Alignments for a candidate for fba in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for fba in Pseudomonas stutzeri RCH2

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate GFF332 Psest_0333 fructose-bisphosphate aldolase, class II, Calvin cycle subtype

Query= BRENDA::Q602L6
         (354 letters)



>FitnessBrowser__psRCH2:GFF332
          Length = 354

 Score =  521 bits (1343), Expect = e-153
 Identities = 257/351 (73%), Positives = 290/351 (82%)

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  D KTPA Y Y
Sbjct: 61  FLRHLILAAIEEFPHIPVCMHQDHGTSPDVCQRSIQLGFSSVMMDGSLQADGKTPADYDY 120

Query: 121 NVETTRKVVEMAHACGVSVEGELGCLGSLETGRAGKEDGHGAEGELDHSLLLTDPDEAAD 180
           NV  T++ V  AHACGVSVEGELGCLGSLETG AG+EDG GAEG LDHS LLTDP+EAAD
Sbjct: 121 NVRVTQQTVAFAHACGVSVEGELGCLGSLETGMAGEEDGVGAEGVLDHSQLLTDPEEAAD 180

Query: 181 FVRQTQVDALAIAIGTSHGAYKFTRKPTGQVLRIDRVKAIHQRIPTIHLVMHGSSSVPEE 240
           FV +T+VDALAIAIGTSHGAYKFT+ PTG  L I R+K IH RIP  HLVMHGSSSVP+E
Sbjct: 181 FVAKTKVDALAIAIGTSHGAYKFTKPPTGDTLSIQRIKEIHARIPDTHLVMHGSSSVPQE 240

Query: 241 WAQMINDYGGDIGQTYGVPVEEIVEGIRHGVRKVNIDTDLRIASYGAMRRFMVEDRKNFD 300
           W Q+IN YGG+IG+TYGVPVEEIVEGI++GVRKVNIDTDLR+AS GA+R FM ++   FD
Sbjct: 241 WLQIINQYGGEIGETYGVPVEEIVEGIKYGVRKVNIDTDLRLASTGAIREFMAKNPSEFD 300

Query: 301 PRKLYKAAQTAMTAICRARYEAFGAAGQAAKIKPLRLEDMSLAYAQGKLDP 351
           PRK +    +AM  IC ARYEAFG AG A+KIKP+ LE M   YA G+LDP
Sbjct: 301 PRKYFAKTVSAMRDICIARYEAFGTAGNASKIKPISLEGMFQRYASGELDP 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: 506
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: 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 GFF332 Psest_0333 (fructose-bisphosphate aldolase, class II, Calvin cycle subtype)
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.18045.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.1e-217  707.8   0.2   1.3e-217  707.7   0.2    1.0  1  lcl|FitnessBrowser__psRCH2:GFF332  Psest_0333 fructose-bisphosphate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF332  Psest_0333 fructose-bisphosphate aldolase, class II, Calvin cycle subtype
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  707.7   0.2  1.3e-217  1.3e-217       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 707.7 bits;  conditional E-value: 1.3e-217
                          TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypdipv 76 
                                        lis+rq+ldhaae+gygvpafnvnnleq++aimeaadktdspvi+qas+gar+yag+++lr+l+laa+ee+p+ipv
  lcl|FitnessBrowser__psRCH2:GFF332   3 LISMRQMLDHAAEFGYGVPAFNVNNLEQMRAIMEAADKTDSPVIVQASAGARKYAGAPFLRHLILAAIEEFPHIPV 78 
                                        69************************************************************************** PP

                          TIGR01521  77 vlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgsletgkg 152
                                        ++hqdhg+sp++c+++iqlgf+svmmdgsl++d+ktpadydynv+vt+++v++aha+g+svegelgclgsletg++
  lcl|FitnessBrowser__psRCH2:GFF332  79 CMHQDHGTSPDVCQRSIQLGFSSVMMDGSLQADGKTPADYDYNVRVTQQTVAFAHACGVSVEGELGCLGSLETGMA 154
                                        **************************************************************************** PP

                          TIGR01521 153 eaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeiherlpdthlv 228
                                        ++edg+g+eg+ld+sqlltdpeeaa+fv+ktkvdala+aigtshgaykft++ptg++l+i+ri+eih+r+pdthlv
  lcl|FitnessBrowser__psRCH2:GFF332 155 GEEDGVGAEGVLDHSQLLTDPEEAADFVAKTKVDALAIAIGTSHGAYKFTKPPTGDTLSIQRIKEIHARIPDTHLV 230
                                        **************************************************************************** PP

                          TIGR01521 229 mhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaakdpsefdprkflk 304
                                        mhgsssvpqewl++in+yggei etygvpveeiv+gik+gvrkvnidtdlrla+t+a+r+++ak+psefdprk++ 
  lcl|FitnessBrowser__psRCH2:GFF332 231 MHGSSSVPQEWLQIINQYGGEIGETYGVPVEEIVEGIKYGVRKVNIDTDLRLASTGAIREFMAKNPSEFDPRKYFA 306
                                        **************************************************************************** PP

                          TIGR01521 305 kaveamkdvckaryeafgtagnaskikvvsleemarryakgel 347
                                        k+v am+d+c+aryeafgtagnaskik++sle+m++rya+gel
  lcl|FitnessBrowser__psRCH2:GFF332 307 KTVSAMRDICIARYEAFGTAGNASKIKPISLEGMFQRYASGEL 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.44
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources