Alignments for a candidate for fbp in Heliobacterium modesticaldum Ice1; ATCC 51547

GapMind for Amino acid biosynthesis

Alignments for a candidate for fbp in Heliobacterium modesticaldum Ice1; ATCC 51547

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_012282027.1 HM1_RS04085 fructose-1,6-bisphosphate aldolase, class II

Query= BRENDA::Q9RHA2
         (305 letters)



>NCBI__GCF_000019165.1:WP_012282027.1
          Length = 284

 Score =  278 bits (712), Expect = 8e-80
 Identities = 150/305 (49%), Positives = 203/305 (66%), Gaps = 24/305 (7%)

Query: 2   LVTGLEILKKAREEGYGVGAFNVNNMEFLQAVLEAAEEQRSPVILALSEGAMKYGGRALT 61
           LV   ++L  A E  Y VGAFN NNME +QA++ AAE +R+PVI+  S+GA+KY G    
Sbjct: 3   LVPVSQLLAAAEEGKYAVGAFNCNNMEIVQAIVAAAEAERAPVIIQASQGAIKYAGLEYI 62

Query: 62  LMAVELAKE-ARVPVAVHLDHGSSYESVLRALRAGFTSVMIDKSHEDFETNVRETRRVVE 120
           +    LA E A VPVA+HLDHG+S+   ++ +R+GFTSVMID S    E N+  T RV+E
Sbjct: 63  VALARLAGETASVPVALHLDHGTSFAQCIQCIRSGFTSVMIDGSKYPLEENIALTNRVLE 122

Query: 121 AAHAVGVTVEAELGRLAGIEEHVAVDEKDALLTNPEEARIFMERTGADYLAVAIGTSHGA 180
            A AVGV+VEAELG++ G E+ + VDE+DA  T+P EA+ F++ T  D LAVAIGT+HG 
Sbjct: 123 VARAVGVSVEAELGKIGGTEDDIHVDERDAFFTDPAEAKQFVDATKVDALAVAIGTAHGQ 182

Query: 181 YKGKGRPFIDHARLERIARLVPAPLVLHGASAVPPELVERFRASGGEIGEAAGIHPEDIK 240
           Y  KGRP +D  RL +I +LV  P+VLHG+S VP                      EDI+
Sbjct: 183 Y--KGRPELDFDRLAKIRQLVNIPIVLHGSSGVP---------------------EEDIQ 219

Query: 241 KAISLGIAKINTDTDLRLAFTALIREALNKNPKEFDPRKYLGPAREAVKEVVKSRMELFG 300
           KAI+LG+ K+N DT+LR AF   ++EA+ KNP+E DPRK LGPA+  + EV++ ++ +FG
Sbjct: 220 KAITLGVRKVNIDTNLREAFVDGVKEAIEKNPREIDPRKILGPAKLKMSEVIREKIRIFG 279

Query: 301 SVGRA 305
           S G+A
Sbjct: 280 SNGKA 284


Lambda     K      H
   0.317    0.134    0.369 

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: 269
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: 305
Length of database: 284
Length adjustment: 26
Effective length of query: 279
Effective length of database: 258
Effective search space:    71982
Effective search space used:    71982
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: 48 (23.1 bits)

Align candidate WP_012282027.1 HM1_RS04085 (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.17461.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     3e-122  393.7   0.6   3.4e-122  393.5   0.6    1.0  1  lcl|NCBI__GCF_000019165.1:WP_012282027.1  HM1_RS04085 fructose-1,6-bisphos


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019165.1:WP_012282027.1  HM1_RS04085 fructose-1,6-bisphosphate aldolase, class II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.5   0.6  3.4e-122  3.4e-122       1     282 []       3     284 .]       3     284 .] 0.98

  Alignments for each domain:
  == domain 1  score: 393.5 bits;  conditional E-value: 3.4e-122
                                 TIGR01859   1 lvkakellekakkekYavgafninnlellqaileaaeeeksPvivqvsegavkYlggikvvvalvkali 69 
                                               lv + +ll++a+++kYavgafn nn+e++qai+ aae+e++Pvi+q+s+ga+kY+g ++ +val + + 
  lcl|NCBI__GCF_000019165.1:WP_012282027.1   3 LVPVSQLLAAAEEGKYAVGAFNCNNMEIVQAIVAAAEAERAPVIIQASQGAIKYAG-LEYIVALARLAG 70 
                                               678899*************************************************9.999999988777 PP

                                 TIGR01859  70 eklsivPvalhLDhGssyescikaikaGfssvmiDashlpleenlketkkvveiahakgvsveaelGkl 138
                                               e++s vPvalhLDhG+s+ +ci++i++Gf+svmiD+s++pleen+++t++v+e+a+a gvsveaelGk+
  lcl|NCBI__GCF_000019165.1:WP_012282027.1  71 ETAS-VPVALHLDHGTSFAQCIQCIRSGFTSVMIDGSKYPLEENIALTNRVLEVARAVGVSVEAELGKI 138
                                               7777.**************************************************************** PP

                                 TIGR01859 139 gGiedd..vvekeaeladideakklvketgvDaLaiaiGtshGkykgepkldferlkeikkllnlPlvl 205
                                               gG+edd  v+e++a ++d+ eak++v+ t+vDaLa+aiGt+hG+ykg+p+ldf+rl++i++l+n+P+vl
  lcl|NCBI__GCF_000019165.1:WP_012282027.1 139 GGTEDDihVDERDAFFTDPAEAKQFVDATKVDALAVAIGTAHGQYKGRPELDFDRLAKIRQLVNIPIVL 207
                                               *****98899*********************************************************** PP

                                 TIGR01859 206 hGasGipeeqlkkaiklgiakvnidtdlrlaftaairkvleekkdeydpRkilaparealkevvkekik 274
                                               hG+sG+pee+++kai+lg+ kvnidt+lr af++ +++ +e++  e+dpRkil+pa+ +++ev++eki+
  lcl|NCBI__GCF_000019165.1:WP_012282027.1 208 HGSSGVPEEDIQKAITLGVRKVNIDTNLREAFVDGVKEAIEKNPREIDPRKILGPAKLKMSEVIREKIR 276
                                               ********************************************************************* PP

                                 TIGR01859 275 vlgsagka 282
                                               ++gs+gka
  lcl|NCBI__GCF_000019165.1:WP_012282027.1 277 IFGSNGKA 284
                                               ******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (282 nodes)
Target sequences:                          1  (284 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.15
//
[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