Alignments for a candidate for tpi in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for tpi 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.carbon/TIGR00419.hmm
# target sequence database:        /tmp/gapView.22678.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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 8.42
//
[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, or view the source code.

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