Alignments for a candidate for fbp in Methylobacterium nodulans ORS 2060

GapMind for Amino acid biosynthesis

Alignments for a candidate for fbp in Methylobacterium nodulans ORS 2060

Align Fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate WP_015933583.1 MNOD_RS34455 fructose-bisphosphate aldolase class II

Query= SwissProt::Q8YNK2
         (359 letters)



>NCBI__GCF_000022085.1:WP_015933583.1
          Length = 362

 Score =  466 bits (1198), Expect = e-136
 Identities = 233/362 (64%), Positives = 285/362 (78%), Gaps = 4/362 (1%)

Query: 1   MALVPLRLLLDHAAENGYGIPAFNVNNLEQIQAILKAAAETDSPVILQASRGARNYAGEN 60
           MA + LR LLDHAAE+GYG+PAFN+NN+EQ  AI+ AA   D+PVILQASRGAR YA + 
Sbjct: 1   MARITLRQLLDHAAEHGYGVPAFNINNMEQGLAIMTAADACDAPVILQASRGARAYANDV 60

Query: 61  FLRHLILAAVETYPEIPIVMHQDHGNAPSTCYSAIKNNFTSVMMDGSLEADAKTPASFEY 120
            L  LI   VE YP IP+ MH DHGN  +TC +AI+  FTSVMMDGSL+AD KTPA + Y
Sbjct: 61  ILAKLIDGLVEIYPHIPVCMHLDHGNNEATCATAIQYGFTSVMMDGSLKADGKTPADYAY 120

Query: 121 NVNVTREVVNVAHALGVSVEGELGCLGSLETGAGEAEDGHGFEGTLDHSQLLTDPDEAVN 180
           NV +TR+V  +AH  GVSVEGELG LGSLE+G GEAEDGHG EG L H QLLTDPDEAV 
Sbjct: 121 NVEITRKVAEMAHWAGVSVEGELGVLGSLESGKGEAEDGHGAEGALSHDQLLTDPDEAVK 180

Query: 181 FVEATQVDALAVAIGTSHGAYKFTRKPTGEILAISRIEEIHRRLPNTHLVMHGSSSVPED 240
           FV+AT+VDALAVA+GTSHGAYKFTRKP G +LA+  IEEI+RRLPNTHLVMHGSSSVP++
Sbjct: 181 FVQATKVDALAVAMGTSHGAYKFTRKPDGAVLAMHVIEEINRRLPNTHLVMHGSSSVPQE 240

Query: 241 LIALINEYGGAIPETYGVPVEEIQKGIKSGVRKVNIDTDNRLAITAAVREALAKNPKEFD 300
           L  +IN+YGG +  T+GVPVEEIQ+GIK GVRK+NIDTDNR+A+T  +R+ L +N  EFD
Sbjct: 241 LQDIINQYGGEMKPTWGVPVEEIQRGIKHGVRKINIDTDNRMAMTGQIRKVLTENKAEFD 300

Query: 301 PRHFLKPSITYMQKVCAERYVQFGTAGNASKIKQVSLETFAAKYAKGELN----AISKAA 356
           PR +LKP++  M K+C +R+ +FGTAG+A KI+ +SL   A +YA G+L+    +  KAA
Sbjct: 301 PRKYLKPAMEAMTKLCKQRFEEFGTAGHAGKIRPISLSEMAKRYASGKLDPSFGSKQKAA 360

Query: 357 AK 358
           A+
Sbjct: 361 AE 362


Lambda     K      H
   0.315    0.132    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: 493
Number of extensions: 17
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: 359
Length of database: 362
Length adjustment: 29
Effective length of query: 330
Effective length of database: 333
Effective search space:   109890
Effective search space used:   109890
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 WP_015933583.1 MNOD_RS34455 (fructose-bisphosphate aldolase class II)
to HMM TIGR01521 (fba: fructose-bisphosphate aldolase, class II, Calvin cycle subtype (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/TIGR01521.hmm
# target sequence database:        /tmp/gapView.727514.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01521  [M=347]
Accession:   TIGR01521
Description: FruBisAldo_II_B: fructose-bisphosphate aldolase, class II, Calvin cycle subtype
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.3e-192  623.4   0.7   6.1e-192  623.2   0.7    1.0  1  NCBI__GCF_000022085.1:WP_015933583.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000022085.1:WP_015933583.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  623.2   0.7  6.1e-192  6.1e-192       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 623.2 bits;  conditional E-value: 6.1e-192
                             TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypd 73 
                                           +i+lrqlldhaae+gygvpafn+nn+eq laim aad++d+pvilqasrgar ya++v+l+kl+ ++ve yp+
  NCBI__GCF_000022085.1:WP_015933583.1   3 RITLRQLLDHAAEHGYGVPAFNINNMEQGLAIMTAADACDAPVILQASRGARAYANDVILAKLIDGLVEIYPH 75 
                                           69*********************************************************************** PP

                             TIGR01521  74 ipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgs 146
                                           ipv++h dhgn+ atc +aiq gftsvmmdgslk+d+ktpady ynv++t +v+++ah  g+svegelg lgs
  NCBI__GCF_000022085.1:WP_015933583.1  76 IPVCMHLDHGNNEATCATAIQYGFTSVMMDGSLKADGKTPADYAYNVEITRKVAEMAHWAGVSVEGELGVLGS 148
                                           ************************************************************************* PP

                             TIGR01521 147 letgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeih 219
                                           le+gkgeaedghg+egal + qlltdp+ea++fv+ tkvdalava+gtshgaykftrkp g vla+++ieei 
  NCBI__GCF_000022085.1:WP_015933583.1 149 LESGKGEAEDGHGAEGALSHDQLLTDPDEAVKFVQATKVDALAVAMGTSHGAYKFTRKPDGAVLAMHVIEEIN 221
                                           ************************************************************************* PP

                             TIGR01521 220 erlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaak 292
                                           +rlp+thlvmhgsssvpqe +d+in+ygge+k t+gvpveei++gik+gvrk+nidtd+r+a+t+ +r+v+++
  NCBI__GCF_000022085.1:WP_015933583.1 222 RRLPNTHLVMHGSSSVPQELQDIINQYGGEMKPTWGVPVEEIQRGIKHGVRKINIDTDNRMAMTGQIRKVLTE 294
                                           ************************************************************************* PP

                             TIGR01521 293 dpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakgel 347
                                           ++ efdprk+lk+a+eam ++ck+r+e+fgtag a ki+++sl ema+rya+g+l
  NCBI__GCF_000022085.1:WP_015933583.1 295 NKAEFDPRKYLKPAMEAMTKLCKQRFEEFGTAGHAGKIRPISLSEMAKRYASGKL 349
                                           *****************************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (347 nodes)
Target sequences:                          1  (362 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: 21.43
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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