Alignments for a candidate for fbp in Desulfovibrio bastinii DSM 16055

GapMind for Amino acid biosynthesis

Alignments for a candidate for fbp in Desulfovibrio bastinii DSM 16055

Align Fructose-bisphosphate aldolase; Glfba; glFBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate WP_027179546.1 G496_RS0112275 fructose-1,6-bisphosphate aldolase, class II

Query= SwissProt::A8B2U2
         (323 letters)



>NCBI__GCF_000429985.1:WP_027179546.1
          Length = 307

 Score =  298 bits (763), Expect = 1e-85
 Identities = 161/310 (51%), Positives = 211/310 (68%), Gaps = 6/310 (1%)

Query: 1   MPLCTLRQMLGEARKHKYGVGAFNVNNMEQIQGIMKAVVQLKSPVILQCSRGALKYSDMI 60
           MPL + ++M   A    Y +GAFNVNNME IQGI++A  + KSP+ILQ S GA KY+   
Sbjct: 1   MPLVSPKEMFKGAYTGGYAIGAFNVNNMEIIQGIIEAGTEEKSPLILQVSAGARKYAGQG 60

Query: 61  YLKKLCEAALEKHPDIPICIHLDHGDTLESVKMAIDLGFSSVMIDASHHPFDENVRITKE 120
           Y+ KL EAAL+   D+P+ +HLDHG   E  K  ID GF+SVMID SH PFDEN+ +TK+
Sbjct: 61  YIIKLMEAALQD-TDLPVVLHLDHGQNFEICKKVIDAGFTSVMIDGSHLPFDENIAVTKK 119

Query: 121 VVAYAHARGVSVEAELGTLGGIEEDVQNTVQL-TEPQDAKKFVELTGVDALAVAIGTSHG 179
           VV YAH +G+ VEAELG L G+E+DV +   + T+P +A +FVE TG D+LA+AIGTSHG
Sbjct: 120 VVEYAHPKGIWVEAELGRLAGVEDDVHSDEHIYTDPDEAVEFVEKTGCDSLAIAIGTSHG 179

Query: 180 AYKFKSESDIRLAIDRVKTISDL-TGIPLVMHGSSSVPKDVKDMINKYGGKMPDAVGVPI 238
           AYKF  +   +L  DR++ IS L    P+V+HG+SSV ++   M N+YGG +  A GVP 
Sbjct: 180 AYKFSGKP--KLDFDRLEKISSLMPDYPIVLHGASSVVQEYVQMANQYGGNIGGAKGVPE 237

Query: 239 ESIVHAIGEGVCKINVDSDSRMAMTGAIRKVFVEHPEKFDPRDYLGPGRDAITEMLIPKI 298
           + +  A    VCKIN+D+D R+AMT  IRK   E+PE FDPR YLG  R A+ +M+  KI
Sbjct: 238 DLLRKAASMAVCKINIDTDIRLAMTAMIRKFLAENPEAFDPRGYLGEARKAVKDMVCHKI 297

Query: 299 K-AFGSAGHA 307
           K   GS+G A
Sbjct: 298 KNVLGSSGKA 307


Lambda     K      H
   0.318    0.135    0.391 

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: 334
Number of extensions: 12
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: 307
Length adjustment: 27
Effective length of query: 296
Effective length of database: 280
Effective search space:    82880
Effective search space used:    82880
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_027179546.1 G496_RS0112275 (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.aa/TIGR01859.hmm
# target sequence database:        /tmp/gapView.29383.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-117  378.4   0.4   3.9e-117  376.9   0.4    1.6  1  lcl|NCBI__GCF_000429985.1:WP_027179546.1  G496_RS0112275 fructose-1,6-bisp


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429985.1:WP_027179546.1  G496_RS0112275 fructose-1,6-bisphosphate aldolase, class II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  376.9   0.4  3.9e-117  3.9e-117       1     282 []       3     307 .]       3     307 .] 0.98

  Alignments for each domain:
  == domain 1  score: 376.9 bits;  conditional E-value: 3.9e-117
                                 TIGR01859   1 lvkakellekakkekYavgafninnlellqaileaaeeeksPvivqvsegavkYlggikvvvalvkali 69 
                                               lv+ ke+++ a++++Ya+gafn+nn+e++q i+ea+ eeksP+i+qvs ga+kY+g    +++l++a++
  lcl|NCBI__GCF_000429985.1:WP_027179546.1   3 LVSPKEMFKGAYTGGYAIGAFNVNNMEIIQGIIEAGTEEKSPLILQVSAGARKYAG-QGYIIKLMEAAL 70 
                                               7999***************************************************9.888999999999 PP

                                 TIGR01859  70 eklsivPvalhLDhGssyescikaikaGfssvmiDashlpleenlketkkvveiahakgvsveaelGkl 138
                                               +++  +Pv+lhLDhG+++e c k i+aGf+svmiD+shlp++en++ tkkvve+ah kg+ veaelG+l
  lcl|NCBI__GCF_000429985.1:WP_027179546.1  71 QDTD-LPVVLHLDHGQNFEICKKVIDAGFTSVMIDGSHLPFDENIAVTKKVVEYAHPKGIWVEAELGRL 138
                                               9888.**************************************************************** PP

                                 TIGR01859 139 gGieddvvekeaeladideakklvketgvDaLaiaiGtshG..kykgepkldferlkeikklln.lPlv 204
                                               +G+eddv ++e  ++d+dea ++v++tg D+LaiaiGtshG  k+ g+pkldf+rl++i+ l++  P+v
  lcl|NCBI__GCF_000429985.1:WP_027179546.1 139 AGVEDDVHSDEHIYTDPDEAVEFVEKTGCDSLAIAIGTSHGayKFSGKPKLDFDRLEKISSLMPdYPIV 207
                                               *****************************************8888899**************999**** PP

                                 TIGR01859 205 lhGas.....................Gipeeqlkkaiklgiakvnidtdlrlaftaairkvleekkdey 252
                                               lhGas                     G+pe+ l+ka++++++k+nidtd+rla+ta irk+l+e+ + +
  lcl|NCBI__GCF_000429985.1:WP_027179546.1 208 LHGASsvvqeyvqmanqyggniggakGVPEDLLRKAASMAVCKINIDTDIRLAMTAMIRKFLAENPEAF 276
                                               ********************************************************************* PP

                                 TIGR01859 253 dpRkilaparealkevvkekik.vlgsagka 282
                                               dpR +l++ar+a+k++v +kik vlgs+gka
  lcl|NCBI__GCF_000429985.1:WP_027179546.1 277 DPRGYLGEARKAVKDMVCHKIKnVLGSSGKA 307
                                               *********************989*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (282 nodes)
Target sequences:                          1  (307 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 3.09
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis