Alignments for a candidate for acn in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Caulobacter crescentus NA1000

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 CCNA_03781 CCNA_03781 aconitate hydratase

Query= SwissProt::P70920
         (906 letters)



>FitnessBrowser__Caulo:CCNA_03781
          Length = 895

 Score = 1209 bits (3128), Expect = 0.0
 Identities = 614/907 (67%), Positives = 718/907 (79%), Gaps = 17/907 (1%)

Query: 1   MTSLDSFKCKKTLKVGAKTYVYYSLPTAEKNGLKGISKLPYSMKVLLENLLRNEDGRSVK 60
           M S+DS K ++ LKVG ++YVYYSL  AE+ GL  +S LP SMKVLLENLLRNEDG SV 
Sbjct: 1   MASVDSLKARRELKVGKQSYVYYSLRAAEEAGLADVSSLPVSMKVLLENLLRNEDGVSVN 60

Query: 61  KADIVAVSKWLRKK-SLEHEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQKLGGDAEKIN 119
           + D+ AV+ WL  K S+EHEI+FRPARVLMQDFTGVPAVVDLAAMR+AM  LG D  KIN
Sbjct: 61  EDDLKAVAAWLNNKGSVEHEISFRPARVLMQDFTGVPAVVDLAAMRDAMVALGADPAKIN 120

Query: 120 PLVPVDLVIDHSVIVNFFGDNKAFAKNVTEEYKQNQERYEFLKWGQAAFSNFSVVPPGTG 179
           PL PVDLVIDHSV+V+ FG+ KA+  NV  EY++N ERY FL+WG +AF+NF VVPPGTG
Sbjct: 121 PLNPVDLVIDHSVMVDNFGNPKAYDDNVKREYERNIERYRFLRWGSSAFNNFRVVPPGTG 180

Query: 180 ICHQVNLEYLSQTVWTKKEKMTVGKKTGTFEVAYPDSLVGTDSHTTMVNGLAVLGWGVGG 239
           ICHQVNLEYL+QTVWT              EVAYPD++VGTDSHTTMVNGLAVLGWGVGG
Sbjct: 181 ICHQVNLEYLAQTVWTNT--------VDGAEVAYPDTVVGTDSHTTMVNGLAVLGWGVGG 232

Query: 240 IEAEACMLGQPLSMLLPNVVGFKLKGAMKEGVTATDLVLTVTQMLRKLGVVGKFVEFFGP 299
           IEAEA MLGQP+ ML+P V+GFKL GAM EG TATDLVLTVTQMLRK GVVGKFVEF+G 
Sbjct: 233 IEAEAAMLGQPIPMLIPEVIGFKLTGAMPEGATATDLVLTVTQMLRKKGVVGKFVEFYGD 292

Query: 300 GLDHLSVADKATIANMAPEYGATCGFFPVDAAAIDYLKTSGRAAPRVALVQAYAKAQGLF 359
            L +L++ D+ATIANMAPEYGATCGFFP+ AA I YLK +GRAA RVALV+AYAK QGL+
Sbjct: 293 ALANLTLEDQATIANMAPEYGATCGFFPISAATIAYLKGTGRAAERVALVEAYAKEQGLW 352

Query: 360 RTAKSADPVFTETLTLDLADVVPSMAGPKRPEGRIALPSVAEGFSVALANEYKKTEEPAK 419
                A+P FT+TL LDL+ V+PS+AGPKRP+ R+ L   A  F+ +LA E+ K E P  
Sbjct: 353 WEPGVAEPTFTDTLELDLSTVLPSLAGPKRPQDRVLLSDAAAKFAESLAGEFGKAENPEL 412

Query: 420 RFAVEGKKYEIGHGDVVIAAITSCTNTSNPSVLIGAGLLARNAAAKGLKAKPWVKTSLAP 479
           R  VEG+ +++GHGDVVIAAITSCTNTSNPSVLI AGLLA+NA AKGLKAKPWVKTSLAP
Sbjct: 413 RAPVEGEDFDVGHGDVVIAAITSCTNTSNPSVLIAAGLLAKNAVAKGLKAKPWVKTSLAP 472

Query: 480 GSQVVAAYLADSGLQAHLDKVGFNLVGFGCTTCIGNSGPLPEEISKSINDNGIVAAAVLS 539
           GSQVV  YLA +GL  HLD +GFNLVG+GCTTCIGNSGPLPE ISK+INDN +VA +VLS
Sbjct: 473 GSQVVTDYLAKAGLTKHLDALGFNLVGYGCTTCIGNSGPLPEAISKTINDNDLVACSVLS 532

Query: 540 GNRNFEGRVSPDVQANYLASPPLVVAHALAGSVTKNLAVEPLGEGKDGKPVYLKDIWPTS 599
           GNRNFEGRV+PDV+ANYLASPPLVVA+ALAGS+  +LA +P+G+ K G  V+LKDIWP++
Sbjct: 533 GNRNFEGRVNPDVRANYLASPPLVVAYALAGSLKIDLATQPIGQDKKGNDVFLKDIWPSN 592

Query: 600 KEINAFMKKFVTASIFKKKYADVFKGDTNWRKIKTVESETYRWNMSSTYVQNPPYFEGMK 659
           ++I A  +K +   +F  +Y DVFKGD NW+ IK    +TY W   STYVQNPPYF  M 
Sbjct: 593 EDIAALQRKAINEKMFATRYGDVFKGDKNWQGIKVTGGQTYAWEADSTYVQNPPYFPNMS 652

Query: 660 KEPEPVTDIVEARILAMFGDKITTDHISPAGSIKLTSPAGKYLSEHQVRPADFNQYGTRR 719
             P PVTDIVEARILA+FGD ITTDHISPAGSIK +SPAGK+L ++ V P DFN YG RR
Sbjct: 653 MTPAPVTDIVEARILAVFGDSITTDHISPAGSIKASSPAGKFLIDNGVEPVDFNGYGARR 712

Query: 720 GNHEVMMRGTFANIRIKNFMLKGADGNIPEGGLTKHWPDGEQMSIYDAAMKYQQEQVPLV 779
           GNH+VMMRGTFANIRI+N +         EGG+TKH+P GE MSIYDAAMKYQ+E  P V
Sbjct: 713 GNHQVMMRGTFANIRIRNRITPDI-----EGGVTKHFPTGEVMSIYDAAMKYQEEGRPAV 767

Query: 780 VFAGAEYGNGSSRDWAAKGTRLLGVRAVICQSFERIHRSNLVGMGVLPLTFEEGTSWSSL 839
           VF G EYG GSSRDWAAKGT+LLGVRAVIC+SFERIHRSNLVGMGVLPL F +   W  L
Sbjct: 768 VFGGKEYGTGSSRDWAAKGTKLLGVRAVICESFERIHRSNLVGMGVLPLQFVQ-DGWQKL 826

Query: 840 GLKGDEKVTLRGLVGDLKPRQKLTAEIV-SGDGSLQRVSLLCRIDTLDELDYYRNGGILH 898
            L G+E V++RGL  DL PR++L  E+    DG + R  + CRIDT  EL+Y++NGG+L+
Sbjct: 827 ELTGEEIVSIRGLT-DLAPRKQLIVELYRPTDGRIARFPVRCRIDTPTELEYFKNGGVLN 885

Query: 899 YVLRKLA 905
           YVLR LA
Sbjct: 886 YVLRNLA 892


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: 2183
Number of extensions: 84
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 CCNA_03781 CCNA_03781 (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.17008.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 1368.9   0.0          0 1368.6   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_03781  CCNA_03781 aconitate hydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_03781  CCNA_03781 aconitate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1368.6   0.0         0         0       2     875 ..      19     891 ..      18     892 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1368.6 bits;  conditional E-value: 0
                             TIGR01341   2 kvyyyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkee.lkdeeiafkparvvlq 72 
                                           ++ yysl+a+ee+ l ++s+lp s+++lle++lrn dg +++e+d++a++ w +++   ++ei+f+parv++q
  lcl|FitnessBrowser__Caulo:CCNA_03781  19 SYVYYSLRAAEEAgLADVSSLPVSMKVLLENLLRNEDGVSVNEDDLKAVAAWLNNKgSVEHEISFRPARVLMQ 91 
                                           578********99789************************************877626799************ PP

                             TIGR01341  73 dftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkw 145
                                           dftGvpavvdlaa+r+a+ +lg dp+kinpl pvdlvidhsv vd++g+ +a + nv++e+ern ery+fl+w
  lcl|FitnessBrowser__Caulo:CCNA_03781  92 DFTGVPAVVDLAAMRDAMVALGADPAKINPLNPVDLVIDHSVMVDNFGNPKAYDDNVKREYERNIERYRFLRW 164
                                           ************************************************************************* PP

                             TIGR01341 146 akkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaea 218
                                           ++ af+n++vvppgtGi+hqvnleyla+ v++++ dg ++aypd++vGtdshttm+nGl vlGwGvGGieaea
  lcl|FitnessBrowser__Caulo:CCNA_03781 165 GSSAFNNFRVVPPGTGICHQVNLEYLAQTVWTNTVDGAEVAYPDTVVGTDSHTTMVNGLAVLGWGVGGIEAEA 237
                                           ************************************************************************* PP

                             TIGR01341 219 allGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmap 291
                                           a+lGqp+ + +peviG+kltG + eG tatdlvltvt++lrkkgvvgkfvef+G++l++l+l d+atianmap
  lcl|FitnessBrowser__Caulo:CCNA_03781 238 AMLGQPIPMLIPEVIGFKLTGAMPEGATATDLVLTVTQMLRKKGVVGKFVEFYGDALANLTLEDQATIANMAP 310
                                           ************************************************************************* PP

                             TIGR01341 292 eyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd.dseepkytdvveldlsdveasvaGpkrp 363
                                           eyGat++ffpi + t+ yl+ tgr  ++v lve+y+k q+l+ +   +ep++td++eldls+v +s+aGpkrp
  lcl|FitnessBrowser__Caulo:CCNA_03781 311 EYGATCGFFPISAATIAYLKGTGRAAERVALVEAYAKEQGLWWEpGVAEPTFTDTLELDLSTVLPSLAGPKRP 383
                                           *******************************************98899************************* PP

                             TIGR01341 364 qdrvalkevkaafksslesnagekglalrkeakekklegkeaelkdgavviaaitsctntsnpsvllgaglla 436
                                           qdrv l++  a+f++sl  + g+ +    +   +  +eg++  + +g+vviaaitsctntsnpsvl++aglla
  lcl|FitnessBrowser__Caulo:CCNA_03781 384 QDRVLLSDAAAKFAESLAGEFGKAE----NPELRAPVEGEDFDVGHGDVVIAAITSCTNTSNPSVLIAAGLLA 452
                                           *****************99999877....445566679*********************************** PP

                             TIGR01341 437 kkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikendl 509
                                           k av  Glk kp+vktslapGs+vvtdyla++gl+++l++lGfnlvGyGcttciGnsGpl+e+++++i++ndl
  lcl|FitnessBrowser__Caulo:CCNA_03781 453 KNAVAKGLKAKPWVKTSLAPGSQVVTDYLAKAGLTKHLDALGFNLVGYGCTTCIGNSGPLPEAISKTINDNDL 525
                                           ************************************************************************* PP

                             TIGR01341 510 evsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiael 582
                                           ++ +vlsGnrnfegr++p+v+anylaspplvvayalaG+++idl+++pig+dk+G++v+lkdiwps+++ia+l
  lcl|FitnessBrowser__Caulo:CCNA_03781 526 VACSVLSGNRNFEGRVNPDVRANYLASPPLVVAYALAGSLKIDLATQPIGQDKKGNDVFLKDIWPSNEDIAAL 598
                                           ************************************************************************* PP

                             TIGR01341 583 vkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeevedikgarillllG 655
                                            +ka+++++f  +y  v++g+++w+ ++vt +++y+w+ +sty+++pp+f +++++p+ v+di +aril+++G
  lcl|FitnessBrowser__Caulo:CCNA_03781 599 QRKAINEKMFATRYGDVFKGDKNWQGIKVTGGQTYAWEADSTYVQNPPYFPNMSMTPAPVTDIVEARILAVFG 671
                                           ************************************************************************* PP

                             TIGR01341 656 dsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvyl 728
                                           dsittdhispaGsik  spa+k+l+++Gve+ dfn yG+rrGnh+vm+rGtfaniri+n++ +  eGg+t+++
  lcl|FitnessBrowser__Caulo:CCNA_03781 672 DSITTDHISPAGSIKASSPAGKFLIDNGVEPVDFNGYGARRGNHQVMMRGTFANIRIRNRITPDIEGGVTKHF 744
                                           ************************************************************************* PP

                             TIGR01341 729 pdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlple 801
                                           p++ev+s+ydaamky++eg+p vv  GkeyG+GssrdwaakgtkllGv+avi+esferihrsnlvgmGvlpl+
  lcl|FitnessBrowser__Caulo:CCNA_03781 745 PTGEVMSIYDAAMKYQEEGRPAVVFGGKEYGTGSSRDWAAKGTKLLGVRAVICESFERIHRSNLVGMGVLPLQ 817
                                           ************************************************************************* PP

                             TIGR01341 802 fkqgedaetlgltgeetidvddieelkpkkevtvelvk.edgeketveavlridtevelayvkkgGilqyvlr 873
                                           f q    + l+ltgee + + ++++l p+k++ vel + +dg    + +++ridt++el+y+k+gG+l+yvlr
  lcl|FitnessBrowser__Caulo:CCNA_03781 818 FVQDGW-QKLELTGEEIVSIRGLTDLAPRKQLIVELYRpTDGRIARFPVRCRIDTPTELEYFKNGGVLNYVLR 889
                                           *88665.68*************************987637999****************************** PP

                             TIGR01341 874 kl 875
                                           +l
  lcl|FitnessBrowser__Caulo:CCNA_03781 890 NL 891
                                           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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 11.35
//
[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