Alignments for a candidate for acn in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Dechlorosoma suillum PS

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate Dsui_2347 Dsui_2347 aconitate hydratase 1

Query= BRENDA::A0A090AMG4
         (901 letters)



>FitnessBrowser__PS:Dsui_2347
          Length = 898

 Score = 1161 bits (3004), Expect = 0.0
 Identities = 581/883 (65%), Positives = 701/883 (79%), Gaps = 9/883 (1%)

Query: 21  YYSLPALGKSLGID-VQRLPVSIRIVLESVLRNCDGKKVTEEHVKQLANWQANARREDEI 79
           ++SLPAL ++ GI  V RLPVS+RIVLE++LR+CDG++VT  HV QLANWQ  A R +EI
Sbjct: 22  FHSLPAL-EAAGIGPVSRLPVSLRIVLEALLRHCDGRRVTPRHVLQLANWQPRAERTEEI 80

Query: 80  PFVVARVVLQDFTGVPLLADIAAMRSVADKMGKSPKSIEPLVPVDLVVDHSVMIDYFGTK 139
           PFVVARVVLQDFTGVPLL D+AAMR  A   G  PK IEPLVPVDLVVDHSV +D +GT 
Sbjct: 81  PFVVARVVLQDFTGVPLLCDLAAMRDAAAAQGTDPKRIEPLVPVDLVVDHSVQVDEYGTP 140

Query: 140 NALDLNMKLEFKRNQERYQFMKWGMQAFDTFGVVPPGFGIVHQVNLEYLARGVHLDKKNN 199
            AL  NM+LEF+RN ERYQFMKWGMQAFDTF VVPPG GIVHQVNLEYL RGV   ++  
Sbjct: 141 TALRRNMELEFQRNAERYQFMKWGMQAFDTFKVVPPGIGIVHQVNLEYLFRGVR--RQGE 198

Query: 200 VYYPDSLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQPVYFLTPDVVGVELKGQLRGG 259
           + +PD+LVGTDSHTTMING+GVVGWGVGGIEAEA MLGQPVYFLTPDVVGVEL+G+L  G
Sbjct: 199 LLFPDTLVGTDSHTTMINGVGVVGWGVGGIEAEAAMLGQPVYFLTPDVVGVELRGRLNEG 258

Query: 260 VTATDLVLTITEMLRREKVVGKFVEFCGEGTASLSVAERATIGNMAPEYGATMGFFPVDE 319
           VTATDLVLT+TE+LRREKVVGKFVEF G G+ SLS+ +RATI NMAPEYGAT+GFFPVDE
Sbjct: 259 VTATDLVLTVTELLRREKVVGKFVEFFGPGSTSLSLTDRATIANMAPEYGATLGFFPVDE 318

Query: 320 RTIDYFRGTGRTEAEIAAFEAYFKAQKMFGVPKAADINFTKLLTLDLSTVAPSLAGPKRP 379
           +T+DY R TGR EAE+ AFEAYF+AQ +FG P+A DI+++  L+LDL+T+ PSLAGPKRP
Sbjct: 319 KTVDYLRQTGRNEAEVEAFEAYFRAQGLFGAPRAGDIDYSTQLSLDLATIVPSLAGPKRP 378

Query: 380 QDRIEIGNVKNTFIDLYSKPVAENGFNQPAEKLAQTFTTS-AGTQVKNGDILIAAITSCT 438
           QDRI++ ++  +F  L+S+P + NGF +PAE+L Q   T+ AG  + +GD+LIAAITSCT
Sbjct: 379 QDRIDLSDMGRSFDTLFSQPTSANGFGKPAEQLPQRQPTARAGVDLGHGDVLIAAITSCT 438

Query: 439 NTSNPSVLLAAGLLAKKAVEAGLTVPKHIKTSLAPGSRVVTEYLTKTGLLPYLEKLGFDV 498
           NTSNP+VL+AAGLLAKKAV+ GL+V  HIKTSLAPGSRVVT+YL K GLL  L +LGF +
Sbjct: 439 NTSNPAVLIAAGLLAKKAVDKGLSVQPHIKTSLAPGSRVVTDYLEKAGLLAPLARLGFAL 498

Query: 499 AAYGCTTCIGNAGDLTPDLNEAIIGNDLICSAVLSGNRNFEARIHPNIKANFLASPPLVV 558
           A YGCTTCIGNAGDL P+ N+AI   DL+ +AVLSGNRNFEARIHP I+AN+LASPPLVV
Sbjct: 499 AGYGCTTCIGNAGDLAPEFNQAIAERDLVVAAVLSGNRNFEARIHPAIRANYLASPPLVV 558

Query: 559 AYALAGTVTRDLMTEPVGRGKNGD-VWLGDIWPTTEEIESLLKYALDPKAFEANYGQVKS 617
           A+A+AG V  DL T P+G G++G  V+L +IWP++EEI ++L +A DP  +   Y    +
Sbjct: 559 AFAIAGRVNVDLTTTPLGTGRDGQPVYLREIWPSSEEIATVLPFAQDPATYRRLYADF-T 617

Query: 618 NPGKLWENTKGVTGDTYNWPDSTYIAEPPFFEGFGMTPGAMPAVKGARALGVFGDSVTTD 677
               LW       G  Y+WP STYIA PPFF+GF + P  +  + GARAL V GDSVTTD
Sbjct: 618 RDHDLWNAVPAPEGQIYDWPPSTYIARPPFFDGFTVEPPPLAPINGARALLVLGDSVTTD 677

Query: 678 HISPAGSIKETSPAGKWLKENGVMKADFNSYGSRRGNHEIMMRGTFANVRIKNLMIPALP 737
           HISPAGS K  +PAG+WL   GV   DFNSYGSRRG+HE+M+RGTFANVR+KNLM+P   
Sbjct: 678 HISPAGSFKAATPAGQWLTAQGVKSLDFNSYGSRRGHHEVMVRGTFANVRVKNLMLPPKA 737

Query: 738 DGSRFEGGETLFQPTGEQMSIYDAAMKYVSAGTPTVVFGGEEYGTGSSRDWAAKGTQLLG 797
           DGS  EGG TL    G+Q+++++AA  Y   G PT+VF GEEYGTGSSRDWAAKGT+LLG
Sbjct: 738 DGSPVEGGYTLLD--GQQVTVFEAASAYQQRGIPTLVFAGEEYGTGSSRDWAAKGTRLLG 795

Query: 798 VKAVITRSFERIHRSNLVGMGVLPLQFKGADSVQSLGITGEETYDISGLEDGIKPMQDVT 857
           V+AV+ RSFERIHR+NLVGMGVLPLQFK   S  SLG+ G E +D+ G +  ++  QD+ 
Sbjct: 796 VRAVVARSFERIHRANLVGMGVLPLQFKAGTSAASLGLDGSEHFDLPGADGPLQAQQDLM 855

Query: 858 LTITRKDGSKQDVTVLLRIDTPIEVDYYQHGGILPFVLRQLLA 900
           L ITR DG  + V +L RIDTPIEV+Y++HGGILP+VLRQLL+
Sbjct: 856 LRITRSDGRVEQVPLLCRIDTPIEVEYFRHGGILPYVLRQLLS 898


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: 2245
Number of extensions: 92
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: 898
Length adjustment: 43
Effective length of query: 858
Effective length of database: 855
Effective search space:   733590
Effective search space used:   733590
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 Dsui_2347 Dsui_2347 (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.26190.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 1237.5   0.0          0 1237.3   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_2347  Dsui_2347 aconitate hydratase 1


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_2347  Dsui_2347 aconitate hydratase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1237.3   0.0         0         0       5     876 .]      22     897 ..      19     897 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1237.3 bits;  conditional E-value: 0
                         TIGR01341   5 yyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlqdftGvpav 80 
                                       ++sl+ale + ++ +s+lp slri+le++lr++dg++++ ++v +l++w+  + + eei+f +arvvlqdftGvp++
  lcl|FitnessBrowser__PS:Dsui_2347  22 FHSLPALEAAgIGPVSRLPVSLRIVLEALLRHCDGRRVTPRHVLQLANWQPRAERTEEIPFVVARVVLQDFTGVPLL 98 
                                       68999999876899*************************************************************** PP

                         TIGR01341  81 vdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwakkafknlkvvp 157
                                        dlaa+r+a ++ g dp++i+plvpvdlv+dhsvqvd++g+ +al+ n+elef+rn+ery+f+kw+ +af  +kvvp
  lcl|FitnessBrowser__PS:Dsui_2347  99 CDLAAMRDAAAAQGTDPKRIEPLVPVDLVVDHSVQVDEYGTPTALRRNMELEFQRNAERYQFMKWGMQAFDTFKVVP 175
                                       ***************************************************************************** PP

                         TIGR01341 158 pgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaallGqpvslsvpeviG 234
                                       pg Givhqvnleyl + v ++     +l++pd+lvGtdshttminG+Gv+GwGvGGieaeaa+lGqpv++  p+v+G
  lcl|FitnessBrowser__PS:Dsui_2347 176 PGIGIVHQVNLEYLFRGVRRQG----ELLFPDTLVGTDSHTTMINGVGVVGWGVGGIEAEAAMLGQPVYFLTPDVVG 248
                                       ***************9997655....689************************************************ PP

                         TIGR01341 235 vkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmapeyGataaffpiddvtlqylr 311
                                       v l G+l+eGvtatdlvltvtellr++ vvgkfveffG+g ++lsl+dratianmapeyGat +ffp+d++t++ylr
  lcl|FitnessBrowser__PS:Dsui_2347 249 VELRGRLNEGVTATDLVLTVTELLRREKVVGKFVEFFGPGSTSLSLTDRATIANMAPEYGATLGFFPVDEKTVDYLR 325
                                       ***************************************************************************** PP

                         TIGR01341 312 ltgrdedkvelvekylkaqelfvd.dseepkytdvveldlsdveasvaGpkrpqdrvalkevkaafksslesnagek 387
                                        tgr+e +ve  e+y +aq+lf    + ++ y++ + ldl ++ +s+aGpkrpqdr++l+++ ++f + ++++++ +
  lcl|FitnessBrowser__PS:Dsui_2347 326 QTGRNEAEVEAFEAYFRAQGLFGApRAGDIDYSTQLSLDLATIVPSLAGPKRPQDRIDLSDMGRSFDTLFSQPTSAN 402
                                       ***********************98999************************************************* PP

                         TIGR01341 388 glalr..keakekklegkeaelkdgavviaaitsctntsnpsvllgagllakkavelGlkvkpyvktslapGskvvt 462
                                       g++ +  + ++++        l +g+v iaaitsctntsnp+vl++agllakkav+ Gl v+p++ktslapGs+vvt
  lcl|FitnessBrowser__PS:Dsui_2347 403 GFGKPaeQLPQRQPTARAGVDLGHGDVLIAAITSCTNTSNPAVLIAAGLLAKKAVDKGLSVQPHIKTSLAPGSRVVT 479
                                       **987446677777789999********************************************************* PP

                         TIGR01341 463 dylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikendlevsavlsGnrnfegrihplvkanylasppl 539
                                       dyl ++gll  l +lGf l GyGcttciGn+G+l  e ++ai+e dl+v+avlsGnrnfe+rihp ++anylasppl
  lcl|FitnessBrowser__PS:Dsui_2347 480 DYLEKAGLLAPLARLGFALAGYGCTTCIGNAGDLAPEFNQAIAERDLVVAAVLSGNRNFEARIHPAIRANYLASPPL 556
                                       ***************************************************************************** PP

                         TIGR01341 540 vvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdl 616
                                       vva+a+aG+v++dl++ p+gt++dG++vyl++iwps +eia++   a  +  +++ y+ +t + + wn + ++++++
  lcl|FitnessBrowser__PS:Dsui_2347 557 VVAFAIAGRVNVDLTTTPLGTGRDGQPVYLREIWPSSEEIATVLPFAQDPATYRRLYADFTRDHDLWNAVPAPEGQI 633
                                       ***************************************************************************** PP

                         TIGR01341 617 yewdekstyireppffeelklepeevedikgarillllGdsittdhispaGsikkdspaakylkekGverrdfnsyG 693
                                       y+w   styi +ppff+++++ep  + +i+gar ll+lGds+ttdhispaGs k  +pa+++l+ +Gv+  dfnsyG
  lcl|FitnessBrowser__PS:Dsui_2347 634 YDWP-PSTYIARPPFFDGFTVEPPPLAPINGARALLVLGDSVTTDHISPAGSFKAATPAGQWLTAQGVKSLDFNSYG 709
                                       ***6.59********************************************************************** PP

                         TIGR01341 694 srrGnhevmlrGtfaniriknklvkgk......eGgltvylpdsevvsvydaamkykkegvplvvlaGkeyGsGssr 764
                                       srrG hevm+rGtfan+r+kn +++ k      eGg+t  l d+++v+v++aa  y++ g+p++v aG+eyG+Gssr
  lcl|FitnessBrowser__PS:Dsui_2347 710 SRRGHHEVMVRGTFANVRVKNLMLPPKadgspvEGGYT--LLDGQQVTVFEAASAYQQRGIPTLVFAGEEYGTGSSR 784
                                       ***********************986522223367777..5699********************************* PP

                         TIGR01341 765 dwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltgeetidvdd.ieelkpkkevtvelvke 840
                                       dwaakgt+llGv+av+a+sferihr+nlvgmGvlpl+fk+g++a +lgl+g+e+ d+++    l+ ++++ ++++++
  lcl|FitnessBrowser__PS:Dsui_2347 785 DWAAKGTRLLGVRAVVARSFERIHRANLVGMGVLPLQFKAGTSAASLGLDGSEHFDLPGaDGPLQAQQDLMLRITRS 861
                                       **********************************************************93457************** PP

                         TIGR01341 841 dgeketveavlridtevelayvkkgGilqyvlrkll 876
                                       dg +e v   +ridt++e++y+++gGil yvlr+ll
  lcl|FitnessBrowser__PS:Dsui_2347 862 DGRVEQVPLLCRIDTPIEVEYFRHGGILPYVLRQLL 897
                                       *********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (898 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: 00:00:00.06
# Mc/sec: 12.37
//
[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:

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