Alignments for a candidate for fba in Calditerrivibrio nitroreducens DSM 19672

GapMind for catabolism of small carbon sources

Alignments for a candidate for fba in Calditerrivibrio nitroreducens DSM 19672

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_013452043.1 CALNI_RS09785 fructose-1,6-bisphosphate aldolase, class II

Query= BRENDA::O97447
         (323 letters)



>NCBI__GCF_000183405.1:WP_013452043.1
          Length = 324

 Score =  279 bits (714), Expect = 6e-80
 Identities = 151/315 (47%), Positives = 204/315 (64%), Gaps = 10/315 (3%)

Query: 3   LCTLRQMLGEARKHKYGVGAFNVNNMEQIQGIMKAVVQLKSPVILQCSRGALKYSDMIYL 62
           L   R+M  +A + KY V A+N NN+EQ+Q I++A V+ KSPVILQ S+GA +Y++   L
Sbjct: 10  LVNTREMFKKAMEGKYAVPAYNFNNLEQLQAIIQACVETKSPVILQVSKGAREYANATIL 69

Query: 63  KKLC----EAALEKHPDIPICIHLDHGDTLESVKMAIDLGFSSVMIDASHHPFDENVRIT 118
           + L     + A E    IPI +HLDHGD+ E  K  +D GFSSVMID SH PF+EN+ +T
Sbjct: 70  RYLALGATQLAEEMGHKIPIALHLDHGDSFEICKSCVDYGFSSVMIDGSHLPFEENIAVT 129

Query: 119 KEVVAYAHARSVSVEAELGTLGGIEEDVQ-NTVQLTEPQDAKKFVELTGVDALAVAIGTS 177
           ++VV YAH   V+VE ELG L GIE+DV       T+P   ++FV  TGVD+LA++IGTS
Sbjct: 130 RKVVEYAHQFDVTVEGELGVLAGIEDDVSAEHSHYTDPAQVEEFVAKTGVDSLAISIGTS 189

Query: 178 HGAYKFK---SESDIRLAIDRVKTISD-LTGIPLVMHGSSSVPKDVKDMINKYGGKMPDA 233
           HGAYKFK    E    L  D ++ +   L G P+V+HG+SSV  +  ++INKYGGK+  A
Sbjct: 190 HGAYKFKVKPGEEVPPLRFDILEEVEKRLPGFPIVLHGASSVVPEYVELINKYGGKLEGA 249

Query: 234 VGVPIESIVHAIGEGVCKINVDSDSRMAMTGAIRKVFVEHPEKFDPRDYLGPGRDAITEM 293
           VGVP E +  A    VCKIN+DSD R+A T  +R+    +P++FDPR YL P R+ + ++
Sbjct: 250 VGVPEEQLRRAAASAVCKINIDSDGRLAFTAKVREYLANNPKEFDPRKYLKPAREELVKL 309

Query: 294 LIPK-IKAFGSAGHA 307
              K I   GSAG A
Sbjct: 310 YKHKNINVLGSAGKA 324


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: 300
Number of extensions: 15
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: 323
Length of database: 324
Length adjustment: 28
Effective length of query: 295
Effective length of database: 296
Effective search space:    87320
Effective search space used:    87320
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_013452043.1 CALNI_RS09785 (fructose-1,6-bisphosphate aldolase, class II)
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.6551.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.1e-118  379.6   0.1   7.3e-118  379.3   0.1    1.1  1  lcl|NCBI__GCF_000183405.1:WP_013452043.1  CALNI_RS09785 fructose-1,6-bisph


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000183405.1:WP_013452043.1  CALNI_RS09785 fructose-1,6-bisphosphate aldolase, class II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.3   0.1  7.3e-118  7.3e-118       1     282 []      10     324 .]      10     324 .] 0.95

  Alignments for each domain:
  == domain 1  score: 379.3 bits;  conditional E-value: 7.3e-118
                                 TIGR01859   1 lvkakellekakkekYavgafninnlellqaileaaeeeksPvivqvsegavkYlg..gikvvvalvka 67 
                                               lv+++e+++ka ++kYav+a+n+nnle+lqai++a+ e+ksPvi+qvs+ga++Y++   ++ ++   ++
  lcl|NCBI__GCF_000183405.1:WP_013452043.1  10 LVNTREMFKKAMEGKYAVPAYNFNNLEQLQAIIQACVETKSPVILQVSKGAREYANatILRYLALGATQ 78 
                                               79******************************************************4333344444678 PP

                                 TIGR01859  68 lieklsi.vPvalhLDhGssyescikaikaGfssvmiDashlpleenlketkkvveiahakgvsveael 135
                                               l+e++ + +P+alhLDhG+s+e c ++++ GfssvmiD+shlp+een++ t+kvve+ah+  v+ve el
  lcl|NCBI__GCF_000183405.1:WP_013452043.1  79 LAEEMGHkIPIALHLDHGDSFEICKSCVDYGFSSVMIDGSHLPFEENIAVTRKVVEYAHQFDVTVEGEL 147
                                               99999999************************************************************* PP

                                 TIGR01859 136 GklgGieddvvekeaeladideakklvketgvDaLaiaiGtshGkykge.......pkldferlkeikk 197
                                               G+l+Gieddv +++++++d+ +++++v +tgvD+Lai+iGtshG yk +       p l+f+ l+e++k
  lcl|NCBI__GCF_000183405.1:WP_013452043.1 148 GVLAGIEDDVSAEHSHYTDPAQVEEFVAKTGVDSLAISIGTSHGAYKFKvkpgeevPPLRFDILEEVEK 216
                                               ********************************************666555599999************* PP

                                 TIGR01859 198 lln.lPlvlhGas.....................Gipeeqlkkaiklgiakvnidtdlrlaftaairkv 244
                                               +l+ +P+vlhGas                     G+peeql++a+ ++++k+nid+d rlafta++r++
  lcl|NCBI__GCF_000183405.1:WP_013452043.1 217 RLPgFPIVLHGASsvvpeyvelinkyggklegavGVPEEQLRRAAASAVCKINIDSDGRLAFTAKVREY 285
                                               **99***************************************************************** PP

                                 TIGR01859 245 leekkdeydpRkilaparealkevvkekik.vlgsagka 282
                                               l+++ +e+dpRk+l+pare+l +++k+k+  vlgsagka
  lcl|NCBI__GCF_000183405.1:WP_013452043.1 286 LANNPKEFDPRKYLKPAREELVKLYKHKNInVLGSAGKA 324
                                               ***************************9755******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (282 nodes)
Target sequences:                          1  (324 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 9.23
//
[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