GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Caldicellulosiruptor hydrothermalis 108

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_013289899.1 CALHY_RS10305 class II fructose-1,6-bisphosphate aldolase

Query= BRENDA::O97447
         (323 letters)



>NCBI__GCF_000166355.1:WP_013289899.1
          Length = 323

 Score =  310 bits (793), Expect = 4e-89
 Identities = 174/325 (53%), Positives = 221/325 (68%), Gaps = 12/325 (3%)

Query: 1   MPLCTLRQMLGEARKHKYGVGAFNVNNMEQIQGIMKAVVQLKSPVILQCSRGALKYSDMI 60
           MPL T R+M  +A + KY +GAFNVNNME IQGI++A  + ++P+ILQ S GA KY+  I
Sbjct: 1   MPLVTTREMFKKAAEGKYAIGAFNVNNMEIIQGIVEAAKEEQAPLILQVSAGARKYAKHI 60

Query: 61  YLKKLCEAALEKHPDIPICIHLDHGDTLESVKMAIDLGFSSVMIDASHHPFDENVRITKE 120
           YL KL EAALE   D+PI +HLDHG+  E  K  ID GF+SVMID S  PF+EN+ +TK+
Sbjct: 61  YLIKLVEAALEDSGDLPIALHLDHGEDFEICKACIDGGFTSVMIDGSRLPFEENIALTKK 120

Query: 121 VVAYAHARSVSVEAELGTLGGIEEDV---QNTVQLTEPQDAKKFVELTGVDALAVAIGTS 177
           VV YAH R V VEAELG L GIE++V   ++    T+P  A +FVE TGVD+LAVAIGTS
Sbjct: 121 VVEYAHERGVVVEAELGKLAGIEDNVKVAEHEAAFTDPDQAAEFVERTGVDSLAVAIGTS 180

Query: 178 HGAYKFKSESDIRLAIDRVKTISDL--TGIPLVMHGSSSVPKDVKDMINKYGGKMPDAVG 235
           HGAYKFK   D RL  +R++ I +      P+V+HG+S+V  +  +M NKYGG +P A G
Sbjct: 181 HGAYKFK--GDPRLDFERLQKIVEKLPKDFPIVLHGASTVLPEFVEMCNKYGGNIPGAKG 238

Query: 236 VPIESIVHAIGEGVCKINVDSDSRMAMTGAIRKVFVEHPEKFDPRDYLGPGRDAITEMLI 295
           VP + +  A   GV KIN+D+D R+AMT AIRK   EHP+ FDPR YL  GRDAI EM+ 
Sbjct: 239 VPEDMLRKAAELGVRKINIDTDLRLAMTAAIRKHLYEHPDHFDPRQYLKDGRDAIKEMVK 298

Query: 296 PKIK-AFGSAGHAGDYKVVSLEEAK 319
            K++   G AG A +     LEE K
Sbjct: 299 HKLRNVLGCAGKAPEI----LEEIK 319


Lambda     K      H
   0.318    0.135    0.389 

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: 331
Number of extensions: 8
Number of successful extensions: 3
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: 323
Length of database: 323
Length adjustment: 28
Effective length of query: 295
Effective length of database: 295
Effective search space:    87025
Effective search space used:    87025
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: 48 (23.1 bits)

Align candidate WP_013289899.1 CALHY_RS10305 (class II fructose-1,6-bisphosphate aldolase)
to HMM TIGR01859 (fba: fructose-1,6-bisphosphate aldolase, class II (EC 4.1.2.13))

# 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/TIGR01859.hmm
# target sequence database:        /tmp/gapView.3589792.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01859  [M=282]
Accession:   TIGR01859
Description: fruc_bis_ald_: fructose-1,6-bisphosphate aldolase, class II
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-118  381.5   0.2   1.8e-118  381.3   0.2    1.1  1  NCBI__GCF_000166355.1:WP_013289899.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166355.1:WP_013289899.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  381.3   0.2  1.8e-118  1.8e-118       1     282 []       3     311 ..       3     311 .. 0.98

  Alignments for each domain:
  == domain 1  score: 381.3 bits;  conditional E-value: 1.8e-118
                             TIGR01859   1 lvkakellekakkekYavgafninnlellqaileaaeeeksPvivqvsegavkYlggikvvvalvkaliekls 73 
                                           lv+++e+++ka ++kYa+gafn+nn+e++q i+eaa+ee++P+i+qvs ga+kY+     +++lv+a++e+  
  NCBI__GCF_000166355.1:WP_013289899.1   3 LVTTREMFKKAAEGKYAIGAFNVNNMEIIQGIVEAAKEEQAPLILQVSAGARKYAK-HIYLIKLVEAALEDSG 74 
                                           79*****************************************************9.667889********** PP

                             TIGR01859  74 ivPvalhLDhGssyescikaikaGfssvmiDashlpleenlketkkvveiahakgvsveaelGklgGiedd.. 144
                                           ++P+alhLDhG+++e c ++i+ Gf+svmiD+s+lp+een+++tkkvve+ah++gv veaelGkl+Gied+  
  NCBI__GCF_000166355.1:WP_013289899.1  75 DLPIALHLDHGEDFEICKACIDGGFTSVMIDGSRLPFEENIALTKKVVEYAHERGVVVEAELGKLAGIEDNvk 147
                                           ***********************************************************************88 PP

                             TIGR01859 145 vvekeaeladideakklvketgvDaLaiaiGtshG..kykgepkldferlkeikklln..lPlvlhGas.... 209
                                           v e+ea ++d+d+a ++v++tgvD+La+aiGtshG  k+kg+p+ldferl++i ++l+  +P+vlhGas    
  NCBI__GCF_000166355.1:WP_013289899.1 148 VAEHEAAFTDPDQAAEFVERTGVDSLAVAIGTSHGayKFKGDPRLDFERLQKIVEKLPkdFPIVLHGAStvlp 220
                                           8899*******************************9999999************999878************* PP

                             TIGR01859 210 .................GipeeqlkkaiklgiakvnidtdlrlaftaairkvleekkdeydpRkilapareal 265
                                                            G+pe++l+ka++lg+ k+nidtdlrla+taairk+l e+ d++dpR++l+++r+a+
  NCBI__GCF_000166355.1:WP_013289899.1 221 efvemcnkyggnipgakGVPEDMLRKAAELGVRKINIDTDLRLAMTAAIRKHLYEHPDHFDPRQYLKDGRDAI 293
                                           ************************************************************************* PP

                             TIGR01859 266 kevvkekik.vlgsagka 282
                                           ke+vk+k++ vlg agka
  NCBI__GCF_000166355.1:WP_013289899.1 294 KEMVKHKLRnVLGCAGKA 311
                                           ********9899*99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (282 nodes)
Target sequences:                          1  (323 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: 00:00:00.00
# Mc/sec: 18.14
//
[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:

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:

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:

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:

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