Alignments for a candidate for acn in Desulfatitalea tepidiphila S28bF

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Desulfatitalea tepidiphila S28bF

Align aconitate hydratase; EC 4.2.1.3 (characterized)
to candidate WP_054031160.1 DFT_RS10550 aconitate hydratase

Query= CharProtDB::CH_122731
         (777 letters)



>NCBI__GCF_001293685.1:WP_054031160.1
          Length = 652

 Score =  285 bits (729), Expect = 5e-81
 Identities = 219/719 (30%), Positives = 330/719 (45%), Gaps = 84/719 (11%)

Query: 60  LTYAEKLLYGHLDDPHNQEIERGVSYLKLRPDRVACQDATAQMAILQFMSAGIPQVATP- 118
           +   +KL+  HL +   +  E     + LR D+   QDAT  M +L+F +  + +V T  
Sbjct: 3   MNVTQKLIVSHLVNGRMRPGEE----IGLRIDQTLTQDATGTMVMLEFEAMQVGRVKTEL 58

Query: 119 STVHCDHLIQAQVGGPKDLARAIDLNKEVYDFLSTACAKYNLGFWKPGSGIIHQIVLENY 178
           S  + DH          +L +    N + + FL +AC K+ + + +PG+G+ H + ++ +
Sbjct: 59  SAQYVDH----------NLLQTDYRNADDHLFLRSACQKFGIWYSRPGNGVSHPVHMQRF 108

Query: 179 AFPGALLIGTDSHTPNAGGLGQLAIGVGGADAVDVMSGLPWELKAPKIIGVKLTGKMSGW 238
             PG  LIG+DSHTP AG LG LA G GG +   VM+G P  ++ P+++G++LTG++  W
Sbjct: 109 GIPGKTLIGSDSHTPAAGALGMLAFGAGGLEVATVMAGEPMYVRMPEVLGIRLTGRLPDW 168

Query: 239 TSPKDIILKLAGITTVKGGTGSIVEYFGSGVDTFSCTGMGTICNMGAEIGATTSVFPFND 298
            S KD+IL++     V GG G I+EYFG G+D  S      I NMG E+GATT+VFP +D
Sbjct: 169 VSAKDVILEMLRRYGVDGGRGKIIEYFGPGLDDLSAMDRHVIANMGTELGATTTVFPSDD 228

Query: 299 SMVDYLNATGRSEIAQFAQVYKKDFLSADEGAEYDQVIEIDLNTLEPHINGPFTPDLATP 358
           ++  +L+   R E+ +         + AD  A YDQ   IDL TLEP I  P +P    P
Sbjct: 229 AVRRFLDTQQRGEVWR--------EVKADADAGYDQTDHIDLGTLEPLIALPSSPGNVVP 280

Query: 359 VSKMKETAIANGWPLEVKVGLIGSCTNSSYEDMTRAASIIKDAGAHGLKSKALYTVSPGS 418
           V ++    I   +        IGS  N    D    A ++       +     + V+P S
Sbjct: 281 VREVIGRPIYQAY--------IGSSANPGLRDFAVPALMV---AGRRIPDHISFDVNPTS 329

Query: 419 EQVRATIARDGQLKTFEDFGGVVMANACGPCIGQWDRQDIKKGDKNTIVSSFNRNFTARN 478
            Q+   +   G +    + G       C  CIG        K    T+     RNF  R+
Sbjct: 330 RQLIENMIELGLMAHLINCGARFHQAGCNGCIGMGQAPATGKISLRTV----PRNFPGRS 385

Query: 479 DGNPATHAFVASPEMATVYAISGDLGFNPITDTLVGADGKEFKLKEPQGVGLPPDGYDPG 538
            G      ++ SPE AT  A++G      ITD           L  P      P+     
Sbjct: 386 -GTIEDQVYLCSPETATASALNG-----VITDPRT--------LSMPYPRFKEPERLSVN 431

Query: 539 ENTYQAPPEDRASVEVVISPTSDRLQKLSPFKPWDG-KDAERLPILIKAVGKTTTDHISM 597
                 P E+   VE+   P       + P   +D   D    P+L+K     +TD I  
Sbjct: 432 TTLLLGPLENSEGVELEKGP------NIKPLPEFDALPDRIEGPVLLKMGDNISTDEIMP 485

Query: 598 AG-PWLKYRGHLENISNNYMIGAINAENGKANEVRNHYTGKYDGVPQTAAAYRDAGHKWV 656
           AG   L +R ++  IS  +    I+ +      +R   TG +                  
Sbjct: 486 AGASVLPFRSNIPEIS-RFAFSRIDLDY-YDRTIRYQKTGSF------------------ 525

Query: 657 VIGDENFGEGSSREHAALEPRFLGGFAIITKSFARIHETNLKKQGLLPLNFKNPADYDKI 716
           VIG +N+G+GSSREHAAL PR+LG  A+I KSFARIH  NL   G++PL F+N  D+ ++
Sbjct: 526 VIGGDNYGQGSSREHAALAPRYLGLRAVIAKSFARIHAQNLINFGIVPLTFENGDDWRRV 585

Query: 717 NFDDEVDLIGLTT-LAPGKDVILRVHPKEGEAWEAVLTHTFNSEQLEWFKHGSALNFIK 774
              D++ + GL   L  G+   +    +    W   +    +  QLE    G  +N I+
Sbjct: 586 EQGDQLRMTGLVARLKAGEPFDIENLTRN---WAFRVGFALSQRQLEVLLAGGLINHIR 641


Lambda     K      H
   0.316    0.134    0.401 

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: 1181
Number of extensions: 63
Number of successful extensions: 4
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: 777
Length of database: 652
Length adjustment: 39
Effective length of query: 738
Effective length of database: 613
Effective search space:   452394
Effective search space used:   452394
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: 55 (25.8 bits)

Align candidate WP_054031160.1 DFT_RS10550 (aconitate hydratase)
to HMM TIGR01342 (putative aconitate hydratase (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/TIGR01342.hmm
# target sequence database:        /tmp/gapView.2805534.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01342  [M=655]
Accession:   TIGR01342
Description: acon_putative: putative aconitate hydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.4e-253  827.5   0.0   4.2e-253  827.3   0.0    1.0  1  NCBI__GCF_001293685.1:WP_054031160.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001293685.1:WP_054031160.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  827.3   0.0  4.2e-253  4.2e-253       2     647 ..       5     642 ..       4     650 .. 0.98

  Alignments for each domain:
  == domain 1  score: 827.3 bits;  conditional E-value: 4.2e-253
                             TIGR01342   2 laekilddhlvegdlepgeeiaikidqtlsqdatgtmvylefealevdevktelavsyidhqtlqtdfknadd 74 
                                           +++k++  hlv+g ++pgeei+++idqtl+qdatgtmv lefea++v  vktel+++y+dh++lqtd++nadd
  NCBI__GCF_001293685.1:WP_054031160.1   5 VTQKLIVSHLVNGRMRPGEEIGLRIDQTLTQDATGTMVMLEFEAMQVGRVKTELSAQYVDHNLLQTDYRNADD 77 
                                           899********************************************************************** PP

                             TIGR01342  75 hkylrsvakkygiylskpgngichqvhkerfakpgktllgsdshtptagglgqlaigaggldvavamageayy 147
                                           h +lrs+ +k+gi++s+pgng+ h vh++rf  pgktl+gsdshtp+ag lg+la gaggl+va+ mage++y
  NCBI__GCF_001293685.1:WP_054031160.1  78 HLFLRSACQKFGIWYSRPGNGVSHPVHMQRFGIPGKTLIGSDSHTPAAGALGMLAFGAGGLEVATVMAGEPMY 150
                                           ************************************************************************* PP

                             TIGR01342 148 lkmpkvvnvrlkgklpewvtakdvilellrrlsvkgglgkvleytgegvkelsvperatitnmgaelgatssi 220
                                           ++mp+v+++rl g+lp+wv+akdvile+lrr  v gg gk++ey+g+g+++ls  +r  i+nmg+elgat+++
  NCBI__GCF_001293685.1:WP_054031160.1 151 VRMPEVLGIRLTGRLPDWVSAKDVILEMLRRYGVDGGRGKIIEYFGPGLDDLSAMDRHVIANMGTELGATTTV 223
                                           ************************************************************************* PP

                             TIGR01342 221 fpsdeitedylaafdreeefvelladadaeydevivvdlselepliaepsspdnvvpvrevegikveqvvvgs 293
                                           fpsd+  + +l +++r e + e++adada yd+   +dl  leplia pssp nvvpvrev g  + q  +gs
  NCBI__GCF_001293685.1:WP_054031160.1 224 FPSDDAVRRFLDTQQRGEVWREVKADADAGYDQTDHIDLGTLEPLIALPSSPGNVVPVREVIGRPIYQAYIGS 296
                                           ************************************************************************* PP

                             TIGR01342 294 ctnsayvdllraakllegrevskdvvlivapgskqalellaregallellkagvrileaacgacigigfvpas 366
                                            +n    d    a ++ gr++ +++ + v p s+q +e + + g +++l++ g+r+ +a c  cig+g +pa+
  NCBI__GCF_001293685.1:WP_054031160.1 297 SANPGLRDFAVPALMVAGRRIPDHISFDVNPTSRQLIENMIELGLMAHLINCGARFHQAGCNGCIGMGQAPAT 369
                                           ************************************************************************* PP

                             TIGR01342 367 dsvslrsfnrnfkgragieddkvylaspevavaaaiageivdprdlaedeglkairvemgekysygdeadidi 439
                                             +slr+  rnf gr+g+ +d+vyl+spe+a+a+a+ g i dpr l+    + ++r++ +e+ s      + +
  NCBI__GCF_001293685.1:WP_054031160.1 370 GKISLRTVPRNFPGRSGTIEDQVYLCSPETATASALNGVITDPRTLS----MPYPRFKEPERLSVNTTLLLGP 438
                                           *********************************************98....689**********987766666 PP

                             TIGR01342 440 ltkeeridvelikgpnikslpvkeplgedvegevllkvednittdhiipatadilklrsniealseyvlsrvd 512
                                           l  e+++ vel kgpnik+lp+++ l++ +eg vllk+ dni+td i+pa+a +l++rsni  +s +++sr+d
  NCBI__GCF_001293685.1:WP_054031160.1 439 L--ENSEGVELEKGPNIKPLPEFDALPDRIEGPVLLKMGDNISTDEIMPAGASVLPFRSNIPEISRFAFSRID 509
                                           5..788899**************************************************************** PP

                             TIGR01342 513 defverakkldekgkagvlvagenygqgssrehaalaprflgveavlaksfarihkanlvnfgvlpleidnke 585
                                            ++ +r+ + ++      +++g+nygqgssrehaalapr+lg++av+aksfarih  nl+nfg++pl ++n +
  NCBI__GCF_001293685.1:WP_054031160.1 510 LDYYDRTIRYQK--TGSFVIGGDNYGQGSSREHAALAPRYLGLRAVIAKSFARIHAQNLINFGIVPLTFENGD 580
                                           ******999988..45689****************************************************** PP

                             TIGR01342 586 dydkielgdevevvdliealkdgeeilvvrktddeeilatldlsevekeiliaggklslikq 647
                                           d+ ++e+gd++ ++ l+++lk ge   + + t ++   + + ls+++ e+l+agg +++i++
  NCBI__GCF_001293685.1:WP_054031160.1 581 DWRRVEQGDQLRMTGLVARLKAGEPFDIENLTRNWAFRVGFALSQRQLEVLLAGGLINHIRH 642
                                           ************************999999****************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (655 nodes)
Target sequences:                          1  (652 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 24.69
//
[ok]

This GapMind analysis is from Sep 24 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