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.22289.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: 7.05
//
[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:

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:

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:

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:

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