GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tpiA in Pseudomonas putida KT2440

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate PP_4715 PP_4715 triose phosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__Putida:PP_4715
          Length = 251

 Score =  240 bits (613), Expect = 2e-68
 Identities = 129/250 (51%), Positives = 164/250 (65%), Gaps = 2/250 (0%)

Query: 1   MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM 60
           MR P+V GNWK++G+R  V EL   L   LA  +G  VA+ PP ++I+       G  I 
Sbjct: 1   MRRPMVAGNWKMHGTRASVAELTKGL-SNLALPSGVEVAVFPPALFINQVIDGLAGKEIT 59

Query: 61  LGAQNVDLNLS-GAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQ 119
           +GAQN  +    GA TGE +   L + G + ++IGHSERR    E+DE++ +KFA  + +
Sbjct: 60  VGAQNSAVQPEQGALTGEVAPEQLVEAGCKLVLIGHSERRQIIGETDEVLNRKFAAAQAK 119

Query: 120 GLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSAT 179
           GL PVLCIGET  E EAGKT EV  RQ+ ++++  G  AF  AVIAYEPVWAIGTG +AT
Sbjct: 120 GLKPVLCIGETLEEREAGKTLEVVGRQLSSIIEAFGVKAFADAVIAYEPVWAIGTGLTAT 179

Query: 180 PAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKA 239
           P QAQ VH  IR  +A  DA +A +V + YGGSV A+NAAELF  PDIDG L+GGASL A
Sbjct: 180 PQQAQDVHAAIRGQLAAEDAEVAAKVQLLYGGSVKAANAAELFGMPDIDGGLIGGASLNA 239

Query: 240 DAFAVIVKAA 249
           D F  I +AA
Sbjct: 240 DEFGAICRAA 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: 188
Number of extensions: 7
Number of successful extensions: 3
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 PP_4715 PP_4715 (triose phosphate 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.29172.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    1.9e-69  220.0   2.2    2.2e-69  219.7   2.2    1.0  1  lcl|FitnessBrowser__Putida:PP_4715  PP_4715 triose phosphate isomera


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4715  PP_4715 triose phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.7   2.2   2.2e-69   2.2e-69       1     228 []       5     240 ..       5     240 .. 0.92

  Alignments for each domain:
  == domain 1  score: 219.7 bits;  conditional E-value: 2.2e-69
                           TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdav.ksGaftGei 73 
                                         +v +n+K+++++ +v+++   l  ++a ++gvevav pp ++++ v d +   ei+v+Aqn  ++ ++Ga tGe+
  lcl|FitnessBrowser__Putida:PP_4715   5 MVAGNWKMHGTRASVAELTKGL-SNLALPSGVEVAVFPPALFINQVIDGLAgKEITVGAQNSAVQpEQGALTGEV 78 
                                         699************9877776.68************************9989********9886479******* PP

                           TIGR00419  74 sAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartinnvatt 141
                                           e l+++G+k vligHsErR ++ e+de+++ k+a ++++glk+v+C+getleere       ++r++  + + 
  lcl|FitnessBrowser__Putida:PP_4715  79 APEQLVEAGCKLVLIGHSERRQIIGETDEVLNRKFAAAQAKGLKPVLCIGETLEEREagktlevVGRQLSSIIEA 153
                                         *********************************************************444444444444445555 PP

                           TIGR00419 142 aaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvd 216
                                          ++ A+ ++v+A+EPv++iGtG ++++ +a+ v++ +r  l+  ++eva +v++lyG+sv+aa++ael+  +d+d
  lcl|FitnessBrowser__Putida:PP_4715 154 FGVKAFADAVIAYEPVWAIGTGLTATPQQAQDVHAAIRGQLAAEDAEVAAKVQLLYGGSVKAANAAELFGMPDID 228
                                         56666********************************************************************** PP

                           TIGR00419 217 GvLlasavlkae 228
                                         G L+++a+l a+
  lcl|FitnessBrowser__Putida:PP_4715 229 GGLIGGASLNAD 240
                                         *********997 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: 10.41
//
[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