Alignments for a candidate for fba in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for fba in Sinorhizobium meliloti 1021

Align Fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate SM_b20199 SM_b20199 fructose-1,6-bisphosphate aldolase

Query= SwissProt::Q56815
         (354 letters)



>FitnessBrowser__Smeli:SM_b20199
          Length = 359

 Score =  477 bits (1227), Expect = e-139
 Identities = 235/349 (67%), Positives = 282/349 (80%)

Query: 1   MALVSMRQLLDHAADDSYGLPAFNVNNMEQVKAIMDAARATSSPVILQGSAGARKYAGEP 60
           MA +++RQLLDHAA+ SYG+PAFN+NNMEQ  AIM+AARA+ +PVILQ S GAR YA + 
Sbjct: 1   MARITLRQLLDHAAERSYGVPAFNINNMEQGLAIMEAARASDAPVILQVSRGARSYANDV 60

Query: 61  FLRHLIAAAVEAYPEIPVVMHQDHGASPAVCMGAIKSGFSSVMMDGSLKEDGKTPADYDY 120
            L  ++ A  E YP+IP+ +HQDHG + A C+ AI+ GF+SVMMDGSLKED KTPADYDY
Sbjct: 61  MLAKMMEALEEMYPDIPLCIHQDHGNNVATCLTAIQHGFTSVMMDGSLKEDAKTPADYDY 120

Query: 121 NVSVTAKVVELAHAVGVSVEGELGCLGSLETGKGEAEDGHGAEEALDHSKLLTDPDEAAQ 180
           NVS+TA+V  LAH VG SVEGELGCLGSLETG GEAEDGHG E ALD S+LLTDPDEAA+
Sbjct: 121 NVSITAEVSRLAHMVGASVEGELGCLGSLETGHGEAEDGHGFEGALDRSQLLTDPDEAAR 180

Query: 181 FVKATQCDALAIAIGTSHGAYKFTRKPTGDILAIDRIKAIHQRIPTTHLVMHGSSSVPQE 240
           FV  T  DALA+AIGTSHGAYKFTRKPTG++LA+D I+ IH+R+P TH+VMHGSSSVPQE
Sbjct: 181 FVAETGVDALAVAIGTSHGAYKFTRKPTGEVLAMDVIEKIHERLPDTHIVMHGSSSVPQE 240

Query: 241 LLEEIRTYGGDIKETYGVPVEEIQEGIRYGVRKVNIDTDIRLAMTAAIRRVGAKNKSEFD 300
             +    +GG ++ETYGVPVEEI  GIR+GVRKVNIDTD+RLA  AA RRV   ++SEFD
Sbjct: 241 WQDVFNAHGGQMRETYGVPVEEIVRGIRFGVRKVNIDTDLRLAAAAAFRRVADTSRSEFD 300

Query: 301 PRKFMAAAMEEAKKVCIARFEAFGSAGKAEKIRAIELDEMAKRYASGEL 349
           PRKF+  AM+    VC ARFEAFG+AG A +I+ + + EMA+RYASG L
Sbjct: 301 PRKFLKPAMDAMSAVCKARFEAFGTAGNASRIKVVPMPEMARRYASGSL 349


Lambda     K      H
   0.316    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: 458
Number of extensions: 14
Number of successful extensions: 2
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: 354
Length of database: 359
Length adjustment: 29
Effective length of query: 325
Effective length of database: 330
Effective search space:   107250
Effective search space used:   107250
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 SM_b20199 SM_b20199 (fructose-1,6-bisphosphate aldolase)
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.carbon/TIGR01521.hmm
# target sequence database:        /tmp/gapView.16372.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   7.3e-220  715.0   0.6   8.2e-220  714.8   0.6    1.0  1  lcl|FitnessBrowser__Smeli:SM_b20199  SM_b20199 fructose-1,6-bisphosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SM_b20199  SM_b20199 fructose-1,6-bisphosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  714.8   0.6  8.2e-220  8.2e-220       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 714.8 bits;  conditional E-value: 8.2e-220
                            TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypdi 74 
                                          +i+lrqlldhaaer+ygvpafn+nn+eq laimeaa+++d+pvilq+srgarsya++v+l+k+++a++e+ypdi
  lcl|FitnessBrowser__Smeli:SM_b20199   3 RITLRQLLDHAAERSYGVPAFNINNMEQGLAIMEAARASDAPVILQVSRGARSYANDVMLAKMMEALEEMYPDI 76 
                                          69************************************************************************ PP

                            TIGR01521  75 pvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgsle 148
                                          p+++hqdhgn++atcl+aiq+gftsvmmdgslkedaktpadydynvs+taev++lah+vgasvegelgclgsle
  lcl|FitnessBrowser__Smeli:SM_b20199  77 PLCIHQDHGNNVATCLTAIQHGFTSVMMDGSLKEDAKTPADYDYNVSITAEVSRLAHMVGASVEGELGCLGSLE 150
                                          ************************************************************************** PP

                            TIGR01521 149 tgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeiherl 222
                                          tg+geaedghgfegaldrsqlltdp+eaa+fv++t+vdalavaigtshgaykftrkptgevla+d+ie+iherl
  lcl|FitnessBrowser__Smeli:SM_b20199 151 TGHGEAEDGHGFEGALDRSQLLTDPDEAARFVAETGVDALAVAIGTSHGAYKFTRKPTGEVLAMDVIEKIHERL 224
                                          ************************************************************************** PP

                            TIGR01521 223 pdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaakdpse 296
                                          pdth+vmhgsssvpqew+dv+n++gg+++etygvpveeiv+gi+fgvrkvnidtdlrlaa+aa+rrva++++se
  lcl|FitnessBrowser__Smeli:SM_b20199 225 PDTHIVMHGSSSVPQEWQDVFNAHGGQMRETYGVPVEEIVRGIRFGVRKVNIDTDLRLAAAAAFRRVADTSRSE 298
                                          ************************************************************************** PP

                            TIGR01521 297 fdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakgel 347
                                          fdprkflk+a++am++vckar+eafgtagnas+ikvv+++emarrya+g+l
  lcl|FitnessBrowser__Smeli:SM_b20199 299 FDPRKFLKPAMDAMSAVCKARFEAFGTAGNASRIKVVPMPEMARRYASGSL 349
                                          *************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (347 nodes)
Target sequences:                          1  (359 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: 10.40
//
[ok]

This GapMind analysis is from Sep 17 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