Alignments for a candidate for acn in Sphingomonas histidinilytica UM2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Sphingomonas histidinilytica UM2

Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_079648606.1 B5X82_RS13120 aconitate hydratase AcnA

Query= SwissProt::P37032
         (891 letters)



>NCBI__GCF_900167915.1:WP_079648606.1
          Length = 894

 Score = 1199 bits (3102), Expect = 0.0
 Identities = 602/892 (67%), Positives = 701/892 (78%), Gaps = 4/892 (0%)

Query: 3   VGQDSLSTKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTVTT 62
           VGQD+L T+S L VDGK Y YYSL +A  K    I+RLP+S+KVLLENLLRFEDG TVTT
Sbjct: 4   VGQDTLKTRSTLNVDGKHYAYYSLAKAAEK-LGDISRLPFSMKVLLENLLRFEDGTTVTT 62

Query: 63  KDIKAIADWLHNKTSQHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISPL 122
            D++AI DW   +TS+ EI +RP RVLMQDFTGVP VVDLAAMR A+  +GG+A KI+PL
Sbjct: 63  DDVQAIVDWQKERTSEREIQYRPARVLMQDFTGVPCVVDLAAMRDAMNTLGGDAQKINPL 122

Query: 123 SPVDLVIDHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGIC 182
            PV LVIDHSVMVD F +  A + N  +E  RN ERYEFLRWG KA +NF+VVPPGTGIC
Sbjct: 123 VPVHLVIDHSVMVDSFGNPKAFDENVALEYARNGERYEFLRWGSKALNNFKVVPPGTGIC 182

Query: 183 HQVNLEYLGKTVWNS-ENDGQLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLG 241
           HQVNLE L + VW+S +  G   AYPDT VGTDSHTTMINGLGVLGWGVGGIEAEAAMLG
Sbjct: 183 HQVNLENLAQAVWSSADGSGVEVAYPDTCVGTDSHTTMINGLGVLGWGVGGIEAEAAMLG 242

Query: 242 QPVSMLIPEVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLAD 301
           QPVSMLIPEV+GFKLSG L EGITATDLVLTVTQMLR KGVVG+FVEFYGPGL+ L LAD
Sbjct: 243 QPVSMLIPEVVGFKLSGTLNEGITATDLVLTVTQMLRAKGVVGRFVEFYGPGLDALSLAD 302

Query: 302 RATISNMAPEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEEPV 361
           RATI+NMAPEYGATCGFFP+D  T+ Y+ LTGR    +ALVEAYAK QG W D    +PV
Sbjct: 303 RATIANMAPEYGATCGFFPIDDATLVYMRLTGRSAENVALVEAYAKEQGFWRDATAPDPV 362

Query: 362 FTDSLHLDLGSVEPSLAGPKRPQDKVNLSSLPVEFNNFLIEVGKE-KEKEKTFAVKNKDF 420
           FTD+LHLD+ +V+PSLAGPKRPQD+V L+S+   FN+ L    K+  E +K  AV+  DF
Sbjct: 363 FTDTLHLDMSTVQPSLAGPKRPQDRVLLASVDEGFNSELATGYKKGDESDKRVAVEGTDF 422

Query: 421 QMKHGHVVIAAITSCTNTSNPSVLMAAGLVAKKAIEKGLQRKPWVKSSLAPGSKVVTDYL 480
            + HG VVIAAITSCTNTSNPSVL+AAGLVA+KA   GL+ KPWVK+SLAPGS+VVTDYL
Sbjct: 423 DLGHGDVVIAAITSCTNTSNPSVLVAAGLVARKANALGLKAKPWVKTSLAPGSQVVTDYL 482

Query: 481 RHAGLQTYLDQLGFNLVGYGCTTCIGNSGPLPDDISHCVAEHDLVVSSVLSGNRNFEGRV 540
             AGLQ  LD +GFNLVGYGCTTCIGNSGPLPD IS  +  +DLV S+VLSGNRNFEGRV
Sbjct: 483 EKAGLQKDLDAIGFNLVGYGCTTCIGNSGPLPDPISKAINGNDLVASAVLSGNRNFEGRV 542

Query: 541 HPQVRANWLASPPLVVAYALCGTTCSDLSREPIGQDKEGNDVYLKDIWPSNEEIAAEVAK 600
            P VRAN+LASPPLVVAYAL GTT  D++++PIG   +G  VYLKDIWP+  E+A  VA 
Sbjct: 543 SPDVRANYLASPPLVVAYALFGTTAKDITQDPIGTSTDGKPVYLKDIWPTTAEVANTVAA 602

Query: 601 -VSGTMFRKEYAEVFKGDAHWQAIQTSSGQTYEWNPDSTYIQHPPFFENLSLKPEPLKPI 659
            +   MF   YA VF+GD +WQAI      TY W   STY+ +PP+FE +S+ P P++ I
Sbjct: 603 AIDSEMFASRYANVFQGDKNWQAIDVEGSDTYTWRAGSTYVANPPYFEGMSMTPAPVRDI 662

Query: 660 KQAYVLALFGDSITTDHISPAGSIKASSPAGLYLKSKGVDEKDFNSYGSRRGNHEVMMRG 719
            +A  LA+F DSITTDHISPAGSIK  SPAG YL    V + DFNSYG+RRGNHEVMMRG
Sbjct: 663 VEARPLAIFADSITTDHISPAGSIKVDSPAGRYLTEHQVTKADFNSYGARRGNHEVMMRG 722

Query: 720 TFANIRIRNEMTPGQEGGVTRYVPTGETMSIYDAAMRYQENQQDLVIIAGKEYGTGSSRD 779
           TFANIRI+N+M PG EGG+T+++P+GE M+IYDAAM+Y++    LV++AGKEYGTGSSRD
Sbjct: 723 TFANIRIKNQMIPGIEGGLTKHIPSGEVMAIYDAAMKYKQEGTPLVVVAGKEYGTGSSRD 782

Query: 780 WAAKGTNLLGVKAVITESFERIHRSNLIGMGILPLQFKEGTTRKTLKLDGSERISIEISD 839
           WAAKGTNLLGV+AVI ESFERIHRSNL+GMG+LPLQF EG  R TLKLDG+E  +IE   
Sbjct: 783 WAAKGTNLLGVRAVIAESFERIHRSNLVGMGVLPLQFAEGVDRNTLKLDGTETFTIEDVA 842

Query: 840 KLTPGAMVPVTIERQDGDIEKIETLCRIDTADELEYYKNGGILQYVLRKISS 891
            L P   V V + R DG  E  ET CRIDT +ELEY+ NGGILQYVLRK+++
Sbjct: 843 GLRPRQTVSVKLTRADGSTETFETRCRIDTVNELEYFLNGGILQYVLRKLAA 894


Lambda     K      H
   0.316    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: 2076
Number of extensions: 87
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: 891
Length of database: 894
Length adjustment: 43
Effective length of query: 848
Effective length of database: 851
Effective search space:   721648
Effective search space used:   721648
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_079648606.1 B5X82_RS13120 (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.2642102.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 1398.6   0.0          0 1398.4   0.0    1.0  1  NCBI__GCF_900167915.1:WP_079648606.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900167915.1:WP_079648606.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1398.4   0.0         0         0       1     875 [.      20     892 ..      20     893 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1398.4 bits;  conditional E-value: 0
                             TIGR01341   1 kkvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlqd 73 
                                           k++ yysl +++e+l++is+lp s+++lle++lr  dg++++ +dv+a+++w+ke ++++ei+++parv++qd
  NCBI__GCF_900167915.1:WP_079648606.1  20 KHYAYYSLAKAAEKLGDISRLPFSMKVLLENLLRFEDGTTVTTDDVQAIVDWQKERTSEREIQYRPARVLMQD 92 
                                           5789********************************************************************* PP

                             TIGR01341  74 ftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwa 146
                                           ftGvp vvdlaa+r+a+++lg+d++kinplvpv lvidhsv vd +g+ +a+++nv le+ rn ery+fl+w+
  NCBI__GCF_900167915.1:WP_079648606.1  93 FTGVPCVVDLAAMRDAMNTLGGDAQKINPLVPVHLVIDHSVMVDSFGNPKAFDENVALEYARNGERYEFLRWG 165
                                           ************************************************************************* PP

                             TIGR01341 147 kkafknlkvvppgtGivhqvnleylakvvfeae.kdgellaypdslvGtdshttminGlGvlGwGvGGieaea 218
                                           +ka++n+kvvppgtGi+hqvnle la++v+++    g ++aypd+ vGtdshttminGlGvlGwGvGGieaea
  NCBI__GCF_900167915.1:WP_079648606.1 166 SKALNNFKVVPPGTGICHQVNLENLAQAVWSSAdGSGVEVAYPDTCVGTDSHTTMINGLGVLGWGVGGIEAEA 238
                                           ******************************875157899********************************** PP

                             TIGR01341 219 allGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmap 291
                                           a+lGqpvs+ +pev+G+kl G l+eG+tatdlvltvt++lr kgvvg+fvef+G+gl+ lsladratianmap
  NCBI__GCF_900167915.1:WP_079648606.1 239 AMLGQPVSMLIPEVVGFKLSGTLNEGITATDLVLTVTQMLRAKGVVGRFVEFYGPGLDALSLADRATIANMAP 311
                                           ************************************************************************* PP

                             TIGR01341 292 eyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd.dseepkytdvveldlsdveasvaGpkrp 363
                                           eyGat++ffpidd tl y+rltgr+ ++v lve+y+k q++++d  + +p++td++ ld+s+v++s+aGpkrp
  NCBI__GCF_900167915.1:WP_079648606.1 312 EYGATCGFFPIDDATLVYMRLTGRSAENVALVEAYAKEQGFWRDaTAPDPVFTDTLHLDMSTVQPSLAGPKRP 384
                                           ********************************************77788************************ PP

                             TIGR01341 364 qdrvalkevkaafksslesnagekglalrkeakekklegkeaelkdgavviaaitsctntsnpsvllgaglla 436
                                           qdrv l +v++ f+s l +   +     +   k+ ++eg++  l +g+vviaaitsctntsnpsvl++agl+a
  NCBI__GCF_900167915.1:WP_079648606.1 385 QDRVLLASVDEGFNSELATGYKKG----DESDKRVAVEGTDFDLGHGDVVIAAITSCTNTSNPSVLVAAGLVA 453
                                           ***************998654444....467788899************************************ PP

                             TIGR01341 437 kkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikendl 509
                                           +ka  lGlk kp+vktslapGs+vvtdyl ++gl++ l+++GfnlvGyGcttciGnsGpl++ +++ai+ ndl
  NCBI__GCF_900167915.1:WP_079648606.1 454 RKANALGLKAKPWVKTSLAPGSQVVTDYLEKAGLQKDLDAIGFNLVGYGCTTCIGNSGPLPDPISKAINGNDL 526
                                           ************************************************************************* PP

                             TIGR01341 510 evsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiael 582
                                           ++savlsGnrnfegr+ p+v+anylaspplvvayal Gt   d++++pigt +dGk+vylkdiwp++ e+a++
  NCBI__GCF_900167915.1:WP_079648606.1 527 VASAVLSGNRNFEGRVSPDVRANYLASPPLVVAYALFGTTAKDITQDPIGTSTDGKPVYLKDIWPTTAEVANT 599
                                           ************************************************************************* PP

                             TIGR01341 583 vkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeevedikgarillllG 655
                                           v  a+ +e+f  +y++v++g+++w+ ++v  sd+y+w   sty+ +pp+fe+++++p+ v di +ar l+ + 
  NCBI__GCF_900167915.1:WP_079648606.1 600 VAAAIDSEMFASRYANVFQGDKNWQAIDVEGSDTYTWRAGSTYVANPPYFEGMSMTPAPVRDIVEARPLAIFA 672
                                           ************************************************************************* PP

                             TIGR01341 656 dsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvyl 728
                                           dsittdhispaGsik dspa++yl+e+ v + dfnsyG+rrGnhevm+rGtfanirikn++++g eGglt+++
  NCBI__GCF_900167915.1:WP_079648606.1 673 DSITTDHISPAGSIKVDSPAGRYLTEHQVTKADFNSYGARRGNHEVMMRGTFANIRIKNQMIPGIEGGLTKHI 745
                                           ************************************************************************* PP

                             TIGR01341 729 pdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlple 801
                                           p +ev+++ydaamkyk+eg+plvv+aGkeyG+Gssrdwaakgt+llGv+aviaesferihrsnlvgmGvlpl+
  NCBI__GCF_900167915.1:WP_079648606.1 746 PSGEVMAIYDAAMKYKQEGTPLVVVAGKEYGTGSSRDWAAKGTNLLGVRAVIAESFERIHRSNLVGMGVLPLQ 818
                                           ************************************************************************* PP

                             TIGR01341 802 fkqgedaetlgltgeetidvddieelkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrk 874
                                           f +g d++tl l+g+et  ++d+  l+p+++v+v+l+++dg+ et+e+++ridt  el+y+ +gGilqyvlrk
  NCBI__GCF_900167915.1:WP_079648606.1 819 FAEGVDRNTLKLDGTETFTIEDVAGLRPRQTVSVKLTRADGSTETFETRCRIDTVNELEYFLNGGILQYVLRK 891
                                           ************************************************************************9 PP

                             TIGR01341 875 l 875
                                           l
  NCBI__GCF_900167915.1:WP_079648606.1 892 L 892
                                           6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (894 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 31.28
//
[ok]

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

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Steps (tab-delimited)
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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 2024 update 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