GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Snodgrassella alvi wkB2

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_025331513.1 SALWKB2_RS09870 fructose-bisphosphate aldolase class II

Query= BRENDA::Q602L6
         (354 letters)



>NCBI__GCF_000600005.1:WP_025331513.1
          Length = 354

 Score =  509 bits (1310), Expect = e-149
 Identities = 251/354 (70%), Positives = 294/354 (83%)

Query: 1   MALISLRQLLDHAAEHGYGLPAFNVNNMEQIKAIMEAASAVDAPVILQGSAGARTYAGEP 60
           MAL+S+RQLLDHAAE+ YGLPAFNVNN+EQ++AIMEAA  V+APVI+Q SAGAR YAG P
Sbjct: 1   MALVSMRQLLDHAAENSYGLPAFNVNNLEQMRAIMEAADEVNAPVIVQASAGARKYAGAP 60

Query: 61  FLRHLVRAAIEMYPHIPVCMHQDHGASPAVCIRSIQSGFSSVMMDGSLLEDMKTPASYAY 120
           FLRHL+ AAIE +PHIPV MHQDHGASP VC RSIQ GFSSVMMDGSLL D KTP++Y Y
Sbjct: 61  FLRHLILAAIEEFPHIPVVMHQDHGASPEVCQRSIQLGFSSVMMDGSLLSDAKTPSTYEY 120

Query: 121 NVETTRKVVEMAHACGVSVEGELGCLGSLETGRAGKEDGHGAEGELDHSLLLTDPDEAAD 180
           NV+ TRK V MAHACGVSVEGE+GCLG+LETG AG+EDG GA G+L H  +LT  DEAA 
Sbjct: 121 NVDVTRKTVYMAHACGVSVEGEIGCLGNLETGDAGEEDGVGAAGKLSHEQMLTSVDEAAR 180

Query: 181 FVRQTQVDALAIAIGTSHGAYKFTRKPTGQVLRIDRVKAIHQRIPTIHLVMHGSSSVPEE 240
           FV+ T VDALAIAIGTSHGAYKFTRKPTG+VLRIDR++ IH+R+P  HLVMHGSSSVP+E
Sbjct: 181 FVQDTGVDALAIAIGTSHGAYKFTRKPTGEVLRIDRIREIHERLPNTHLVMHGSSSVPQE 240

Query: 241 WAQMINDYGGDIGQTYGVPVEEIVEGIRHGVRKVNIDTDLRIASYGAMRRFMVEDRKNFD 300
           W Q+IN++GG+I +TYGVPVEEIVEGI++GVRKVNIDTDLR+AS GA+RRF+      FD
Sbjct: 241 WLQVINEFGGNIPETYGVPVEEIVEGIKYGVRKVNIDTDLRLASTGAIRRFLATHPAEFD 300

Query: 301 PRKLYKAAQTAMTAICRARYEAFGAAGQAAKIKPLRLEDMSLAYAQGKLDPIVR 354
           PRK +     AM  +C  RY AFGAAG A++IKP+ LE M+  YA G+L  IV+
Sbjct: 301 PRKYFTETIKAMKQVCIDRYVAFGAAGHASQIKPISLEKMANRYAAGELVQIVK 354


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: 493
Number of extensions: 13
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: 354
Length adjustment: 29
Effective length of query: 325
Effective length of database: 325
Effective search space:   105625
Effective search space used:   105625
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 WP_025331513.1 SALWKB2_RS09870 (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.carbon/TIGR01521.hmm
# target sequence database:        /tmp/gapView.1531118.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.5e-199  647.0   0.3     4e-199  646.8   0.3    1.0  1  NCBI__GCF_000600005.1:WP_025331513.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000600005.1:WP_025331513.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  646.8   0.3    4e-199    4e-199       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 646.8 bits;  conditional E-value: 4e-199
                             TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypd 73 
                                           l+s+rqlldhaae++yg+pafnvnnleq++aimeaad+ ++pvi+qas+gar+yag+++lr+l+laa+ee+p+
  NCBI__GCF_000600005.1:WP_025331513.1   3 LVSMRQLLDHAAENSYGLPAFNVNNLEQMRAIMEAADEVNAPVIVQASAGARKYAGAPFLRHLILAAIEEFPH 75 
                                           69*********************************************************************** PP

                             TIGR01521  74 ipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgs 146
                                           ipvv+hqdhg+sp++c+++iqlgf+svmmdgsl  daktp+ y+ynv+vt ++v +aha+g+svege+gclg 
  NCBI__GCF_000600005.1:WP_025331513.1  76 IPVVMHQDHGASPEVCQRSIQLGFSSVMMDGSLLSDAKTPSTYEYNVDVTRKTVYMAHACGVSVEGEIGCLGN 148
                                           ************************************************************************* PP

                             TIGR01521 147 letgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeih 219
                                           letg +++edg+g+ g+l + q+lt  +eaa+fv++t+vdala+aigtshgaykftrkptgevl idri+eih
  NCBI__GCF_000600005.1:WP_025331513.1 149 LETGDAGEEDGVGAAGKLSHEQMLTSVDEAARFVQDTGVDALAIAIGTSHGAYKFTRKPTGEVLRIDRIREIH 221
                                           ************************************************************************* PP

                             TIGR01521 220 erlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaak 292
                                           erlp+thlvmhgsssvpqewl+vine+gg+i+etygvpveeiv+gik+gvrkvnidtdlrla+t+a+rr++a+
  NCBI__GCF_000600005.1:WP_025331513.1 222 ERLPNTHLVMHGSSSVPQEWLQVINEFGGNIPETYGVPVEEIVEGIKYGVRKVNIDTDLRLASTGAIRRFLAT 294
                                           ************************************************************************* PP

                             TIGR01521 293 dpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakgel 347
                                           +p efdprk++ ++++amk+vc++ry afg+ag as+ik++sle+ma+rya gel
  NCBI__GCF_000600005.1:WP_025331513.1 295 HPAEFDPRKYFTETIKAMKQVCIDRYVAFGAAGHASQIKPISLEKMANRYAAGEL 349
                                           *****************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (347 nodes)
Target sequences:                          1  (354 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: 00:00:00.00
# Mc/sec: 26.53
//
[ok]

This GapMind analysis is from Sep 24 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