GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Sphingomonas koreensis DSMZ 15582

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate Ga0059261_0254 Ga0059261_0254 triosephosphate isomerase (EC 5.3.1.1)

Query= SwissProt::Q8L1Z5
         (254 letters)



>FitnessBrowser__Korea:Ga0059261_0254
          Length = 248

 Score =  221 bits (564), Expect = 8e-63
 Identities = 123/245 (50%), Positives = 163/245 (66%), Gaps = 5/245 (2%)

Query: 6   RPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGGENILL 65
           R  +AGNWKM+G   +L E+ AIA   +   G   +A +CVPATL++ A  +     + +
Sbjct: 3   RKLVAGNWKMHGLIAALPEIEAIAQAAAVTPG--VDAALCVPATLIAPAVTVAA--RMPI 58

Query: 66  GGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAAWRAGL 125
           GGQ+CH  D G +TG ISA ML+EAGA+  I+GHSERR    E+DA V+ K +AA R GL
Sbjct: 59  GGQDCHAADQGAHTGCISAAMLREAGAALTIVGHSERRANQGETDADVKGKAEAAHRHGL 118

Query: 126 VALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTATSADV 185
            A++CVGETLE+R + +   V+T QL GS+P+GA A+ + IAYEPVWA+GTG T T ADV
Sbjct: 119 NAILCVGETLEQRDAGQAEAVVTAQLAGSMPEGAAADWLSIAYEPVWAIGTGRTPTEADV 178

Query: 186 AEVHAFIHHKMHSRFGDE-GAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLKAIDF 244
           A +H  I  K+    G E  A +R+LYGGSV  +NA  LL  A V+GAL+GGASL A  F
Sbjct: 179 AAMHGAIRAKLTELLGGETAAAMRVLYGGSVNGANAASLLGCADVDGALVGGASLTAEKF 238

Query: 245 LTICD 249
           + I +
Sbjct: 239 VPIIE 243


Lambda     K      H
   0.320    0.137    0.403 

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: 233
Number of extensions: 8
Number of successful extensions: 4
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: 254
Length of database: 248
Length adjustment: 24
Effective length of query: 230
Effective length of database: 224
Effective search space:    51520
Effective search space used:    51520
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: 46 (22.3 bits)

Align candidate Ga0059261_0254 Ga0059261_0254 (triosephosphate isomerase (EC 5.3.1.1))
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.2471067.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.3e-50  158.4   5.8    1.5e-50  158.2   5.8    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_0254  Ga0059261_0254 triosephosphate i


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_0254  Ga0059261_0254 triosephosphate isomerase (EC 5.3.1.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.2   5.8   1.5e-50   1.5e-50       1     228 []       5     236 ..       5     236 .. 0.89

  Alignments for each domain:
  == domain 1  score: 158.2 bits;  conditional E-value: 1.5e-50
                                 TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeveseiqvaAqnvdavksGaf 69 
                                               lv +n+K+++ +     e+  +a+  a + gv  a+ +p   +  ++  +  +++++ q+++a ++Ga+
  lcl|FitnessBrowser__Korea:Ga0059261_0254   5 LVAGNWKMHGLIAAL-PEIEAIAQAAAVTPGVDAALCVPATLIAPAVTVAA-RMPIGGQDCHAADQGAH 71 
                                               799******999876.57899***99********99988877765554333.6**************** PP

                                 TIGR00419  70 tGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnv 138
                                               tG isA+ml+++Ga+ +++gHsErR+   e+d  ++ k   ++  gl++++Cvgetle+r+a++   +v
  lcl|FitnessBrowser__Korea:Ga0059261_0254  72 TGCISAAMLREAGAALTIVGHSERRANQGETDADVKGKAEAAHRHGLNAILCVGETLEQRDAGQAEAVV 140
                                               *******************************999***************************99775555 PP

                                 TIGR00419 139 attaaa.....aAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasv 201
                                               + + a      aA +   +A+EPv++iGtG++ ++A+  ++++ +r  l++    e a  +rvlyG+sv
  lcl|FitnessBrowser__Korea:Ga0059261_0254 141 TAQLAGsmpegAAADWLSIAYEPVWAIGTGRTPTEADVAAMHGAIRAKLTElLGGETAAAMRVLYGGSV 209
                                               544432222224566778*******************************998999************** PP

                                 TIGR00419 202 taaedaelaaqldvdGvLlasavlkae 228
                                               ++a++a l    dvdG+L+++a+l ae
  lcl|FitnessBrowser__Korea:Ga0059261_0254 210 NGANAASLLGCADVDGALVGGASLTAE 236
                                               ************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (248 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 14.68
//
[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:

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