GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Paraburkholderia bryophila 376MFSha3.1

Align Fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate H281DRAFT_01311 H281DRAFT_01311 fructose-bisphosphate aldolase

Query= SwissProt::Q56815
         (354 letters)



>FitnessBrowser__Burk376:H281DRAFT_01311
          Length = 345

 Score =  474 bits (1220), Expect = e-138
 Identities = 239/344 (69%), Positives = 280/344 (81%)

Query: 1   MALVSMRQLLDHAADDSYGLPAFNVNNMEQVKAIMDAARATSSPVILQGSAGARKYAGEP 60
           MA +++RQLLDHAA+  YG+PAFNVNNMEQ+ AIM AA  T+SPVILQ SAGARKYAGEP
Sbjct: 1   MAFIALRQLLDHAAEHGYGVPAFNVNNMEQIHAIMQAAEETASPVILQASAGARKYAGEP 60

Query: 61  FLRHLIAAAVEAYPEIPVVMHQDHGASPAVCMGAIKSGFSSVMMDGSLKEDGKTPADYDY 120
           +LRHL+ AA+EA+P+IP+V+HQDHGASPAVC  AI+SGF+SVMMDGSL  D KTPA YDY
Sbjct: 61  YLRHLVLAALEAHPDIPLVLHQDHGASPAVCQQAIRSGFTSVMMDGSLLPDQKTPATYDY 120

Query: 121 NVSVTAKVVELAHAVGVSVEGELGCLGSLETGKGEAEDGHGAEEALDHSKLLTDPDEAAQ 180
           NV V+ +VV+ AHAVGVSVEGELGCLGSLETG    EDG GA+  L    LLTDP EA  
Sbjct: 121 NVEVSRRVVDAAHAVGVSVEGELGCLGSLETGMAGEEDGVGAQGQLTRDDLLTDPREAQI 180

Query: 181 FVKATQCDALAIAIGTSHGAYKFTRKPTGDILAIDRIKAIHQRIPTTHLVMHGSSSVPQE 240
           FV++T  DALAIAIGTSHGAYKF+R+PTGDILAI RI  IH+RIP THLVMHGSSSVPQE
Sbjct: 181 FVESTGVDALAIAIGTSHGAYKFSREPTGDILAIGRIVEIHERIPNTHLVMHGSSSVPQE 240

Query: 241 LLEEIRTYGGDIKETYGVPVEEIQEGIRYGVRKVNIDTDIRLAMTAAIRRVGAKNKSEFD 300
            L  IR +GG+I  TYGVPVEEIQ GI +GVRKVNIDTDIRLAM+ A+R+  A  ++EFD
Sbjct: 241 WLAIIREFGGEIPTTYGVPVEEIQRGIAHGVRKVNIDTDIRLAMSGAMRKSLANARAEFD 300

Query: 301 PRKFMAAAMEEAKKVCIARFEAFGSAGKAEKIRAIELDEMAKRY 344
           PR  + AA   A+ VC+ RFEAFG AG+A +I+ + LD MA+RY
Sbjct: 301 PRAALKAATAAARGVCVERFEAFGCAGQAPRIKPLPLDAMARRY 344


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: 446
Number of extensions: 11
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: 354
Length of database: 345
Length adjustment: 29
Effective length of query: 325
Effective length of database: 316
Effective search space:   102700
Effective search space used:   102700
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 H281DRAFT_01311 H281DRAFT_01311 (fructose-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.21356.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
     6e-182  590.3   0.1   6.8e-182  590.1   0.1    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_01311  H281DRAFT_01311 fructose-bisphos


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_01311  H281DRAFT_01311 fructose-bisphosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  590.1   0.1  6.8e-182  6.8e-182       2     342 ..       4     344 ..       3     345 .] 1.00

  Alignments for each domain:
  == domain 1  score: 590.1 bits;  conditional E-value: 6.8e-182
                                    TIGR01521   2 islrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaa 67 
                                                  i+lrqlldhaae+gygvpafnvnn+eqi aim+aa++t spvilqas+gar+yage++lr+lvlaa
  lcl|FitnessBrowser__Burk376:H281DRAFT_01311   4 IALRQLLDHAAEHGYGVPAFNVNNMEQIHAIMQAAEETASPVILQASAGARKYAGEPYLRHLVLAA 69 
                                                  89**************************************************************** PP

                                    TIGR01521  68 veeypdipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahav 133
                                                   e +pdip+vlhqdhg+spa+c++ai+ gftsvmmdgsl  d ktpa ydynv+v+ +vv  ahav
  lcl|FitnessBrowser__Burk376:H281DRAFT_01311  70 LEAHPDIPLVLHQDHGASPAVCQQAIRSGFTSVMMDGSLLPDQKTPATYDYNVEVSRRVVDAAHAV 135
                                                  ****************************************************************** PP

                                    TIGR01521 134 gasvegelgclgsletgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgay 199
                                                  g+svegelgclgsletg++++edg+g++g+l r +lltdp ea  fv+ t+vdala+aigtshgay
  lcl|FitnessBrowser__Burk376:H281DRAFT_01311 136 GVSVEGELGCLGSLETGMAGEEDGVGAQGQLTRDDLLTDPREAQIFVESTGVDALAIAIGTSHGAY 201
                                                  ****************************************************************** PP

                                    TIGR01521 200 kftrkptgevlaidrieeiherlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgi 265
                                                  kf+r+ptg++lai ri eiher+p+thlvmhgsssvpqewl++i e+ggei+ tygvpveei++gi
  lcl|FitnessBrowser__Burk376:H281DRAFT_01311 202 KFSREPTGDILAIGRIVEIHERIPNTHLVMHGSSSVPQEWLAIIREFGGEIPTTYGVPVEEIQRGI 267
                                                  ****************************************************************** PP

                                    TIGR01521 266 kfgvrkvnidtdlrlaataalrrvaakdpsefdprkflkkaveamkdvckaryeafgtagnaskik 331
                                                   +gvrkvnidtd rla+++a+r+ +a+ + efdpr  lk a  a + vc++r+eafg ag+a +ik
  lcl|FitnessBrowser__Burk376:H281DRAFT_01311 268 AHGVRKVNIDTDIRLAMSGAMRKSLANARAEFDPRAALKAATAAARGVCVERFEAFGCAGQAPRIK 333
                                                  ****************************************************************** PP

                                    TIGR01521 332 vvsleemarry 342
                                                  +++l+ marry
  lcl|FitnessBrowser__Burk376:H281DRAFT_01311 334 PLPLDAMARRY 344
                                                  **********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (347 nodes)
Target sequences:                          1  (345 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: 00:00:00.03
# Mc/sec: 3.62
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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