GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Pseudomonas fluorescens FW300-N1B4

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate Pf1N1B4_2402 Fructose-bisphosphate aldolase class II (EC 4.1.2.13)

Query= BRENDA::Q602L6
         (354 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2402
          Length = 354

 Score =  524 bits (1349), Expect = e-153
 Identities = 258/350 (73%), Positives = 291/350 (83%)

Query: 1   MALISLRQLLDHAAEHGYGLPAFNVNNMEQIKAIMEAASAVDAPVILQGSAGARTYAGEP 60
           MALIS+RQ+LDHAAE GYG+PAFNVNN+EQ++AIMEAA   D+PVI+Q SAGAR YAG P
Sbjct: 1   MALISMRQMLDHAAEFGYGVPAFNVNNLEQMRAIMEAADKTDSPVIVQASAGARKYAGAP 60

Query: 61  FLRHLVRAAIEMYPHIPVCMHQDHGASPAVCIRSIQSGFSSVMMDGSLLEDMKTPASYAY 120
           FLRHL+ AAIE +PHIPVCMHQDHG SP VC RSIQ GFSSVMMDGSL ED KTP  Y Y
Sbjct: 61  FLRHLILAAIEEFPHIPVCMHQDHGTSPDVCQRSIQLGFSSVMMDGSLGEDGKTPTDYDY 120

Query: 121 NVETTRKVVEMAHACGVSVEGELGCLGSLETGRAGKEDGHGAEGELDHSLLLTDPDEAAD 180
           NV  T++ V MAHACGVSVEGELGCLGSLETG AG+EDG GAEG LDHS +LTDP+EAAD
Sbjct: 121 NVRVTQQTVAMAHACGVSVEGELGCLGSLETGMAGEEDGIGAEGVLDHSQMLTDPEEAAD 180

Query: 181 FVRQTQVDALAIAIGTSHGAYKFTRKPTGQVLRIDRVKAIHQRIPTIHLVMHGSSSVPEE 240
           FV++TQVDALAIAIGTSHGAYKFT+ PTG VL IDR+K IH+RIP  HLVMHGSSSVP+E
Sbjct: 181 FVKRTQVDALAIAIGTSHGAYKFTKPPTGDVLAIDRIKEIHKRIPNTHLVMHGSSSVPQE 240

Query: 241 WAQMINDYGGDIGQTYGVPVEEIVEGIRHGVRKVNIDTDLRIASYGAMRRFMVEDRKNFD 300
           W  +IN YGGDI +TYGVPVEEIVEGI+HGVRKVNIDTDLR+AS GAMRR M  +   FD
Sbjct: 241 WLAIINQYGGDIKETYGVPVEEIVEGIKHGVRKVNIDTDLRLASTGAMRRLMATNPSEFD 300

Query: 301 PRKLYKAAQTAMTAICRARYEAFGAAGQAAKIKPLRLEDMSLAYAQGKLD 350
           PRK + A  TAM  +C ARYE FG AG A+KIKP+ LE M   Y +G+L+
Sbjct: 301 PRKFFGATVTAMRDVCIARYEQFGTAGNASKIKPISLEAMYQRYLKGELN 350


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: 489
Number of extensions: 16
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 Pf1N1B4_2402 (Fructose-bisphosphate aldolase class II (EC 4.1.2.13))
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.666.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   5.6e-214  695.6   0.2   6.3e-214  695.5   0.2    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2402  Fructose-bisphosphate aldolase c


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2402  Fructose-bisphosphate aldolase class II (EC 4.1.2.13)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  695.5   0.2  6.3e-214  6.3e-214       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 695.5 bits;  conditional E-value: 6.3e-214
                                      TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklv 64 
                                                    lis+rq+ldhaae+gygvpafnvnnleq++aimeaadktdspvi+qas+gar+yag+++lr+l+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2402   3 LISMRQMLDHAAEFGYGVPAFNVNNLEQMRAIMEAADKTDSPVIVQASAGARKYAGAPFLRHLI 66 
                                                    69************************************************************** PP

                                      TIGR01521  65 laaveeypdipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvk 128
                                                    laa+ee+p+ipv++hqdhg+sp++c+++iqlgf+svmmdgsl ed+ktp+dydynv+vt+++v+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2402  67 LAAIEEFPHIPVCMHQDHGTSPDVCQRSIQLGFSSVMMDGSLGEDGKTPTDYDYNVRVTQQTVA 130
                                                    **************************************************************** PP

                                      TIGR01521 129 lahavgasvegelgclgsletgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavai 192
                                                    +aha+g+svegelgclgsletg++++edg g+eg+ld+sq+ltdpeeaa+fvk+t+vdala+ai
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2402 131 MAHACGVSVEGELGCLGSLETGMAGEEDGIGAEGVLDHSQMLTDPEEAADFVKRTQVDALAIAI 194
                                                    **************************************************************** PP

                                      TIGR01521 193 gtshgaykftrkptgevlaidrieeiherlpdthlvmhgsssvpqewldvineyggeiketygv 256
                                                    gtshgaykft++ptg+vlaidri+eih+r+p+thlvmhgsssvpqewl++in+ygg+iketygv
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2402 195 GTSHGAYKFTKPPTGDVLAIDRIKEIHKRIPNTHLVMHGSSSVPQEWLAIINQYGGDIKETYGV 258
                                                    **************************************************************** PP

                                      TIGR01521 257 pveeivkgikfgvrkvnidtdlrlaataalrrvaakdpsefdprkflkkaveamkdvckaryea 320
                                                    pveeiv+gik+gvrkvnidtdlrla+t+a+rr++a++psefdprkf+  +v am+dvc+arye+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2402 259 PVEEIVEGIKHGVRKVNIDTDLRLASTGAMRRLMATNPSEFDPRKFFGATVTAMRDVCIARYEQ 322
                                                    **************************************************************** PP

                                      TIGR01521 321 fgtagnaskikvvsleemarryakgel 347
                                                    fgtagnaskik++sle m++ry kgel
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2402 323 FGTAGNASKIKPISLEAMYQRYLKGEL 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.05
//
[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