Alignments for a candidate for fbp in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for fbp in Echinicola vietnamensis KMM 6221, DSM 17526

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate Echvi_2849 Echvi_2849 fructose-bisphosphate aldolase, class II, yeast/E. coli subtype

Query= BRENDA::D0ZEE4
         (358 letters)



>FitnessBrowser__Cola:Echvi_2849
          Length = 353

 Score =  479 bits (1234), Expect = e-140
 Identities = 228/348 (65%), Positives = 279/348 (80%)

Query: 9   KPGVIFGDDVQKVFQVAKENKFALPAVNCVGTDSVNAVMEAAAKVRAPIIVQFSNGGAAF 68
           KPG+ FG++++ + + AKE++FALPAVN + T + NAV+E A KV +P+IVQFSNGGA F
Sbjct: 4   KPGIKFGEELKDLLEYAKESEFALPAVNVINTSTANAVLETAKKVNSPVIVQFSNGGAQF 63

Query: 69  IAGKGLKLEGQQAAILGAISGAHHVHQMAEYYGVPVILHTDHCAKKLLPWLDGLLDAGEK 128
            AGKGL  + QQA+I GA+SGA HVH+MAE YGVPVILHTDH AKKL+PW+DG+L+AG++
Sbjct: 64  FAGKGLANDKQQASIAGAVSGAMHVHKMAEAYGVPVILHTDHAAKKLIPWVDGMLEAGKE 123

Query: 129 HFAATGKPLFSSHMIDLSEESLEENIEICSQYLARMSKIGMTLELELGCTGGEEDGVDNS 188
           ++AA  KPLFSSHM+DLSEE +EENIE   +YLA   K+ M LE+ELG TGGEEDGVDN+
Sbjct: 124 YYAAFKKPLFSSHMLDLSEEPIEENIETSVKYLAEFKKLEMALEIELGVTGGEEDGVDNT 183

Query: 189 HLDNSALYTQPEDVDYAFTKLSAISPRFTIAASFGNVHGVYKPGNVQLTPVILKNSQEYV 248
            +D+S LYTQPE+V YA+ KL   S  FTIAA+FGNVHGVYKPGNV L P ILKNSQ+Y+
Sbjct: 184 DIDSSKLYTQPEEVAYAYEKLREQSELFTIAAAFGNVHGVYKPGNVSLQPKILKNSQDYI 243

Query: 249 SKKHNLPHNSLNFVFHGGSGSTAAEIKEAVSYGVVKMNIDTDTQWATWEGVLKYYKKNEG 308
            +K  L    ++FVFHGGSGS+  EI+EA  YG +KMNIDTD QWA WEGVLKYYK+NEG
Sbjct: 244 CEKFGLSGKPVSFVFHGGSGSSVEEIREATGYGSIKMNIDTDMQWAFWEGVLKYYKENEG 303

Query: 309 YLQGQLGNPEGDDKPNKKYYDPRVWLRAGQTGMIERLELAFKELNCID 356
           YLQ QLGNPEG D PNKK YDPRVWLR G+   ++RLE+AF  LN +D
Sbjct: 304 YLQTQLGNPEGPDVPNKKKYDPRVWLRKGEENFVKRLEVAFDMLNAVD 351


Lambda     K      H
   0.317    0.135    0.400 

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: 414
Number of extensions: 10
Number of successful extensions: 1
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: 358
Length of database: 353
Length adjustment: 29
Effective length of query: 329
Effective length of database: 324
Effective search space:   106596
Effective search space used:   106596
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: 49 (23.5 bits)

Align candidate Echvi_2849 Echvi_2849 (fructose-bisphosphate aldolase, class II, yeast/E. coli subtype)
to HMM TIGR01520 (fbaA: fructose-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/TIGR01520.hmm
# target sequence database:        /tmp/gapView.3845.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01520  [M=357]
Accession:   TIGR01520
Description: FruBisAldo_II_A: fructose-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   2.3e-169  549.0   0.6   2.6e-169  548.8   0.6    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2849  Echvi_2849 fructose-bisphosphate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2849  Echvi_2849 fructose-bisphosphate aldolase, class II, yeast/E. coli subtype
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  548.8   0.6  2.6e-169  2.6e-169       5     356 ..       3     352 ..       1     353 [] 0.99

  Alignments for each domain:
  == domain 1  score: 548.8 bits;  conditional E-value: 2.6e-169
                            TIGR01520   5 lktgvilgedvaklfevakeekfaiPainvvssetvnaaleaardakspiilqfsnggaafiaGkGvkdeaeka 78 
                                           k+g+  ge++++l+e+ake +fa+Pa+nv+ ++t+na+le+a++++sp+i+qfsngga+f+aGkG+ +++++a
  lcl|FitnessBrowser__Cola:Echvi_2849   3 FKPGIKFGEELKDLLEYAKESEFALPAVNVINTSTANAVLETAKKVNSPVIVQFSNGGAQFFAGKGLANDKQQA 76 
                                          689********************************************************************999 PP

                            TIGR01520  79 asiaGaiaaaeyvrsiaekygvpvvlhtdhCakkllpyvdglleadekyfkkegkPlfsshmldlseepieeni 152
                                           siaGa+++a++v+++ae+ygvpv+lhtdh akkl+p+vdg+lea+++y+++ +kPlfsshmldlseepieeni
  lcl|FitnessBrowser__Cola:Echvi_2849  77 -SIAGAVSGAMHVHKMAEAYGVPVILHTDHAAKKLIPWVDGMLEAGKEYYAAFKKPLFSSHMLDLSEEPIEENI 149
                                          .************************************************************************* PP

                            TIGR01520 153 eiakkylkrmakiklileieiGitGGeedGvdneeadkeelytkPedvekvyeelskispkfsiaaafGnvhGv 226
                                          e+++kyl    k+++ leie+G+tGGeedGvdn + d+++lyt+Pe+v ++ye+l++ s  f+iaaafGnvhGv
  lcl|FitnessBrowser__Cola:Echvi_2849 150 ETSVKYLAEFKKLEMALEIELGVTGGEEDGVDNTDIDSSKLYTQPEEVAYAYEKLREQSELFTIAAAFGNVHGV 223
                                          ************************************************************************** PP

                            TIGR01520 227 ykpGnvklrPdiladgqeyvaeklglkeakplsfvfhGGsGstkeeikealsyGvvkvnvdtdtqyaalegild 300
                                          ykpGnv l+P+il+++q+y+ ek gl   kp+sfvfhGGsGs++eei+ea  yG +k+n+dtd+q+a++eg+l+
  lcl|FitnessBrowser__Cola:Echvi_2849 224 YKPGNVSLQPKILKNSQDYICEKFGLS-GKPVSFVFHGGSGSSVEEIREATGYGSIKMNIDTDMQWAFWEGVLK 296
                                          **************************9.9********************************************* PP

                            TIGR01520 301 yvlknedylqsqvGnpkgeekpnkkvydPrvwlreaeksmkarvekaleelnaink 356
                                          y+++ne ylq+q+Gnp+g+++pnkk+ydPrvwlr++e+   +r+e a++ lna+++
  lcl|FitnessBrowser__Cola:Echvi_2849 297 YYKENEGYLQTQLGNPEGPDVPNKKKYDPRVWLRKGEENFVKRLEVAFDMLNAVDR 352
                                          ****************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (357 nodes)
Target sequences:                          1  (353 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.64
//
[ok]

This GapMind analysis is from Apr 09 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