Alignments for a candidate for tpi in Sphingomonas koreensis DSMZ 15582

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.13253.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: 6.43
//
[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
the source code
instructions for running GapMind on your computer

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