Aligments for a candidate for acn in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Aligments for a candidate for acn in Sinorhizobium meliloti 1021

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 SMc03846 SMc03846 aconitate hydratase

Query= SwissProt::P70920
         (906 letters)



>FitnessBrowser__Smeli:SMc03846
          Length = 896

 Score = 1298 bits (3359), Expect = 0.0
 Identities = 652/905 (72%), Positives = 742/905 (81%), Gaps = 13/905 (1%)

Query: 3   SLDSFKCKKTLKVGAKTYVYYSLPTAEKNGLKGISKLPYSMKVLLENLLRNEDGRSVKKA 62
           SLDSF C+ TL V    YVYYSLP AE NGL GISKLPYSMKVLLENLLRNEDGRSV K 
Sbjct: 4   SLDSFNCRSTLTVNGVDYVYYSLPKAEANGLAGISKLPYSMKVLLENLLRNEDGRSVTKK 63

Query: 63  DIVAVSKWLRKK-SLEHEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQKLGGDAEKINPL 121
           DI  ++ WL  K + E+EIA+RPARVLMQDFTGVPAVVDLAAMR+AM  LGGD EKINPL
Sbjct: 64  DIENIAAWLGDKGTAENEIAYRPARVLMQDFTGVPAVVDLAAMRDAMVSLGGDPEKINPL 123

Query: 122 VPVDLVIDHSVIVNFFGDNKAFAKNVTEEYKQNQERYEFLKWGQAAFSNFSVVPPGTGIC 181
           VPVDLVIDHSVIV+ FG   AFA+NV  EY++N ERY FLKWGQ AF NF VVPPGTGIC
Sbjct: 124 VPVDLVIDHSVIVDEFGTPTAFARNVELEYQRNGERYRFLKWGQQAFKNFRVVPPGTGIC 183

Query: 182 HQVNLEYLSQTVWTKKEKMTVGKKTGTFEVAYPDSLVGTDSHTTMVNGLAVLGWGVGGIE 241
           HQVNLEYL Q VWT++E   V         AYPD+ VGTDSHTTM+NGL VLGWGVGGIE
Sbjct: 184 HQVNLEYLGQAVWTREEDGEV--------TAYPDTCVGTDSHTTMINGLGVLGWGVGGIE 235

Query: 242 AEACMLGQPLSMLLPNVVGFKLKGAMKEGVTATDLVLTVTQMLRKLGVVGKFVEFFGPGL 301
           AEA MLGQP+SMLLP V+GFKL G +KEGVTATDLVLTV QMLRK GVV KFVEFFGPGL
Sbjct: 236 AEAAMLGQPVSMLLPEVIGFKLTGKLKEGVTATDLVLTVVQMLRKKGVVSKFVEFFGPGL 295

Query: 302 DHLSVADKATIANMAPEYGATCGFFPVDAAAIDYLKTSGRAAPRVALVQAYAKAQGLFRT 361
           D++++AD+ATI NM PEYGATCGFFPVDA  I+YL  SGR   R+ALV+AY+KAQG++R 
Sbjct: 296 DNMTLADRATIGNMGPEYGATCGFFPVDAETINYLTISGREEQRIALVEAYSKAQGMWRE 355

Query: 362 AKSADPVFTETLTLDLADVVPSMAGPKRPEGRIALPSVAEGFSVALANEYKKTEEPAKRF 421
              ++ VFT+TL LDL DVVPSMAGPKRPEGRIAL ++A GF+ AL N+YKK  + A R+
Sbjct: 356 GDGSELVFTDTLELDLGDVVPSMAGPKRPEGRIALENIASGFAAALDNDYKKPGQLANRY 415

Query: 422 AVEGKKYEIGHGDVVIAAITSCTNTSNPSVLIGAGLLARNAAAKGLKAKPWVKTSLAPGS 481
           AVEG  Y++GHGDV IAAITSCTNTSNPSVLI AGLLARNA AKGLK +PWVKTSLAPGS
Sbjct: 416 AVEGTDYDLGHGDVAIAAITSCTNTSNPSVLIAAGLLARNAVAKGLKTQPWVKTSLAPGS 475

Query: 482 QVVAAYLADSGLQAHLDKVGFNLVGFGCTTCIGNSGPLPEEISKSINDNGIVAAAVLSGN 541
           QVVA YL+ SGLQ  LDK+GFNLVGFGCTTCIGNSGPLP EISK+IND G++AA VLSGN
Sbjct: 476 QVVAEYLSKSGLQTDLDKLGFNLVGFGCTTCIGNSGPLPTEISKTINDKGLIAAGVLSGN 535

Query: 542 RNFEGRVSPDVQANYLASPPLVVAHALAGSVTKNLAVEPLGEGKDGKPVYLKDIWPTSKE 601
           RNFEGR+SPDVQANYLASPPLVVA+ALAGSV K+L  EP+GE +DG+PVYL+DIWPTS+E
Sbjct: 536 RNFEGRISPDVQANYLASPPLVVAYALAGSVQKDLTKEPIGEDRDGQPVYLRDIWPTSQE 595

Query: 602 INAFMKKFVTASIFKKKYADVFKGDTNWRKIKTVESETYRWNMSSTYVQNPPYFEGMKKE 661
           I  F+ ++VT  ++  KYADVFKGD NW+ ++    +TY W+  STYVQNPPYF GM K+
Sbjct: 596 IQDFIFRYVTRELYATKYADVFKGDANWQAVQVPAGQTYAWDEGSTYVQNPPYFVGMGKK 655

Query: 662 PEPVTDIVEARILAMFGDKITTDHISPAGSIKLTSPAGKYLSEHQVRPADFNQYGTRRGN 721
              ++DI  AR+L +FGDKITTDHISPAGSIK  SPAG YL EH V  ADFNQYGTRRGN
Sbjct: 656 GAGISDIKNARVLGLFGDKITTDHISPAGSIKAASPAGAYLLEHGVGIADFNQYGTRRGN 715

Query: 722 HEVMMRGTFANIRIKNFMLKGADGNIPEGGLTKHWPDGEQMSIYDAAMKYQQEQVPLVVF 781
           HEVMMRGTFANIRI+N ML G +G   EGG T H+P  E+MSIYDAAM+Y++E VPLV+F
Sbjct: 716 HEVMMRGTFANIRIRNHML-GPNGK--EGGYTIHYPSKEEMSIYDAAMQYKEEGVPLVIF 772

Query: 782 AGAEYGNGSSRDWAAKGTRLLGVRAVICQSFERIHRSNLVGMGVLPLTFEEGTSWSSLGL 841
           AG EYGNGSSRDWAAKGT LLGV+AVI QSFERIHRSNLVGMGV+P  FEEG +W SLGL
Sbjct: 773 AGVEYGNGSSRDWAAKGTNLLGVKAVIAQSFERIHRSNLVGMGVVPFVFEEGMTWESLGL 832

Query: 842 KGDEKVTLRGLVGDLKPRQKLTAEIVSGDGSLQRVSLLCRIDTLDELDYYRNGGILHYVL 901
           KGDE VT+  L  +++PR+K  A+I  GDGS++ V L+CRIDTLDE+ Y  NGGIL  VL
Sbjct: 833 KGDEVVTIENL-ANVQPREKRVAKITYGDGSVKEVPLICRIDTLDEVTYVNNGGILQTVL 891

Query: 902 RKLAA 906
           R LAA
Sbjct: 892 RDLAA 896


Lambda     K      H
   0.317    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: 2261
Number of extensions: 88
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: 906
Length of database: 896
Length adjustment: 43
Effective length of query: 863
Effective length of database: 853
Effective search space:   736139
Effective search space used:   736139
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 SMc03846 SMc03846 (aconitate hydratase)
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.20950.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 1380.3   0.0          0 1380.1   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc03846  SMc03846 aconitate hydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc03846  SMc03846 aconitate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1380.1   0.0         0         0       3     875 ..      21     894 ..      19     895 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1380.1 bits;  conditional E-value: 0
                           TIGR01341   3 vyyyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkke.elkdeeiafkparvvlqdft 75 
                                         + yysl+++e + l  isklp+s+++lle++lrn dg++++++d+e+++ w  +  ++++eia++parv++qdft
  lcl|FitnessBrowser__Smeli:SMc03846  21 YVYYSLPKAEANgLAGISKLPYSMKVLLENLLRNEDGRSVTKKDIENIAAWLGDkGTAENEIAYRPARVLMQDFT 95 
                                         78******99876899***********************************86515899**************** PP

                           TIGR01341  76 Gvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwakkaf 150
                                         Gvpavvdlaa+r+a+ +lg+dpekinplvpvdlvidhsv vd++g+ +a++ nvele++rn ery+flkw+++af
  lcl|FitnessBrowser__Smeli:SMc03846  96 GVPAVVDLAAMRDAMVSLGGDPEKINPLVPVDLVIDHSVIVDEFGTPTAFARNVELEYQRNGERYRFLKWGQQAF 170
                                         *************************************************************************** PP

                           TIGR01341 151 knlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaallGqpv 225
                                         kn++vvppgtGi+hqvnleyl+++v++ e+dge +aypd+ vGtdshttminGlGvlGwGvGGieaeaa+lGqpv
  lcl|FitnessBrowser__Smeli:SMc03846 171 KNFRVVPPGTGICHQVNLEYLGQAVWTREEDGEVTAYPDTCVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPV 245
                                         *************************************************************************** PP

                           TIGR01341 226 slsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmapeyGataaff 300
                                         s+ +peviG+kltGkl+eGvtatdlvltv ++lrkkgvv+kfveffG+gl++++ladrati nm peyGat++ff
  lcl|FitnessBrowser__Smeli:SMc03846 246 SMLLPEVIGFKLTGKLKEGVTATDLVLTVVQMLRKKGVVSKFVEFFGPGLDNMTLADRATIGNMGPEYGATCGFF 320
                                         *************************************************************************** PP

                           TIGR01341 301 piddvtlqylrltgrdedkvelvekylkaqelfvd.dseepkytdvveldlsdveasvaGpkrpqdrvalkevka 374
                                         p+d++t++yl ++gr+e+++ lve+y kaq+++++ d++e ++td++eldl dv +s+aGpkrp+ r+al+++ +
  lcl|FitnessBrowser__Smeli:SMc03846 321 PVDAETINYLTISGREEQRIALVEAYSKAQGMWREgDGSELVFTDTLELDLGDVVPSMAGPKRPEGRIALENIAS 395
                                         ***********************************99************************************** PP

                           TIGR01341 375 afksslesnagekglalrkeakekklegkeaelkdgavviaaitsctntsnpsvllgagllakkavelGlkvkpy 449
                                          f+++l+++  + g    + a+++++eg+++ l +g+v+iaaitsctntsnpsvl++aglla+ av  Glk +p+
  lcl|FitnessBrowser__Smeli:SMc03846 396 GFAAALDNDYKKPG----QLANRYAVEGTDYDLGHGDVAIAAITSCTNTSNPSVLIAAGLLARNAVAKGLKTQPW 466
                                         ********998888....889999*************************************************** PP

                           TIGR01341 450 vktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikendlevsavlsGnrnfegr 524
                                         vktslapGs+vv++yl++sgl++ l++lGfnlvG+GcttciGnsGpl+ e++++i++++l ++ vlsGnrnfegr
  lcl|FitnessBrowser__Smeli:SMc03846 467 VKTSLAPGSQVVAEYLSKSGLQTDLDKLGFNLVGFGCTTCIGNSGPLPTEISKTINDKGLIAAGVLSGNRNFEGR 541
                                         *************************************************************************** PP

                           TIGR01341 525 ihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeev 599
                                         i p+v+anylaspplvvayalaG+v+ dl+kepig d+dG++vyl+diwp+ +ei++++ ++v++el+  +y+ v
  lcl|FitnessBrowser__Smeli:SMc03846 542 ISPDVQANYLASPPLVVAYALAGSVQKDLTKEPIGEDRDGQPVYLRDIWPTSQEIQDFIFRYVTRELYATKYADV 616
                                         *************************************************************************** PP

                           TIGR01341 600 tegnerwnelevtssdlyewdekstyireppffeelklepeevedikgarillllGdsittdhispaGsikkdsp 674
                                         ++g+++w+ ++v+ +++y+wde sty+++pp+f ++  + + ++dik+ar+l l+Gd+ittdhispaGsik  sp
  lcl|FitnessBrowser__Smeli:SMc03846 617 FKGDANWQAVQVPAGQTYAWDEGSTYVQNPPYFVGMGKKGAGISDIKNARVLGLFGDKITTDHISPAGSIKAASP 691
                                         *************************************************************************** PP

                           TIGR01341 675 aakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklv..kgkeGgltvylpdsevvsvydaamkykkeg 747
                                         a+ yl e+Gv   dfn yG+rrGnhevm+rGtfaniri+n+++  +gkeGg+t+++p +e++s+ydaam+yk+eg
  lcl|FitnessBrowser__Smeli:SMc03846 692 AGAYLLEHGVGIADFNQYGTRRGNHEVMMRGTFANIRIRNHMLgpNGKEGGYTIHYPSKEEMSIYDAAMQYKEEG 766
                                         ******************************************96679**************************** PP

                           TIGR01341 748 vplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltgeetidvd 822
                                         vplv+ aG eyG Gssrdwaakgt+llGvkavia+sferihrsnlvgmGv+p+ f++g + e+lgl+g+e + ++
  lcl|FitnessBrowser__Smeli:SMc03846 767 VPLVIFAGVEYGNGSSRDWAAKGTNLLGVKAVIAQSFERIHRSNLVGMGVVPFVFEEGMTWESLGLKGDEVVTIE 841
                                         *************************************************************************** PP

                           TIGR01341 823 dieelkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkl 875
                                         ++ +++p+++   +++  dg+++ v   +ridt  e++yv++gGilq vlr+l
  lcl|FitnessBrowser__Smeli:SMc03846 842 NLANVQPREKRVAKITYGDGSVKEVPLICRIDTLDEVTYVNNGGILQTVLRDL 894
                                         **************************************************985 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: 0.07u 0.02s 00:00:00.09 Elapsed: 00:00:00.09
# Mc/sec: 8.48
//
[ok]

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

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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, 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

GapMind for catabolism of small carbon sources