aconitate hydratase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1327.8   0.0         0         0       3     876 .]      19     922 ..      17     922 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1327.8 bits;  conditional E-value: 0
                            TIGR01341   3 vyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlqdftG 76 
                                           +y+sl al+e+++ki++lp s+rille++lrn d++ i++e+ e+ll+wk e  +d+++++kparv++qdftG
  lcl|FitnessBrowser__Cola:Echvi_4039  19 LNYWSLAALQEQGHKINELPFSIRILLENALRNYDDFAITKEHTETLLNWKPE-ASDKDVPYKPARVLMQDFTG 91 
                                          68************************************************998.89****************** PP

                            TIGR01341  77 vpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwakkaf 150
                                          vpavvd+a+lr +  + gkdp+kinpl+pvdlv+dhsvqvd++g++++ ++nv++e+ern ery+flkwa+k+f
  lcl|FitnessBrowser__Cola:Echvi_4039  92 VPAVVDIASLRAEAVRKGKDPQKINPLIPVDLVVDHSVQVDYFGTNYSYKKNVDVEYERNGERYEFLKWAQKSF 165
                                          ************************************************************************** PP

                            TIGR01341 151 knlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaallGqp 224
                                           n++vvppg Gi+hqvnleylak v+e +  g   ++pd+lvGtdsht m+nG+Gv+GwGvGGieaeaallGqp
  lcl|FitnessBrowser__Cola:Echvi_4039 166 DNFSVVPPGMGICHQVNLEYLAKGVIERD--G--NVFPDTLVGTDSHTPMVNGIGVVGWGVGGIEAEAALLGQP 235
                                          *************************9866..5..58************************************** PP

                            TIGR01341 225 vslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmapeyGataa 298
                                          +++ +p+v+G+kltG+l  G+tatd+vlt+tellrk+gvvgkfve fG+gl++l+++drati+nm+pe+G t++
  lcl|FitnessBrowser__Cola:Echvi_4039 236 IYFIMPQVVGLKLTGELPLGTTATDMVLTITELLRKHGVVGKFVEVFGPGLDTLTVPDRATISNMSPEFGCTVT 309
                                          ************************************************************************** PP

                            TIGR01341 299 ffpiddvtlqylrltgrdedkvelvekylkaqelfvddseepkytdvveldlsdveasvaGpkrpqdrvalkev 372
                                          +fpidd+tl+y+  t+r++d+++lve y+ka+ l+++d e++ky+++veldl +ve++v+Gpkrpqd++ +++ 
  lcl|FitnessBrowser__Cola:Echvi_4039 310 YFPIDDRTLDYMSKTNRSKDQIKLVEDYAKANMLWREDEESVKYSSLVELDLGTVEPTVSGPKRPQDKILVRNF 383
                                          ************************************************************************** PP

                            TIGR01341 373 kaafksslesnagekglalr...................................keakekklegkeaelkdga 411
                                          k++f + le+  g + + ++                                    +++e k++++e  l+dg+
  lcl|FitnessBrowser__Cola:Echvi_4039 384 KEKFGELLEEVHGREYIPIDkrdksrwfsegggqpvdkpgdlpedveiatktkngLKTVEVKINNEEFALSDGS 457
                                          ***************99998899999*******************9999988665456677889********** PP

                            TIGR01341 412 vviaaitsctntsnpsvllgagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyG 485
                                          +viaaitsctntsnpsv++gagl+a+ka e Gl vkp+vktslapGskvvtdyl  sgll+ le+l f++vGyG
  lcl|FitnessBrowser__Cola:Echvi_4039 458 IVIAAITSCTNTSNPSVMIGAGLVAQKARERGLDVKPWVKTSLAPGSKVVTDYLEASGLLDDLEALRFHVVGYG 531
                                          ************************************************************************** PP

                            TIGR01341 486 cttciGnsGpleeeveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepig 559
                                          ct+ciGnsGpl++++++a+ endl+v++vlsGnrnfe+r+hp+vk nyl+sp+lvvayalaG+vd+dl++ep+g
  lcl|FitnessBrowser__Cola:Echvi_4039 532 CTSCIGNSGPLPKHIAHAVEENDLVVASVLSGNRNFEARVHPQVKMNYLMSPMLVVAYALAGRVDVDLNEEPLG 605
                                          ************************************************************************** PP

                            TIGR01341 560 tdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffe 633
                                          +d + ++vylkdiwps++ei e++ k +++  f k+y e++egne+w++l+++s+++y+w ekstyi+e+pff+
  lcl|FitnessBrowser__Cola:Echvi_4039 606 FDPNLEPVYLKDIWPSNDEIFEVMGKVLSPGDFDKNYGEIFEGNEQWKNLQAPSDKVYNWSEKSTYIKEAPFFQ 679
                                          ************************************************************************** PP

                            TIGR01341 634 elklepeevedikgarillllGdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtf 707
                                          +l+ e  e ++i+gar+ll+lGdsittdhispaG+ ++ spa++yl  +Gve++dfnsyGsrrGn+evm+rGtf
  lcl|FitnessBrowser__Cola:Echvi_4039 680 GLSNEVPEPQNIQGARVLLKLGDSITTDHISPAGAFAESSPAGQYLVGRGVEKKDFNSYGSRRGNDEVMVRGTF 753
                                          ************************************************************************** PP

                            TIGR01341 708 aniriknklvkgkeGgltvylpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkavia 781
                                          an+rikn+l+  +eGg+t+++p +e+++v++a+ ky+k+++plvvlaGkeyGsGssrdwaakgt+llG++avia
  lcl|FitnessBrowser__Cola:Echvi_4039 754 ANVRIKNQLAS-REGGYTTHIPSGEEMTVFEASEKYQKDDTPLVVLAGKEYGSGSSRDWAAKGTTLLGIHAVIA 826
                                          *********99.************************************************************** PP

                            TIGR01341 782 esferihrsnlvgmGvlplefkqgedaetlgltgeetidvddi.eelkpkkevtvelvkedgeketveavlrid 854
                                          es+erihrsnlvgmGvlpl+f +g++a++lgl+g+e+i +++i e l p k+++ ++ k+ g +  +++v+r+d
  lcl|FitnessBrowser__Cola:Echvi_4039 827 ESYERIHRSNLVGMGVLPLQFAEGQSASSLGLDGKEEITIEGItEGLTPLKNLKATAKKDGGAVVNFDVVCRLD 900
                                          ******************************************7256**************************** PP

                            TIGR01341 855 tevelayvkkgGilqyvlrkll 876
                                          +eve+ay+k+gGil+yvlr++l
  lcl|FitnessBrowser__Cola:Echvi_4039 901 SEVEIAYYKNGGILHYVLREFL 922
                                          *******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (925 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: 0.14u 0.02s 00:00:00.16 Elapsed: 00:00:00.16
# Mc/sec: 5.06
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources