Alignments for a candidate for acn in Halobacillus alkaliphilus FP5

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Halobacillus alkaliphilus FP5

Align Aconitate hydratase, mitochondrial; Aconitase; Citrate hydro-lyase; EC 4.2.1.3 (characterized)
to candidate WP_089751514.1 BMZ06_RS07900 aconitate hydratase

Query= SwissProt::P20004
         (780 letters)



>NCBI__GCF_900113125.1:WP_089751514.1
          Length = 649

 Score =  285 bits (729), Expect = 5e-81
 Identities = 222/714 (31%), Positives = 328/714 (45%), Gaps = 76/714 (10%)

Query: 65  LSEKIVYGHLDDPANQEIERGKTYLRLRPDRVAMQDATAQMAMLQFISSGLPKVAVPSTI 124
           +++K++  HL      E+  G T + L+ D+   QDAT  M ML+  + G+ +    ++ 
Sbjct: 5   VTQKLIKDHL---VKGEMTPG-TEIGLKIDQTLTQDATGTMVMLELEAMGIERAQTEASA 60

Query: 125 -HCDHLIEAQLGGEKDLRRAKDINQEVYNFLATAGAKYGVGFWRPGSGIIHQIILENYAY 183
            + DH          +L +    N + + FL +A  ++G+ F RPG+G+ H + ++  A 
Sbjct: 61  QYVDH----------NLIQEDSKNPDDHLFLESAAKRFGLHFSRPGNGVSHPVHMQRLAT 110

Query: 184 PGVLLIGTDSHTPNGGGLGGICIGVGGADAVDVMAGIPWELKCPKVIGVKLTGSLSGWTS 243
           PG  L+G+DSHT   G +G + +G GG D    +AG P+ +K PKV GVK+TG    W S
Sbjct: 111 PGKTLLGSDSHTCANGCMGMLAMGAGGIDVAMAIAGEPFYVKMPKVWGVKVTGEFPDWVS 170

Query: 244 PKDVILKVAGILTVKGGTGAIVEYHGPGVDSISCTGMATICNMGAEIGATTSVFPYNHRM 303
            KD IL++     VKG T  + EY+GPG+ +++      I NMGAE+GAT +VFP +   
Sbjct: 171 AKDAILEMLRRHGVKGATNHVFEYYGPGLKNLTAMDRHVIANMGAELGATGTVFPSDEET 230

Query: 304 KKYLSKTGRADIANLADEFKDHLVPDSGCHYDQLIEINLSELKPHINGPFTPDLAHPVAE 363
           K+++   GR D     D  +  L  D G  YD   E+NLSEL P I  P +P    P+ E
Sbjct: 231 KRFMKLQGRED-----DWIE--LKADDGASYDVHDELNLSELGPMIAKPSSPGNVVPIEE 283

Query: 364 VGSVAEKEGWPLDIRVGLIGSCTNSSYEDMGRSAAVAKQALAHGLQCKSQFTITPGSEQI 423
           V      EG    I    IGS  N  Y D    A  +K    H +     F + P S Q+
Sbjct: 284 V------EG--ESIYQSYIGSSANPGYRDF---AVASKIVEGHRIADGVSFDLNPTSRQM 332

Query: 424 RATIERDGYAQILRDVGGIVLANACGPCIGQWDRKDIKKGEKNTIVTSYNRNFTGRNDAN 483
              + ++G+       GG +    C  CIG        +    T      RNF GR+   
Sbjct: 333 LIDLSQEGHIANFLQSGGRLHQAGCNGCIGMGQAPATGRNSLRTT----PRNFPGRS-GT 387

Query: 484 PETHAFVTSPEIVTALAIAGTLKFNPETDFLTGKDGKKFKLEAPDADELPRAEFDPGQDT 543
            E   F+ SPE     A+ G +            D +K   + P   EL     D     
Sbjct: 388 KEDSVFLCSPETAAVSALTGKI-----------TDPRKSDFDYPSIKELEEPTIDTRLLD 436

Query: 544 YQHPPKDSSGQQVDVSPTSQRLQLLEPFDKWDGRDLEDLQILIKVKGKCTTDHISAAGP- 602
              P +++   ++   P    +  ++        D+E L IL+K+    +TD I A G  
Sbjct: 437 DPLPYEEAKEVELVKGPNIASIPKMDELP----NDME-LPILLKMGNDISTDEILAGGAR 491

Query: 603 WLKFRGHLDNISNNLLIGAINVENGKANSVRNAVTQEFGPVPDTARYYKKHGIRWVVIGD 662
            L +R +L  IS           + +A  +R+                   G   VV G 
Sbjct: 492 VLPYRSNLPEISKFTFEIVDETYHDRAMEIRD------------------QGGHAVVAG- 532

Query: 663 ENYGEGSSREHAALEPRHLGGRAIITKSFARIHETNLKKQGLLPLTFADPADYNKIHPVD 722
            NYG+GSSREHAAL P++LG +  I K FARIH  NL   G+LPLTF +  D  ++   D
Sbjct: 533 MNYGQGSSREHAALAPKYLGLKVAIVKDFARIHWQNLANFGVLPLTFVNEEDLEELEQGD 592

Query: 723 KLTIKGLKDFAPGKPLTCIIKHPNGTQETILLNHTFNETQIEWFRAGSALNRMK 776
            L  KGL+D    K    +     G  +T+ L H  +E QIE  + G  +N +K
Sbjct: 593 VLVFKGLRDGI--KQSNQVEVEVKGKDKTLKLEHALSERQIEIMQMGGLINWVK 644


Lambda     K      H
   0.317    0.136    0.411 

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: 1259
Number of extensions: 63
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: 780
Length of database: 649
Length adjustment: 39
Effective length of query: 741
Effective length of database: 610
Effective search space:   452010
Effective search space used:   452010
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 (21.7 bits)
S2: 55 (25.8 bits)

Align candidate WP_089751514.1 BMZ06_RS07900 (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.289733.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-234  765.2   0.0   2.8e-234  765.0   0.0    1.0  1  NCBI__GCF_900113125.1:WP_089751514.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900113125.1:WP_089751514.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  765.0   0.0  2.8e-234  2.8e-234       2     649 ..       5     647 ..       4     649 .] 0.97

  Alignments for each domain:
  == domain 1  score: 765.0 bits;  conditional E-value: 2.8e-234
                             TIGR01342   2 laekilddhlvegdlepgeeiaikidqtlsqdatgtmvylefealevdevktelavsyidhqtlqtdfknadd 74 
                                           +++k+++dhlv+g++ pg ei++kidqtl+qdatgtmv le+ea++++  +te +++y+dh+++q d kn dd
  NCBI__GCF_900113125.1:WP_089751514.1   5 VTQKLIKDHLVKGEMTPGTEIGLKIDQTLTQDATGTMVMLELEAMGIERAQTEASAQYVDHNLIQEDSKNPDD 77 
                                           899********************************************************************** PP

                             TIGR01342  75 hkylrsvakkygiylskpgngichqvhkerfakpgktllgsdshtptagglgqlaigaggldvavamageayy 147
                                           h +l s+ak++g+++s+pgng+ h vh++r+a+pgktllgsdsht + g +g+la+gagg+dva+a+age++y
  NCBI__GCF_900113125.1:WP_089751514.1  78 HLFLESAAKRFGLHFSRPGNGVSHPVHMQRLATPGKTLLGSDSHTCANGCMGMLAMGAGGIDVAMAIAGEPFY 150
                                           ************************************************************************* PP

                             TIGR01342 148 lkmpkvvnvrlkgklpewvtakdvilellrrlsvkgglgkvleytgegvkelsvperatitnmgaelgatssi 220
                                           +kmpkv +v++ g++p+wv+akd ile+lrr  vkg   +v+ey+g+g+k+l+  +r  i+nmgaelgat ++
  NCBI__GCF_900113125.1:WP_089751514.1 151 VKMPKVWGVKVTGEFPDWVSAKDAILEMLRRHGVKGATNHVFEYYGPGLKNLTAMDRHVIANMGAELGATGTV 223
                                           ************************************************************************* PP

                             TIGR01342 221 fpsdeitedylaafdreeefvelladadaeydevivvdlselepliaepsspdnvvpvrevegikveqvvvgs 293
                                           fpsde t+ +++ ++re++++el+ad  a yd   +++lsel p+ia+pssp nvvp+ eveg  + q  +gs
  NCBI__GCF_900113125.1:WP_089751514.1 224 FPSDEETKRFMKLQGREDDWIELKADDGASYDVHDELNLSELGPMIAKPSSPGNVVPIEEVEGESIYQSYIGS 296
                                           ************************************************************************* PP

                             TIGR01342 294 ctnsayvdllraakllegrevskdvvlivapgskqalellaregallellkagvrileaacgacigigfvpas 366
                                            +n  y d   a+k++eg ++ + v + + p s+q l  l++eg ++++l++g r+ +a c  cig+g +pa+
  NCBI__GCF_900113125.1:WP_089751514.1 297 SANPGYRDFAVASKIVEGHRIADGVSFDLNPTSRQMLIDLSQEGHIANFLQSGGRLHQAGCNGCIGMGQAPAT 369
                                           ************************************************************************* PP

                             TIGR01342 367 dsvslrsfnrnfkgragieddkvylaspevavaaaiageivdprdlaedeglkairvemgekysygdeadidi 439
                                              slr+  rnf gr+g+++d+v+l+spe+a+ +a++g+i dpr+       +++ ++  e+ +       d+
  NCBI__GCF_900113125.1:WP_089751514.1 370 GRNSLRTTPRNFPGRSGTKEDSVFLCSPETAAVSALTGKITDPRKSD----FDYPSIKELEEPTIDTRLLDDP 438
                                           ********************************************954....445555444554556677889* PP

                             TIGR01342 440 ltkeeridvelikgpnikslpvkeplgedvegevllkvednittdhiipatadilklrsniealseyvlsrvd 512
                                           l+ ee ++vel+kgpni s+p+++ l++d+e  +llk+ ++i+td i+  +a +l++rsn+  +s+++++ vd
  NCBI__GCF_900113125.1:WP_089751514.1 439 LPYEEAKEVELVKGPNIASIPKMDELPNDMELPILLKMGNDISTDEILAGGARVLPYRSNLPEISKFTFEIVD 511
                                           ************************************************************************* PP

                             TIGR01342 513 defverakkldekgkagvlvagenygqgssrehaalaprflgveavlaksfarihkanlvnfgvlpleidnke 585
                                           +++ +ra ++ ++g    +vag nygqgssrehaalap++lg++  + k farih  nl nfgvlpl + n+e
  NCBI__GCF_900113125.1:WP_089751514.1 512 ETYHDRAMEIRDQGGH-AVVAGMNYGQGSSREHAALAPKYLGLKVAIVKDFARIHWQNLANFGVLPLTFVNEE 583
                                           **********997765.568***************************************************** PP

                             TIGR01342 586 dydkielgdevevvdliealkdgeeilvvrktddeeilatldlsevekeiliaggklslikqkh 649
                                           d + +e+gd +    l + +k+ +++ v  k +d+ +   + lse++ ei+  gg ++++k++ 
  NCBI__GCF_900113125.1:WP_089751514.1 584 DLEELEQGDVLVFKGLRDGIKQSNQVEVEVKGKDKTLKLEHALSERQIEIMQMGGLINWVKNRL 647
                                           *********999999*******99999888999999999***********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (655 nodes)
Target sequences:                          1  (649 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 17.08
//
[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