Alignments for a candidate for acn in Ochrobactrum thiophenivorans DSM 7216

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Ochrobactrum thiophenivorans DSM 7216

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 WP_094506127.1 CEV31_RS06075 aconitate hydratase AcnA

Query= SwissProt::P70920
         (906 letters)



>NCBI__GCF_002252445.1:WP_094506127.1
          Length = 895

 Score = 1299 bits (3362), Expect = 0.0
 Identities = 650/907 (71%), Positives = 750/907 (82%), Gaps = 13/907 (1%)

Query: 1   MTSLDSFKCKKTLKVGAKTYVYYSLPTAEKNGLKGISKLPYSMKVLLENLLRNEDGRSVK 60
           M+ +DSFKC+KTL VG K YVYYSL  AEKNGL G+SKLP+SMKVLLENLLR ED R+VK
Sbjct: 1   MSHIDSFKCRKTLTVGGKEYVYYSLTEAEKNGLTGVSKLPFSMKVLLENLLRFEDDRTVK 60

Query: 61  KADIVAVSKWLRKK-SLEHEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQKLGGDAEKIN 119
           K+DI A++ WL  + S   EIA+RPARVLMQDFTGVPAVVDLAAMR+ ++ LGGD EKIN
Sbjct: 61  KSDIEAIAAWLNDRGSAGAEIAYRPARVLMQDFTGVPAVVDLAAMRDGLKALGGDPEKIN 120

Query: 120 PLVPVDLVIDHSVIVNFFGDNKAFAKNVTEEYKQNQERYEFLKWGQAAFSNFSVVPPGTG 179
           PLVPVDLVIDHSVIV+ FG+  AF  NV  EY++N ERY FLKWGQ AF NF VVPPGTG
Sbjct: 121 PLVPVDLVIDHSVIVDEFGNPSAFKANVDLEYQRNGERYRFLKWGQQAFKNFRVVPPGTG 180

Query: 180 ICHQVNLEYLSQTVWTKKEKMTVGKKTGTFEVAYPDSLVGTDSHTTMVNGLAVLGWGVGG 239
           ICHQVNLEYL+Q VWTK+E            VAYPD+ VGTDSHTTMVNGL VLGWGVGG
Sbjct: 181 ICHQVNLEYLAQAVWTKEEDGET--------VAYPDTCVGTDSHTTMVNGLGVLGWGVGG 232

Query: 240 IEAEACMLGQPLSMLLPNVVGFKLKGAMKEGVTATDLVLTVTQMLRKLGVVGKFVEFFGP 299
           IEAEA MLGQP+SMLLP V+GF+L G +KEGVTATDLVLTVTQMLRK GVVGKFVEFFG 
Sbjct: 233 IEAEAAMLGQPVSMLLPEVIGFRLTGKVKEGVTATDLVLTVTQMLRKKGVVGKFVEFFGE 292

Query: 300 GLDHLSVADKATIANMAPEYGATCGFFPVDAAAIDYLKTSGRAAPRVALVQAYAKAQGLF 359
           GLD++++AD+ATIANM PEYGATCGFFP+D   ++Y+ T+GRA  R+ALV+AY++AQG++
Sbjct: 293 GLDNMTLADRATIANMGPEYGATCGFFPIDNETLNYMNTTGRAEDRMALVEAYSRAQGMW 352

Query: 360 RTAKSADPVFTETLTLDLADVVPSMAGPKRPEGRIALPSVAEGFSVALANEYKKTEEPAK 419
           R A S DPVFT+ L LD+++VVPSMAGPKRPEGRIAL ++  GF+ +L  EYKKT   A 
Sbjct: 353 REAGSEDPVFTDILELDMSEVVPSMAGPKRPEGRIALENIGSGFATSLETEYKKTTGQAA 412

Query: 420 RFAVEGKKYEIGHGDVVIAAITSCTNTSNPSVLIGAGLLARNAAAKGLKAKPWVKTSLAP 479
           R+AVEG+ +++GHGDV IAAITSCTNTSNPSVLI AGLLARNA AKGLK KPWVKTSLAP
Sbjct: 413 RYAVEGEDFDLGHGDVAIAAITSCTNTSNPSVLIAAGLLARNAVAKGLKTKPWVKTSLAP 472

Query: 480 GSQVVAAYLADSGLQAHLDKVGFNLVGFGCTTCIGNSGPLPEEISKSINDNGIVAAAVLS 539
           GSQVVAAYL  +GLQ  LD +GFNLVGFGCTTCIGNSGPLP  ISK+IN+ G++AAAVLS
Sbjct: 473 GSQVVAAYLESAGLQKDLDALGFNLVGFGCTTCIGNSGPLPAPISKTINEKGLIAAAVLS 532

Query: 540 GNRNFEGRVSPDVQANYLASPPLVVAHALAGSVTKNLAVEPLGEGKDGKPVYLKDIWPTS 599
           GNRNFEGRVSPDVQANYLASPPLVVAHALAG+VTK+L  EPLGE ++G PV+L+DIWP+S
Sbjct: 533 GNRNFEGRVSPDVQANYLASPPLVVAHALAGTVTKDLTKEPLGEDQNGNPVFLRDIWPSS 592

Query: 600 KEINAFMKKFVTASIFKKKYADVFKGDTNWRKIKTVESETYRWNMSSTYVQNPPYFEGMK 659
            EI  F+ K VT  IF +KYADVFKGD NW+ ++    +TY W+ +STYVQNPPYF GM 
Sbjct: 593 AEIQEFIAKNVTRKIFSEKYADVFKGDENWQAVQVPAGQTYAWDDNSTYVQNPPYFVGMG 652

Query: 660 KEPEPVTDIVEARILAMFGDKITTDHISPAGSIKLTSPAGKYLSEHQVRPADFNQYGTRR 719
           K    + D+  AR+L +FGDKITTDHISPAGSIK  SPAGKYL +H V  ADFNQYGTRR
Sbjct: 653 KSAGTIADVKGARVLGLFGDKITTDHISPAGSIKAQSPAGKYLIDHGVGIADFNQYGTRR 712

Query: 720 GNHEVMMRGTFANIRIKNFMLKGADGNIPEGGLTKHWPDGEQMSIYDAAMKYQQEQVPLV 779
           GNHEVMMRGTFANIRI+N ML G +G   EGG T H+P  E+ SIYDAAM+Y+ E VPLV
Sbjct: 713 GNHEVMMRGTFANIRIRNHML-GENGR--EGGYTIHYPSKEETSIYDAAMQYKAEGVPLV 769

Query: 780 VFAGAEYGNGSSRDWAAKGTRLLGVRAVICQSFERIHRSNLVGMGVLPLTFEEGTSWSSL 839
           VFAG EYGNGSSRDWAAKGT LLGV+AVI QSFERIHRSNLVGMG++P  FEEGTSW +L
Sbjct: 770 VFAGVEYGNGSSRDWAAKGTNLLGVKAVIAQSFERIHRSNLVGMGIVPFVFEEGTSWQTL 829

Query: 840 GLKGDEKVTLRGLVGDLKPRQKLTAEIVSGDGSLQRVSLLCRIDTLDELDYYRNGGILHY 899
           GLKGDE V++ GL  D++PRQK+ A I   DGS+++V L+CRIDTLDELDY +NGGIL  
Sbjct: 830 GLKGDEIVSIEGL-ADVRPRQKIEASITFADGSVKKVPLICRIDTLDELDYMKNGGILQT 888

Query: 900 VLRKLAA 906
           VLR LAA
Sbjct: 889 VLRDLAA 895


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: 2239
Number of extensions: 92
Number of successful extensions: 5
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 WP_094506127.1 CEV31_RS06075 (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.3293167.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 1377.2   0.0          0 1377.0   0.0    1.0  1  NCBI__GCF_002252445.1:WP_094506127.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002252445.1:WP_094506127.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1377.0   0.0         0         0       1     875 [.      18     893 ..      18     894 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1377.0 bits;  conditional E-value: 0
                             TIGR01341   1 kkvyyyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkee.lkdeeiafkparvvl 71 
                                           k++ yysl ++e++ l+ +sklp s+++lle++lr  d++++k++d+ea++ w ++   +  eia++parv++
  NCBI__GCF_002252445.1:WP_094506127.1  18 KEYVYYSLTEAEKNgLTGVSKLPFSMKVLLENLLRFEDDRTVKKSDIEAIAAWLNDRgSAGAEIAYRPARVLM 90 
                                           6799*******9986789***********************************88752789************ PP

                             TIGR01341  72 qdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflk 144
                                           qdftGvpavvdlaa+r+ +k+lg+dpekinplvpvdlvidhsv vd++g+ +a++anv+le++rn ery+flk
  NCBI__GCF_002252445.1:WP_094506127.1  91 QDFTGVPAVVDLAAMRDGLKALGGDPEKINPLVPVDLVIDHSVIVDEFGNPSAFKANVDLEYQRNGERYRFLK 163
                                           ************************************************************************* PP

                             TIGR01341 145 wakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieae 217
                                           w+++afkn++vvppgtGi+hqvnleyla++v+++e+dge++aypd+ vGtdshttm+nGlGvlGwGvGGieae
  NCBI__GCF_002252445.1:WP_094506127.1 164 WGQQAFKNFRVVPPGTGICHQVNLEYLAQAVWTKEEDGETVAYPDTCVGTDSHTTMVNGLGVLGWGVGGIEAE 236
                                           ************************************************************************* PP

                             TIGR01341 218 aallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianma 290
                                           aa+lGqpvs+ +peviG++ltGk++eGvtatdlvltvt++lrkkgvvgkfveffGegl++++ladratianm 
  NCBI__GCF_002252445.1:WP_094506127.1 237 AAMLGQPVSMLLPEVIGFRLTGKVKEGVTATDLVLTVTQMLRKKGVVGKFVEFFGEGLDNMTLADRATIANMG 309
                                           ************************************************************************* PP

                             TIGR01341 291 peyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd.dseepkytdvveldlsdveasvaGpkr 362
                                           peyGat++ffpid++tl+y+++tgr ed++ lve+y +aq+++++  se+p++td++eld+s+v +s+aGpkr
  NCBI__GCF_002252445.1:WP_094506127.1 310 PEYGATCGFFPIDNETLNYMNTTGRAEDRMALVEAYSRAQGMWREaGSEDPVFTDILELDMSEVVPSMAGPKR 382
                                           ********************************************988999*********************** PP

                             TIGR01341 363 pqdrvalkevkaafksslesnagekglalrkeakekklegkeaelkdgavviaaitsctntsnpsvllgagll 435
                                           p+ r+al+++ + f++sle++  + +     +a ++++eg++  l +g+v+iaaitsctntsnpsvl++agll
  NCBI__GCF_002252445.1:WP_094506127.1 383 PEGRIALENIGSGFATSLETEYKKTT----GQAARYAVEGEDFDLGHGDVAIAAITSCTNTSNPSVLIAAGLL 451
                                           ******************99876655....78889999*********************************** PP

                             TIGR01341 436 akkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikend 508
                                           a+ av  Glk kp+vktslapGs+vv+ yl  +gl++ l++lGfnlvG+GcttciGnsGpl+  ++++i+e++
  NCBI__GCF_002252445.1:WP_094506127.1 452 ARNAVAKGLKTKPWVKTSLAPGSQVVAAYLESAGLQKDLDALGFNLVGFGCTTCIGNSGPLPAPISKTINEKG 524
                                           ************************************************************************* PP

                             TIGR01341 509 levsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiae 581
                                           l ++avlsGnrnfegr+ p+v+anylaspplvva+alaGtv+ dl+kep+g d++G++v+l+diwps  ei+e
  NCBI__GCF_002252445.1:WP_094506127.1 525 LIAAAVLSGNRNFEGRVSPDVQANYLASPPLVVAHALAGTVTKDLTKEPLGEDQNGNPVFLRDIWPSSAEIQE 597
                                           ************************************************************************* PP

                             TIGR01341 582 lvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeevedikgarillll 654
                                           ++ k+v++++f ++y+ v++g+e+w+ ++v+ +++y+wd++sty+++pp+f ++  +   + d+kgar+l l+
  NCBI__GCF_002252445.1:WP_094506127.1 598 FIAKNVTRKIFSEKYADVFKGDENWQAVQVPAGQTYAWDDNSTYVQNPPYFVGMGKSAGTIADVKGARVLGLF 670
                                           ************************************************************************* PP

                             TIGR01341 655 GdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklv..kgkeGglt 725
                                           Gd+ittdhispaGsik  spa+kyl+++Gv   dfn yG+rrGnhevm+rGtfaniri+n+++  +g+eGg+t
  NCBI__GCF_002252445.1:WP_094506127.1 671 GDKITTDHISPAGSIKAQSPAGKYLIDHGVGIADFNQYGTRRGNHEVMMRGTFANIRIRNHMLgeNGREGGYT 743
                                           **************************************************************85579****** PP

                             TIGR01341 726 vylpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvl 798
                                           +++p +e++s+ydaam+yk egvplvv aG eyG Gssrdwaakgt+llGvkavia+sferihrsnlvgmG++
  NCBI__GCF_002252445.1:WP_094506127.1 744 IHYPSKEETSIYDAAMQYKAEGVPLVVFAGVEYGNGSSRDWAAKGTNLLGVKAVIAQSFERIHRSNLVGMGIV 816
                                           ************************************************************************* PP

                             TIGR01341 799 plefkqgedaetlgltgeetidvddieelkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyv 871
                                           p+ f++g++ +tlgl+g+e + ++++ +++p+++++ +++ +dg+++ v   +ridt  el+y+k+gGilq v
  NCBI__GCF_002252445.1:WP_094506127.1 817 PFVFEEGTSWQTLGLKGDEIVSIEGLADVRPRQKIEASITFADGSVKKVPLICRIDTLDELDYMKNGGILQTV 889
                                           ************************************************************************* PP

                             TIGR01341 872 lrkl 875
                                           lr+l
  NCBI__GCF_002252445.1:WP_094506127.1 890 LRDL 893
                                           *985 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 39.05
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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

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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