GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Shewanella amazonensis SB2B

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate 6938653 Sama_2756 fructose-1,6-bisphosphate aldolase (RefSeq)

Query= BRENDA::Q602L6
         (354 letters)



>FitnessBrowser__SB2B:6938653
          Length = 355

 Score =  504 bits (1297), Expect = e-147
 Identities = 249/351 (70%), Positives = 284/351 (80%)

Query: 1   MALISLRQLLDHAAEHGYGLPAFNVNNMEQIKAIMEAASAVDAPVILQGSAGARTYAGEP 60
           MALISLRQLLDHAAEHGYG+PAFNVNN+EQ++AIM+AA A D+PVI+Q SAGAR YA   
Sbjct: 1   MALISLRQLLDHAAEHGYGVPAFNVNNLEQMRAIMQAAEATDSPVIVQASAGARKYARPQ 60

Query: 61  FLRHLVRAAIEMYPHIPVCMHQDHGASPAVCIRSIQSGFSSVMMDGSLLEDMKTPASYAY 120
           FL++L+ AA+E YP IPVC+HQDHG  P VC RSIQ G SSVMMDGSL+ D KTPASY Y
Sbjct: 61  FLKYLMNAALEQYPDIPVCIHQDHGTHPDVCQRSIQLGMSSVMMDGSLMSDGKTPASYDY 120

Query: 121 NVETTRKVVEMAHACGVSVEGELGCLGSLETGRAGKEDGHGAEGELDHSLLLTDPDEAAD 180
           NV+ TRK V  AHACGVSVEGE+GCLGSLETG AG+EDG GA G L H  LLT  +EAA 
Sbjct: 121 NVDVTRKTVAFAHACGVSVEGEIGCLGSLETGTAGEEDGIGAVGVLSHDQLLTTAEEAAR 180

Query: 181 FVRQTQVDALAIAIGTSHGAYKFTRKPTGQVLRIDRVKAIHQRIPTIHLVMHGSSSVPEE 240
           FV  T VDALAIAIGTSHGAYKF+RKPTG VLRIDR+K IH RIP  HLVMHGSSSVP+ 
Sbjct: 181 FVADTHVDALAIAIGTSHGAYKFSRKPTGDVLRIDRIKEIHARIPNTHLVMHGSSSVPQY 240

Query: 241 WAQMINDYGGDIGQTYGVPVEEIVEGIRHGVRKVNIDTDLRIASYGAMRRFMVEDRKNFD 300
           W ++IN YGG+I +TYGVP+EEIVEGI+HGVRKVNIDTDLR+AS GA+R+F+ E+   FD
Sbjct: 241 WLEIINQYGGEIPETYGVPLEEIVEGIKHGVRKVNIDTDLRLASTGAVRKFLAENPSEFD 300

Query: 301 PRKLYKAAQTAMTAICRARYEAFGAAGQAAKIKPLRLEDMSLAYAQGKLDP 351
           PRK  KA+  AM  IC  RYEAFG AG A+KIKPL L+ M   Y  G+LDP
Sbjct: 301 PRKFLKASMEAMADICTERYEAFGCAGMASKIKPLSLQAMYKRYQTGELDP 351


Lambda     K      H
   0.320    0.134    0.391 

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: 486
Number of extensions: 18
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: 355
Length adjustment: 29
Effective length of query: 325
Effective length of database: 326
Effective search space:   105950
Effective search space used:   105950
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate 6938653 Sama_2756 (fructose-1,6-bisphosphate aldolase (RefSeq))
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.2574.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     3e-195  634.1   0.2   3.3e-195  633.9   0.2    1.0  1  lcl|FitnessBrowser__SB2B:6938653  Sama_2756 fructose-1,6-bisphosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6938653  Sama_2756 fructose-1,6-bisphosphate aldolase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  633.9   0.2  3.3e-195  3.3e-195       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 633.9 bits;  conditional E-value: 3.3e-195
                         TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypdipvv 77 
                                       lislrqlldhaae+gygvpafnvnnleq++aim+aa++tdspvi+qas+gar+ya  ++l+ l+ aa e+ypdipv+
  lcl|FitnessBrowser__SB2B:6938653   3 LISLRQLLDHAAEHGYGVPAFNVNNLEQMRAIMQAAEATDSPVIVQASAGARKYARPQFLKYLMNAALEQYPDIPVC 79 
                                       69*************************************************************************** PP

                         TIGR01521  78 lhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgsletgkgea 154
                                       +hqdhg+ p++c+++iqlg++svmmdgsl  d+ktpa+ydynv+vt ++v++aha+g+svege+gclgsletg++++
  lcl|FitnessBrowser__SB2B:6938653  80 IHQDHGTHPDVCQRSIQLGMSSVMMDGSLMSDGKTPASYDYNVDVTRKTVAFAHACGVSVEGEIGCLGSLETGTAGE 156
                                       ***************************************************************************** PP

                         TIGR01521 155 edghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeiherlpdthlvmhg 231
                                       edg g+ g+l + qllt  eeaa+fv++t+vdala+aigtshgaykf+rkptg+vl idri+eih+r+p+thlvmhg
  lcl|FitnessBrowser__SB2B:6938653 157 EDGIGAVGVLSHDQLLTTAEEAARFVADTHVDALAIAIGTSHGAYKFSRKPTGDVLRIDRIKEIHARIPNTHLVMHG 233
                                       ***************************************************************************** PP

                         TIGR01521 232 sssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaakdpsefdprkflkkave 308
                                       sssvpq wl++in+yggei+etygvp+eeiv+gik+gvrkvnidtdlrla+t+a+r+++a++psefdprkflk ++e
  lcl|FitnessBrowser__SB2B:6938653 234 SSSVPQYWLEIINQYGGEIPETYGVPLEEIVEGIKHGVRKVNIDTDLRLASTGAVRKFLAENPSEFDPRKFLKASME 310
                                       ***************************************************************************** PP

                         TIGR01521 309 amkdvckaryeafgtagnaskikvvsleemarryakgel 347
                                       am d+c++ryeafg ag askik++sl+ m++ry  gel
  lcl|FitnessBrowser__SB2B:6938653 311 AMADICTERYEAFGCAGMASKIKPLSLQAMYKRYQTGEL 349
                                       *************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (347 nodes)
Target sequences:                          1  (355 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 11.60
//
[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