GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tpiA in Pseudomonas stutzeri RCH2

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate GFF946 Psest_0975 triosephosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__psRCH2:GFF946
          Length = 251

 Score =  235 bits (600), Expect = 6e-67
 Identities = 123/250 (49%), Positives = 165/250 (66%), Gaps = 2/250 (0%)

Query: 1   MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM 60
           MR P+V GNWK+NG+R  V ELV +LR +   V+   +A+ P  +++       +  H+ 
Sbjct: 1   MRRPMVAGNWKMNGTRASVAELVESLRMQALPVS-VEIAVFPSCLHVAQVLGGVDSKHVA 59

Query: 61  LGAQNVDL-NLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQ 119
           +GAQ+    N  GA TGE SA    ++G +++++GHSERR    E+DE++++KF   +  
Sbjct: 60  VGAQDCAAQNGFGALTGEVSAEQFAEVGCEWVLVGHSERRLVLGETDEVVSRKFLAAQVG 119

Query: 120 GLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSAT 179
           GL PVLC+GET  E EAG+T EV  RQ+  VL   G A FE AVIAYEPVWAIG+G +AT
Sbjct: 120 GLKPVLCLGETLEEREAGRTLEVVGRQLAQVLDDHGIAVFESAVIAYEPVWAIGSGLTAT 179

Query: 180 PAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKA 239
           P QAQ VH  IR+ +++ D  +A  V + YGGSV A NAAELF+  DIDG LVGGASLKA
Sbjct: 180 PEQAQEVHAAIREQLSRQDRQVAAGVRLLYGGSVKADNAAELFSMADIDGGLVGGASLKA 239

Query: 240 DAFAVIVKAA 249
           + F  I +AA
Sbjct: 240 NEFGAICRAA 249


Lambda     K      H
   0.316    0.130    0.366 

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: 180
Number of extensions: 8
Number of successful extensions: 2
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: 255
Length of database: 251
Length adjustment: 24
Effective length of query: 231
Effective length of database: 227
Effective search space:    52437
Effective search space used:    52437
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: 46 (22.3 bits)

Align candidate GFF946 Psest_0975 (triosephosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

# 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/TIGR00419.hmm
# target sequence database:        /tmp/gapView.4664.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00419  [M=228]
Accession:   TIGR00419
Description: tim: triose-phosphate isomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
      2e-68  216.6   2.3    2.4e-68  216.4   2.3    1.0  1  lcl|FitnessBrowser__psRCH2:GFF946  Psest_0975 triosephosphate isome


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF946  Psest_0975 triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.4   2.3   2.4e-68   2.4e-68       1     228 []       5     240 ..       5     240 .. 0.92

  Alignments for each domain:
  == domain 1  score: 216.4 bits;  conditional E-value: 2.4e-68
                          TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavk.sGaftGeis 74 
                                        +v +n+K+n+++ +v+++v +l+ + a +  ve+av p+ +++  v   v+  ++ v+Aq++ a++ +Ga tGe+s
  lcl|FitnessBrowser__psRCH2:GFF946   5 MVAGNWKMNGTRASVAELVESLRMQ-ALPVSVEIAVFPSCLHVAQVLGGVDsKHVAVGAQDCAAQNgFGALTGEVS 79 
                                        699********************98.778899******************9789********986537******** PP

                          TIGR00419  75 AemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaaaA.... 146
                                        Ae  +++G+++vl+gHsErR +l e+de++  k+  ++  glk+v+C+getleerea+rt+++v ++ a +     
  lcl|FitnessBrowser__psRCH2:GFF946  80 AEQFAEVGCEWVLVGHSERRLVLGETDEVVSRKFLAAQVGGLKPVLCLGETLEEREAGRTLEVVGRQLAQVLddhg 155
                                        ********************************************************66666666555443333333 PP

                          TIGR00419 147 ...lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvdGvL 219
                                           +e++v+A+EPv++iG+G ++++ +a++v++ +r+ l++ +++va  vr+lyG+sv+a ++ael+   d+dG L
  lcl|FitnessBrowser__psRCH2:GFF946 156 iavFESAVIAYEPVWAIGSGLTATPEQAQEVHAAIREQLSRQDRQVAAGVRLLYGGSVKADNAAELFSMADIDGGL 231
                                        334************************************************************************* PP

                          TIGR00419 220 lasavlkae 228
                                        +++a+lka+
  lcl|FitnessBrowser__psRCH2:GFF946 232 VGGASLKAN 240
                                        *******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (251 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: 00:00:00.00
# Mc/sec: 9.36
//
[ok]

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

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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