Alignments for a candidate for acn in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Phaeobacter inhibens BS107

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 GFF1856 PGA1_c18830 aconitate hydratase AcnA

Query= SwissProt::P70920
         (906 letters)



>FitnessBrowser__Phaeo:GFF1856
          Length = 895

 Score = 1095 bits (2831), Expect = 0.0
 Identities = 549/903 (60%), Positives = 690/903 (76%), Gaps = 19/903 (2%)

Query: 5   DSFKCKKTLKVGAKTYVYYSLPTAEKNGLKGISKLPYSMKVLLENLLRNEDGR-SVKKAD 63
           D+ K ++ L  G K+  YYS+P A + GL   +KLP ++KV+LEN+LR EDG  SV   D
Sbjct: 8   DNAKTRRKLSAGGKSISYYSIPAATEAGLGDFAKLPAALKVVLENMLRFEDGGFSVSTDD 67

Query: 64  IVAVSKWLRKKSLE-HEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQKLGGDAEKINPLV 122
           I A ++W         EIA+RPARVLMQDFTGVPAVVDLAAMR+ ++ LGGDA+KINPL 
Sbjct: 68  IKAFAEWGANGGKNPREIAYRPARVLMQDFTGVPAVVDLAAMRDGIKALGGDAQKINPLN 127

Query: 123 PVDLVIDHSVIVNFFGDNKAFAKNVTEEYKQNQERYEFLKWGQAAFSNFSVVPPGTGICH 182
           PVDLVIDHSV+++ FG+ +AF  NV  EY++N ERY+FLKWGQ AF+NF VVPPGTGICH
Sbjct: 128 PVDLVIDHSVMIDEFGNPRAFQMNVDREYERNMERYQFLKWGQGAFNNFRVVPPGTGICH 187

Query: 183 QVNLEYLSQTVWTKKEKMTVGKKTGTFEVAYPDSLVGTDSHTTMVNGLAVLGWGVGGIEA 242
           QVNLEYL+QT+W+ +++       G   VAYPD+LVGTDSHTTMVNG AVLGWGVGGIEA
Sbjct: 188 QVNLEYLAQTIWSDEDQ------NGDM-VAYPDTLVGTDSHTTMVNGAAVLGWGVGGIEA 240

Query: 243 EACMLGQPLSMLLPNVVGFKLKGAMKEGVTATDLVLTVTQMLRKLGVVGKFVEFFGPGLD 302
           EA MLGQP+SML+P V+GF+L GAM EG T TDLVL V +MLR  GVVGKFVEF+G GLD
Sbjct: 241 EAAMLGQPISMLIPEVIGFELTGAMVEGTTGTDLVLKVVEMLRAKGVVGKFVEFYGKGLD 300

Query: 303 HLSVADKATIANMAPEYGATCGFFPVDAAAIDYLKTSGRAAPRVALVQAYAKAQGLFRTA 362
            L +AD+ATIANMAPEYGATCGFFP+D   I YL+ +GR   R+ALV+AYAK  G +R A
Sbjct: 301 TLPLADRATIANMAPEYGATCGFFPIDDETIRYLRNTGRDEDRIALVEAYAKENGFWRDA 360

Query: 363 KSADPVFTETLTLDLADVVPSMAGPKRPEGRIALPSVAEGFSVALANEYKKTEEPAKRFA 422
             A P++T+TL+LD+  +VP+++GPKRP+  +AL      F   +   +K+     K  A
Sbjct: 361 DYA-PIYTDTLSLDMGTIVPAISGPKRPQDYVALTGAKAAFQKEMEETFKRPM--GKEIA 417

Query: 423 VEGKKYEIGHGDVVIAAITSCTNTSNPSVLIGAGLLARNAAAKGLKAKPWVKTSLAPGSQ 482
           V+G+ Y +  G VVIA+ITSCTNTSNP V+IGAGL+AR AAA GL  KPWVKTSLAPGSQ
Sbjct: 418 VKGEDYTMESGKVVIASITSCTNTSNPYVMIGAGLVARKAAALGLDRKPWVKTSLAPGSQ 477

Query: 483 VVAAYLADSGLQAHLDKVGFNLVGFGCTTCIGNSGPLPEEISKSINDNGIVAAAVLSGNR 542
           VV+AYL  + LQ  LDK+GFNLVG+GCTTCIGNSGP+ +E+S +I +  +VA +VLSGNR
Sbjct: 478 VVSAYLEAANLQEDLDKIGFNLVGYGCTTCIGNSGPIQQELSDAIAEGDLVATSVLSGNR 537

Query: 543 NFEGRVSPDVQANYLASPPLVVAHALAGSVTKNLAVEPLGEGKDGKPVYLKDIWPTSKEI 602
           NFEGR+SPDV+ANYLASPPLVVA+ALAG++  +LA +P+ + KDG  VYLKDIWP+ KEI
Sbjct: 538 NFEGRISPDVRANYLASPPLVVAYALAGTMDIDLATDPIAQDKDGNDVYLKDIWPSQKEI 597

Query: 603 NAFMKKFVTASIFKKKYADVFKGDTNWRKIKTVESETYRWNMSSTYVQNPPYFEGMKKEP 662
              ++  VT   F  KYADVFKGD  W+ ++T ++ETY W  +STY+QNPPYF+GM  EP
Sbjct: 598 ADLVEATVTREAFLSKYADVFKGDEKWQAVETTDAETYDWPAASTYIQNPPYFQGMGTEP 657

Query: 663 EPVTDIVEARILAMFGDKITTDHISPAGSIKLTSPAGKYLSEHQVRPADFNQYGTRRGNH 722
             +++I +A+ L + GD +TTDHISPAGS   T+PAG+YL + QV+P +FN YG+RRGNH
Sbjct: 658 GTISNIKDAKPLLILGDMVTTDHISPAGSFATTTPAGQYLLDRQVQPREFNSYGSRRGNH 717

Query: 723 EVMMRGTFANIRIKNFMLKGADGNIPEGGLTKHWPDGEQMSIYDAAMKYQQEQVPLVVFA 782
           E+MMRGTFANIRIKN ML G      EGG TK  PDGEQ S+Y+A+M YQ++ +PLVVF 
Sbjct: 718 EIMMRGTFANIRIKNEMLDGV-----EGGYTK-GPDGEQTSVYEASMAYQEQGIPLVVFG 771

Query: 783 GAEYGNGSSRDWAAKGTRLLGVRAVICQSFERIHRSNLVGMGVLPLTFEEGTSWSSLGLK 842
           G +YG GSSRDWAAKGT LLGV+AVI +SFERIHRSNLVGMGV+P  F  G +  SL L 
Sbjct: 772 GEQYGAGSSRDWAAKGTALLGVKAVIAESFERIHRSNLVGMGVIPFEFTGGDTRKSLNLT 831

Query: 843 GDEKVTLRGLVGDLKPRQKLTAEIVSGDGSLQRVSLLCRIDTLDELDYYRNGGILHYVLR 902
           GDE V++ GL   +KP+++++ +I  GDG+ + ++L CRIDT  E++Y  +GG+LHYVLR
Sbjct: 832 GDETVSIHGL-DTIKPQEEVSCDITYGDGTTKTITLKCRIDTAPEIEYIEHGGVLHYVLR 890

Query: 903 KLA 905
            LA
Sbjct: 891 NLA 893


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: 2161
Number of extensions: 112
Number of successful extensions: 8
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: 895
Length adjustment: 43
Effective length of query: 863
Effective length of database: 852
Effective search space:   735276
Effective search space used:   735276
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 GFF1856 PGA1_c18830 (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.12900.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 1341.9   0.0          0 1341.7   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF1856  PGA1_c18830 aconitate hydratase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1856  PGA1_c18830 aconitate hydratase AcnA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1341.7   0.0         0         0       2     875 ..      22     892 ..      21     893 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1341.7 bits;  conditional E-value: 0
                          TIGR01341   2 kvyyyslkalees.lekisklpkslrillesvlrnldg.skikeedveallkwkkeelkd.eeiafkparvvlqdf 74 
                                        ++ yys++a++e+ l++  klp +l+++le++lr  dg ++++ +d++a+++w ++  k+ +eia++parv++qdf
  lcl|FitnessBrowser__Phaeo:GFF1856  22 SISYYSIPAATEAgLGDFAKLPAALKVVLENMLRFEDGgFSVSTDDIKAFAEWGANGGKNpREIAYRPARVLMQDF 97 
                                        689******9998789*******************99549*************998765439************** PP

                          TIGR01341  75 tGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwakkaf 150
                                        tGvpavvdlaa+r+ +k+lg+d++kinpl pvdlvidhsv +d++g+ +a+++nv++e+ern+ery+flkw++ af
  lcl|FitnessBrowser__Phaeo:GFF1856  98 TGVPAVVDLAAMRDGIKALGGDAQKINPLNPVDLVIDHSVMIDEFGNPRAFQMNVDREYERNMERYQFLKWGQGAF 173
                                        **************************************************************************** PP

                          TIGR01341 151 knlkvvppgtGivhqvnleylakvvfeae.kdgellaypdslvGtdshttminGlGvlGwGvGGieaeaallGqpv 225
                                        +n++vvppgtGi+hqvnleyla+ +++ e ++g+++aypd+lvGtdshttm+nG  vlGwGvGGieaeaa+lGqp+
  lcl|FitnessBrowser__Phaeo:GFF1856 174 NNFRVVPPGTGICHQVNLEYLAQTIWSDEdQNGDMVAYPDTLVGTDSHTTMVNGAAVLGWGVGGIEAEAAMLGQPI 249
                                        *************************9865289******************************************** PP

                          TIGR01341 226 slsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmapeyGataaffp 301
                                        s+ +peviG+ ltG + eG+t tdlvl+v e+lr kgvvgkfvef+G+gl++l+ladratianmapeyGat++ffp
  lcl|FitnessBrowser__Phaeo:GFF1856 250 SMLIPEVIGFELTGAMVEGTTGTDLVLKVVEMLRAKGVVGKFVEFYGKGLDTLPLADRATIANMAPEYGATCGFFP 325
                                        **************************************************************************** PP

                          TIGR01341 302 iddvtlqylrltgrdedkvelvekylkaqelfvddseepkytdvveldlsdveasvaGpkrpqdrvalkevkaafk 377
                                        idd+t+ ylr tgrded++ lve+y+k +++++d    p+ytd++ ld+ ++ ++++Gpkrpqd val+  kaaf+
  lcl|FitnessBrowser__Phaeo:GFF1856 326 IDDETIRYLRNTGRDEDRIALVEAYAKENGFWRDADYAPIYTDTLSLDMGTIVPAISGPKRPQDYVALTGAKAAFQ 401
                                        **********************************9999************************************** PP

                          TIGR01341 378 sslesnagekglalrkeakekklegkeaelkdgavviaaitsctntsnpsvllgagllakkavelGlkvkpyvkts 453
                                        + +e++   k        ke +++g+++++++g+vvia+itsctntsnp+v++gagl+a+ka  lGl +kp+vkts
  lcl|FitnessBrowser__Phaeo:GFF1856 402 KEMEETF--KR----PMGKEIAVKGEDYTMESGKVVIASITSCTNTSNPYVMIGAGLVARKAAALGLDRKPWVKTS 471
                                        9988654..33....456778889**************************************************** PP

                          TIGR01341 454 lapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikendlevsavlsGnrnfegrihplv 529
                                        lapGs+vv+ yl  ++l++ l+++GfnlvGyGcttciGnsGp+++e+++ai+e+dl++++vlsGnrnfegri p+v
  lcl|FitnessBrowser__Phaeo:GFF1856 472 LAPGSQVVSAYLEAANLQEDLDKIGFNLVGYGCTTCIGNSGPIQQELSDAIAEGDLVATSVLSGNRNFEGRISPDV 547
                                        **************************************************************************** PP

                          TIGR01341 530 kanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeevtegner 605
                                        +anylaspplvvayalaGt+didl+++pi++dkdG++vylkdiwps+keia+lv+ +v++e f  +y+ v++g+e+
  lcl|FitnessBrowser__Phaeo:GFF1856 548 RANYLASPPLVVAYALAGTMDIDLATDPIAQDKDGNDVYLKDIWPSQKEIADLVEATVTREAFLSKYADVFKGDEK 623
                                        **************************************************************************** PP

                          TIGR01341 606 wnelevtssdlyewdekstyireppffeelklepeevedikgarillllGdsittdhispaGsikkdspaakylke 681
                                        w+ +e+t+ ++y+w   styi++pp+f+++ +ep  +++ik+a+ ll lGd +ttdhispaGs +  +pa++yl +
  lcl|FitnessBrowser__Phaeo:GFF1856 624 WQAVETTDAETYDWPAASTYIQNPPYFQGMGTEPGTISNIKDAKPLLILGDMVTTDHISPAGSFATTTPAGQYLLD 699
                                        **************************************************************************** PP

                          TIGR01341 682 kGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvylpdsevvsvydaamkykkegvplvvlaGke 757
                                        + v++r+fnsyGsrrGnhe+m+rGtfanirikn++++g eGg+t+  pd+e++svy+a+m y+++g+plvv  G++
  lcl|FitnessBrowser__Phaeo:GFF1856 700 RQVQPREFNSYGSRRGNHEIMMRGTFANIRIKNEMLDGVEGGYTK-GPDGEQTSVYEASMAYQEQGIPLVVFGGEQ 774
                                        *******************************************97.6***************************** PP

                          TIGR01341 758 yGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltgeetidvddieelkpkkev 833
                                        yG+Gssrdwaakgt llGvkaviaesferihrsnlvgmGv+p+ef  g+++++l+ltg+et+ +++++++kp++ev
  lcl|FitnessBrowser__Phaeo:GFF1856 775 YGAGSSRDWAAKGTALLGVKAVIAESFERIHRSNLVGMGVIPFEFTGGDTRKSLNLTGDETVSIHGLDTIKPQEEV 850
                                        **************************************************************************** PP

                          TIGR01341 834 tvelvkedgeketveavlridtevelayvkkgGilqyvlrkl 875
                                        +  ++  dg  +t++ ++ridt+ e++y+++gG+l+yvlr+l
  lcl|FitnessBrowser__Phaeo:GFF1856 851 SCDITYGDGTTKTITLKCRIDTAPEIEYIEHGGVLHYVLRNL 892
                                        ****************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (895 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: 0.06u 0.03s 00:00:00.09 Elapsed: 00:00:00.09
# Mc/sec: 8.51
//
[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
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