Alignments for a candidate for acn in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Dinoroseobacter shibae DFL-12

Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate 3608455 Dshi_1851 aconitate hydratase 1 (RefSeq)

Query= reanno::Marino:GFF3491
         (919 letters)



>FitnessBrowser__Dino:3608455
          Length = 928

 Score = 1125 bits (2910), Expect = 0.0
 Identities = 565/925 (61%), Positives = 701/925 (75%), Gaps = 18/925 (1%)

Query: 5   SLSKDSLNTLSSLDAGGKTFHYYSLPKAADT--LGDLNRLPFSLKVLMENLLRNEDG-TT 61
           ++ +D+  T  +L  G ++  YYS+P AA+T  LGD ++LP +LKV++EN+LR EDG  T
Sbjct: 4   TVGQDTAKTRKTLRVGDQSLAYYSIP-AAETAGLGDFSKLPAALKVVLENMLRFEDGGRT 62

Query: 62  VDRSHIDAMVQWM-KDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAM 120
           V    I A   W  K   +  EI +RPARVLMQDFTGVP VVDLAAMR+ +   G D   
Sbjct: 63  VSVDDIRAFADWADKGGQNPREIAYRPARVLMQDFTGVPAVVDLAAMRDGIVGLGGDAEK 122

Query: 121 INPLSPVDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPG 180
           INPL+PVDLVIDHSVM+D+FG+  +F+ NV  E ERN ERY FL+WGQ AF NFRVVPPG
Sbjct: 123 INPLNPVDLVIDHSVMIDEFGNPRAFQMNVDREYERNIERYTFLKWGQSAFANFRVVPPG 182

Query: 181 TGICHQVNLEYLGKTVW-QKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEA 239
           TGICHQVNLEYL + VW   DQ G+ +AYPDTLVGTDSHTTM+NG+ +LGWGVGGIEAEA
Sbjct: 183 TGICHQVNLEYLAQAVWTDTDQSGQEVAYPDTLVGTDSHTTMVNGMAVLGWGVGGIEAEA 242

Query: 240 AMLGQPVSMLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDM 299
           AMLGQP+SMLIPEVVGF++TG++ EG T TDLVL V EMLR KGVVGKFVEFYG GL  +
Sbjct: 243 AMLGQPISMLIPEVVGFELTGEMMEGTTGTDLVLKVVEMLRAKGVVGKFVEFYGAGLDHL 302

Query: 300 PVADRATIANMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGH 359
           P+ADRATIANMAPEYGATCGFFP+D +T++YMR TGR+E ++ LVEAYAK  GLWR   +
Sbjct: 303 PLADRATIANMAPEYGATCGFFPIDGETLRYMRTTGRDEARIALVEAYAKENGLWRGDDY 362

Query: 360 EPVYTDNLELDMGEVEASLAGPKRPQDRVALKNMKSSFELLMETAEGP----AENREANL 415
            PVYTD L LDMG +  +++GPKRPQD VAL     +F   + T + P     E  +A  
Sbjct: 363 APVYTDTLSLDMGTIVPAISGPKRPQDYVALDKAAETFRDYV-TGQRPDWSADEEDKAEW 421

Query: 416 ESEGGQTAVG--VDDSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAG 473
             EGG  A      D  KH  ++   + G    +  G +VIA+ITSCTNTSNP VM+ AG
Sbjct: 422 TDEGGAVAPRDIPGDRGKHKRAR---VRGADYTIHDGTIVIASITSCTNTSNPYVMIGAG 478

Query: 474 LIAQKAVQKGLSTKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNS 533
           L+A+KA   GL+ KPWVKTSLAPGS+VV+ YL+  G Q+DLD +GFNLVGYGCTTCIGNS
Sbjct: 479 LVARKARALGLTRKPWVKTSLAPGSQVVSAYLEAAGLQEDLDAIGFNLVGYGCTTCIGNS 538

Query: 534 GPLPDAVEKAISDGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDL 593
           GP+ + + +AI+DGD+   SVLSGNRNFEGR+ P V+ N+LASPPLVVAYALAG++ +DL
Sbjct: 539 GPIQEELSEAINDGDIIATSVLSGNRNFEGRISPDVRANYLASPPLVVAYALAGDMNVDL 598

Query: 594 SQDPLGNDKDGNPVYLKDLWPSQQEIAEAVEKVKT-DMFRKEYAEVFDGDATWKSIKVPE 652
           ++DPLG D+DGN VYLKD+WPS +EIAE VE+  T + F+ +YA+VF GD  W+S++  +
Sbjct: 599 TRDPLGQDRDGNDVYLKDIWPSTKEIAELVEQTVTREAFQAKYADVFKGDEKWQSVETTD 658

Query: 653 SKVYEWSDKSTYIQHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDT 712
           S  Y+W   STY+Q+PP+F+G+  EP  I +I+ A ILA+LGD +TTDHISPAGSFK  T
Sbjct: 659 SLTYDWPPSSTYVQNPPYFQGMSAEPGTISNIEGAKILAILGDMITTDHISPAGSFKEST 718

Query: 713 PAGKYLQEHGVEPKDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQ 772
           PAG+YL E  V+P++FNSYGSRRGNHEVMMRGTFAN+RIRNEMLDGVEGGYT   P G+Q
Sbjct: 719 PAGRYLTERQVQPREFNSYGSRRGNHEVMMRGTFANIRIRNEMLDGVEGGYT-LGPDGQQ 777

Query: 773 MAIYDAAMKYQEKGTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLI 832
            +I++AAM YQE GTPLV+  G++YG GSSRDWAAKGT LLGVKAV+AES+ERIHRSNL+
Sbjct: 778 TSIFEAAMAYQEMGTPLVIFGGEQYGAGSSRDWAAKGTSLLGVKAVIAESFERIHRSNLV 837

Query: 833 GMGVMPLQFPEGTDRKSLKLTGEETISIEGLSGEIKPGQTLKMTVKYKDGSTETCELKSR 892
           GMGV+P +F  G  RK+L L G+ET+SI GL G+I P   +  T+ Y DG+T    LK R
Sbjct: 838 GMGVIPFEFTGGDTRKTLGLKGDETVSITGLDGKIVPLSEMPCTITYGDGTTREITLKCR 897

Query: 893 IDTANEAVYFKHGGILHYVVREMLR 917
           IDT  E  Y ++GG+LHYV+R + +
Sbjct: 898 IDTEVEIEYIENGGVLHYVLRNLAK 922


Lambda     K      H
   0.315    0.134    0.390 

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: 2345
Number of extensions: 109
Number of successful extensions: 7
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: 919
Length of database: 928
Length adjustment: 43
Effective length of query: 876
Effective length of database: 885
Effective search space:   775260
Effective search space used:   775260
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: 42 (22.0 bits)
S2: 57 (26.6 bits)

Align candidate 3608455 Dshi_1851 (aconitate hydratase 1 (RefSeq))
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.15637.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 1319.5   0.0          0 1319.1   0.0    1.1  1  lcl|FitnessBrowser__Dino:3608455  Dshi_1851 aconitate hydratase 1 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608455  Dshi_1851 aconitate hydratase 1 (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1319.1   0.0         0         0       3     875 ..      23     920 ..      21     921 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1319.1 bits;  conditional E-value: 0
                         TIGR01341   3 vyyyslkalees.lekisklpkslrillesvlrnldg.skikeedveallkwkke.elkdeeiafkparvvlqdftG 76 
                                         yys++a+e + l++ sklp +l+++le++lr  dg ++++ +d+ a+++w  +  ++ +eia++parv++qdftG
  lcl|FitnessBrowser__Dino:3608455  23 LAYYSIPAAETAgLGDFSKLPAALKVVLENMLRFEDGgRTVSVDDIRAFADWADKgGQNPREIAYRPARVLMQDFTG 99 
                                       67*******988789********************96378999*********866156779**************** PP

                         TIGR01341  77 vpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwakkafknl 153
                                       vpavvdlaa+r+ +  lg+d+ekinpl pvdlvidhsv +d++g+ +a+++nv++e+ern ery+flkw++ af n+
  lcl|FitnessBrowser__Dino:3608455 100 VPAVVDLAAMRDGIVGLGGDAEKINPLNPVDLVIDHSVMIDEFGNPRAFQMNVDREYERNIERYTFLKWGQSAFANF 176
                                       ***************************************************************************** PP

                         TIGR01341 154 kvvppgtGivhqvnleylakvvfe.aekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaallGqpvslsv 229
                                       +vvppgtGi+hqvnleyla++v++ +++ g+++aypd+lvGtdshttm+nG+ vlGwGvGGieaeaa+lGqp+s+ +
  lcl|FitnessBrowser__Dino:3608455 177 RVVPPGTGICHQVNLEYLAQAVWTdTDQSGQEVAYPDTLVGTDSHTTMVNGMAVLGWGVGGIEAEAAMLGQPISMLI 253
                                       **********************9626789************************************************ PP

                         TIGR01341 230 peviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmapeyGataaffpiddvt 306
                                       pev+G+ ltG++ eG+t tdlvl+v e+lr kgvvgkfvef+G gl++l+ladratianmapeyGat++ffpid +t
  lcl|FitnessBrowser__Dino:3608455 254 PEVVGFELTGEMMEGTTGTDLVLKVVEMLRAKGVVGKFVEFYGAGLDHLPLADRATIANMAPEYGATCGFFPIDGET 330
                                       ***************************************************************************** PP

                         TIGR01341 307 lqylrltgrdedkvelvekylkaqelfvddseepkytdvveldlsdveasvaGpkrpqdrvalkevkaafksslesn 383
                                       l y+r+tgrde ++ lve+y+k ++l++ d   p+ytd++ ld+ ++ ++++Gpkrpqd val++  ++f+  +  +
  lcl|FitnessBrowser__Dino:3608455 331 LRYMRTTGRDEARIALVEAYAKENGLWRGDDYAPVYTDTLSLDMGTIVPAISGPKRPQDYVALDKAAETFRDYVTGQ 407
                                       *****************************999**************************************9986544 PP

                         TIGR01341 384 agekglalr.....................keakekklegkeaelkdgavviaaitsctntsnpsvllgagllakka 439
                                         + +   +                      + k+  + g +++++dg +via+itsctntsnp+v++gagl+a+ka
  lcl|FitnessBrowser__Dino:3608455 408 RPDWSADEEdkaewtdeggavaprdipgdrGKHKRARVRGADYTIHDGTIVIASITSCTNTSNPYVMIGAGLVARKA 484
                                       333222222233345667777799999986455666779************************************** PP

                         TIGR01341 440 velGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikendlevsavls 516
                                         lGl +kp+vktslapGs+vv+ yl  +gl++ l+++GfnlvGyGcttciGnsGp++ee++eai+++d+ +++vls
  lcl|FitnessBrowser__Dino:3608455 485 RALGLTRKPWVKTSLAPGSQVVSAYLEAAGLQEDLDAIGFNLVGYGCTTCIGNSGPIQEELSEAINDGDIIATSVLS 561
                                       ***************************************************************************** PP

                         TIGR01341 517 GnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiaelvkkavkkelfk 593
                                       Gnrnfegri p+v+anylaspplvvayalaG +++dl+++p+g+d+dG++vylkdiwps+keiaelv+++v++e f+
  lcl|FitnessBrowser__Dino:3608455 562 GNRNFEGRISPDVRANYLASPPLVVAYALAGDMNVDLTRDPLGQDRDGNDVYLKDIWPSTKEIAELVEQTVTREAFQ 638
                                       ***************************************************************************** PP

                         TIGR01341 594 keyeevtegnerwnelevtssdlyewdekstyireppffeelklepeevedikgarillllGdsittdhispaGsik 670
                                       ++y+ v++g+e+w+++e+t+s +y+w + sty+++pp+f+++++ep  +++i+ga+il+ lGd ittdhispaGs k
  lcl|FitnessBrowser__Dino:3608455 639 AKYADVFKGDEKWQSVETTDSLTYDWPPSSTYVQNPPYFQGMSAEPGTISNIEGAKILAILGDMITTDHISPAGSFK 715
                                       ***************************************************************************** PP

                         TIGR01341 671 kdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvylpdsevvsvydaamkykkeg 747
                                       + +pa++yl+e+ v++r+fnsyGsrrGnhevm+rGtfaniri+n++++g eGg+t+  pd++++s+++aam y+++g
  lcl|FitnessBrowser__Dino:3608455 716 ESTPAGRYLTERQVQPREFNSYGSRRGNHEVMMRGTFANIRIRNEMLDGVEGGYTL-GPDGQQTSIFEAAMAYQEMG 791
                                       ******************************************************97.6******************* PP

                         TIGR01341 748 vplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltgeetidvddi 824
                                       +plv+  G++yG+Gssrdwaakgt+llGvkaviaesferihrsnlvgmGv+p+ef  g++++tlgl+g+et+ + ++
  lcl|FitnessBrowser__Dino:3608455 792 TPLVIFGGEQYGAGSSRDWAAKGTSLLGVKAVIAESFERIHRSNLVGMGVIPFEFTGGDTRKTLGLKGDETVSITGL 868
                                       ****************************************************************************8 PP

                         TIGR01341 825 e.elkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkl 875
                                       + ++ p +e++ +++  dg  + ++ ++ridteve++y+++gG+l+yvlr+l
  lcl|FitnessBrowser__Dino:3608455 869 DgKIVPLSEMPCTITYGDGTTREITLKCRIDTEVEIEYIENGGVLHYVLRNL 920
                                       548***********************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (928 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: 8.50
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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