GapMind for Amino acid biosynthesis

 

Alignments for a candidate for fbp 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::A0Q7I9
         (354 letters)



>FitnessBrowser__psRCH2:GFF332
          Length = 354

 Score =  597 bits (1538), Expect = e-175
 Identities = 288/351 (82%), Positives = 320/351 (91%)

Query: 1   MALVSLRQLLDHAAEHGYGLPAFNVNNLEQVRAVMEAADKVNSPVILQGSAGARKYAGAS 60
           MAL+S+RQ+LDHAAE GYG+PAFNVNNLEQ+RA+MEAADK +SPVI+Q SAGARKYAGA 
Sbjct: 1   MALISMRQMLDHAAEFGYGVPAFNVNNLEQMRAIMEAADKTDSPVIVQASAGARKYAGAP 60

Query: 61  FIRHLVLAAIEEYPHIPVCMHQDHGTSPSVCQRSIQLGFSSVMMDGSLKSDGKTPADYEY 120
           F+RHL+LAAIEE+PHIPVCMHQDHGTSP VCQRSIQLGFSSVMMDGSL++DGKTPADY+Y
Sbjct: 61  FLRHLILAAIEEFPHIPVCMHQDHGTSPDVCQRSIQLGFSSVMMDGSLQADGKTPADYDY 120

Query: 121 NVNVTKTVSDMAHACGVSVEGELGCLGSLETGQAGEEDGIGAEGTLSMDQLLTDPEEAAD 180
           NV VT+     AHACGVSVEGELGCLGSLETG AGEEDG+GAEG L   QLLTDPEEAAD
Sbjct: 121 NVRVTQQTVAFAHACGVSVEGELGCLGSLETGMAGEEDGVGAEGVLDHSQLLTDPEEAAD 180

Query: 181 FVRRTKVDALAIAIGTSHGAYKFTKPPTGDVLSIKRVKEIHARIPDTHLVMHGSSSVPQD 240
           FV +TKVDALAIAIGTSHGAYKFTKPPTGD LSI+R+KEIHARIPDTHLVMHGSSSVPQ+
Sbjct: 181 FVAKTKVDALAIAIGTSHGAYKFTKPPTGDTLSIQRIKEIHARIPDTHLVMHGSSSVPQE 240

Query: 241 WLEVINTYGGAMGETYGVPVEEIVEAIKYGVRKINIDTDLRMAATGAIRRFLAENPAEFD 300
           WL++IN YGG +GETYGVPVEEIVE IKYGVRK+NIDTDLR+A+TGAIR F+A+NP+EFD
Sbjct: 241 WLQIINQYGGEIGETYGVPVEEIVEGIKYGVRKVNIDTDLRLASTGAIREFMAKNPSEFD 300

Query: 301 PRKYNAVAKAAMSEICAARYEAFGSAGMASKIKPISLETMFQRYESGELDP 351
           PRKY A   +AM +IC ARYEAFG+AG ASKIKPISLE MFQRY SGELDP
Sbjct: 301 PRKYFAKTVSAMRDICIARYEAFGTAGNASKIKPISLEGMFQRYASGELDP 351


Lambda     K      H
   0.316    0.132    0.380 

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: 543
Number of extensions: 15
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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.aa/TIGR01521.hmm
# target sequence database:        /tmp/gapView.25392.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.24
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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