GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Marinobacter adhaerens HP15

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate GFF2966 HP15_2910 fructose-1,6-bisphosphate aldolase

Query= BRENDA::Q602L6
         (354 letters)



>FitnessBrowser__Marino:GFF2966
          Length = 354

 Score =  540 bits (1390), Expect = e-158
 Identities = 263/354 (74%), Positives = 301/354 (85%)

Query: 1   MALISLRQLLDHAAEHGYGLPAFNVNNMEQIKAIMEAASAVDAPVILQGSAGARTYAGEP 60
           MALIS+RQ+LDHAAEHGYG+PAFNVNN+EQ++AIMEAA   D+PVI+Q SAGAR YAG P
Sbjct: 1   MALISMRQMLDHAAEHGYGVPAFNVNNLEQMRAIMEAADRTDSPVIVQASAGARKYAGAP 60

Query: 61  FLRHLVRAAIEMYPHIPVCMHQDHGASPAVCIRSIQSGFSSVMMDGSLLEDMKTPASYAY 120
           FLRHL+ AAIE +PHIPV MHQDHG SP+VC RSIQ GFSSVMMDGSL ED KTP  Y Y
Sbjct: 61  FLRHLILAAIEEFPHIPVVMHQDHGTSPSVCQRSIQLGFSSVMMDGSLGEDGKTPTDYEY 120

Query: 121 NVETTRKVVEMAHACGVSVEGELGCLGSLETGRAGKEDGHGAEGELDHSLLLTDPDEAAD 180
           NV+ TR+ VEMAHACGVSVEGELGCLGSLETG+AG+EDG GAEG LDHS +LTDP+EAAD
Sbjct: 121 NVDVTRRTVEMAHACGVSVEGELGCLGSLETGQAGEEDGIGAEGTLDHSQMLTDPEEAAD 180

Query: 181 FVRQTQVDALAIAIGTSHGAYKFTRKPTGQVLRIDRVKAIHQRIPTIHLVMHGSSSVPEE 240
           FV++T VDALAIAIGTSHGAYKFTR PTG +L ID++KAIH RIP  HLVMHGSSSVP+E
Sbjct: 181 FVKKTHVDALAIAIGTSHGAYKFTRPPTGDILAIDQIKAIHARIPDTHLVMHGSSSVPQE 240

Query: 241 WAQMINDYGGDIGQTYGVPVEEIVEGIRHGVRKVNIDTDLRIASYGAMRRFMVEDRKNFD 300
           W ++IN+YGG+I +TYGVPVEEIVEGI+HGVRKVNIDTDLR+AS GA+RRF+ E+   FD
Sbjct: 241 WLKIINEYGGEIPETYGVPVEEIVEGIKHGVRKVNIDTDLRLASTGAVRRFLAENPAEFD 300

Query: 301 PRKLYKAAQTAMTAICRARYEAFGAAGQAAKIKPLRLEDMSLAYAQGKLDPIVR 354
           PRK  K    AMT +C ARYEAFG AG A+KIKP+ LE M   YA G+LDP V+
Sbjct: 301 PRKFLKETMKAMTDVCIARYEAFGCAGNASKIKPVNLERMFERYASGELDPKVK 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: 538
Number of extensions: 22
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 GFF2966 HP15_2910 (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.21908.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.7e-210  684.2   0.2   1.9e-210  684.0   0.2    1.0  1  lcl|FitnessBrowser__Marino:GFF2966  HP15_2910 fructose-1,6-bisphosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF2966  HP15_2910 fructose-1,6-bisphosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  684.0   0.2  1.9e-210  1.9e-210       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 684.0 bits;  conditional E-value: 1.9e-210
                           TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypdip 75 
                                         lis+rq+ldhaae+gygvpafnvnnleq++aimeaad+tdspvi+qas+gar+yag+++lr+l+laa+ee+p+ip
  lcl|FitnessBrowser__Marino:GFF2966   3 LISMRQMLDHAAEHGYGVPAFNVNNLEQMRAIMEAADRTDSPVIVQASAGARKYAGAPFLRHLILAAIEEFPHIP 77 
                                         69************************************************************************* PP

                           TIGR01521  76 vvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgsletg 150
                                         vv+hqdhg+sp++c+++iqlgf+svmmdgsl ed+ktp+dy+ynv+vt ++v++aha+g+svegelgclgsletg
  lcl|FitnessBrowser__Marino:GFF2966  78 VVMHQDHGTSPSVCQRSIQLGFSSVMMDGSLGEDGKTPTDYEYNVDVTRRTVEMAHACGVSVEGELGCLGSLETG 152
                                         *************************************************************************** PP

                           TIGR01521 151 kgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeiherlpdt 225
                                         ++++edg g+eg+ld+sq+ltdpeeaa+fvkkt+vdala+aigtshgaykftr+ptg++laid+i+ ih+r+pdt
  lcl|FitnessBrowser__Marino:GFF2966 153 QAGEEDGIGAEGTLDHSQMLTDPEEAADFVKKTHVDALAIAIGTSHGAYKFTRPPTGDILAIDQIKAIHARIPDT 227
                                         *************************************************************************** PP

                           TIGR01521 226 hlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaakdpsefdpr 300
                                         hlvmhgsssvpqewl++ineyggei+etygvpveeiv+gik+gvrkvnidtdlrla+t+a+rr++a++p efdpr
  lcl|FitnessBrowser__Marino:GFF2966 228 HLVMHGSSSVPQEWLKIINEYGGEIPETYGVPVEEIVEGIKHGVRKVNIDTDLRLASTGAVRRFLAENPAEFDPR 302
                                         *************************************************************************** PP

                           TIGR01521 301 kflkkaveamkdvckaryeafgtagnaskikvvsleemarryakgel 347
                                         kflk++++am dvc+aryeafg agnaskik+v+le m++rya+gel
  lcl|FitnessBrowser__Marino:GFF2966 303 KFLKETMKAMTDVCIARYEAFGCAGNASKIKPVNLERMFERYASGEL 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.48
//
[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