Alignments for a candidate for tpiA in Sinorhizobium fredii NGR234

GapMind for Amino acid biosynthesis

Alignments for a candidate for tpiA in Sinorhizobium fredii NGR234

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate YP_002825810.1 NGR_c12760 triosephosphate isomerase

Query= SwissProt::Q8L1Z5
         (254 letters)



>NCBI__GCF_000018545.1:YP_002825810.1
          Length = 256

 Score =  297 bits (761), Expect = 1e-85
 Identities = 149/254 (58%), Positives = 186/254 (73%)

Query: 1   MSPNIRPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGG 60
           M+P+IRP +AGNWKMNGT  SL +++A+A G+   L    E LIC PATLL  A  +   
Sbjct: 1   MTPDIRPLVAGNWKMNGTRASLDQIKAMAEGVKGALSAKVETLICPPATLLYVATALCDD 60

Query: 61  ENILLGGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAA 120
             +++G Q+CH    G +TG+ISA M+ +   +HVI+GHSERRT + E+DA+VRAK +AA
Sbjct: 61  SPLMIGAQDCHQKQSGAHTGEISAEMIADCFGTHVIVGHSERRTDHAETDALVRAKTEAA 120

Query: 121 WRAGLVALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTA 180
             A LVA++C+GET EERKS K LDVL RQL  SLPD ATAEN +IAYEPVWA+GTG T 
Sbjct: 121 HAAALVAIVCIGETEEERKSGKTLDVLKRQLAESLPDAATAENTVIAYEPVWAIGTGLTP 180

Query: 181 TSADVAEVHAFIHHKMHSRFGDEGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLK 240
           T  DV E HAF+  ++ SRFG EG K+R+LYGGSVKPSNA EL+  A+V+GALIGGASLK
Sbjct: 181 TVGDVEEAHAFMRRELVSRFGSEGGKMRILYGGSVKPSNATELMGVANVDGALIGGASLK 240

Query: 241 AIDFLTICDVYRKL 254
           A DFL I   Y +L
Sbjct: 241 AEDFLAIYGAYEEL 254


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: 243
Number of extensions: 9
Number of successful extensions: 1
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: 256
Length adjustment: 24
Effective length of query: 230
Effective length of database: 232
Effective search space:    53360
Effective search space used:    53360
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: 47 (22.7 bits)

Align candidate YP_002825810.1 NGR_c12760 (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.13320.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.8e-55  174.2   1.5    2.1e-55  174.1   1.5    1.0  1  lcl|NCBI__GCF_000018545.1:YP_002825810.1  NGR_c12760 triosephosphate isome


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000018545.1:YP_002825810.1  NGR_c12760 triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.1   1.5   2.1e-55   2.1e-55       1     228 []       8     242 ..       8     242 .. 0.91

  Alignments for each domain:
  == domain 1  score: 174.1 bits;  conditional E-value: 2.1e-55
                                 TIGR00419   1 lviinfKlnesvgkvelevaklae.evaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksG 67 
                                               lv +n+K+n+++ + +++ a  +  + a +a+ve  + pp   l v++   + s ++++Aq+++ ++sG
  lcl|NCBI__GCF_000018545.1:YP_002825810.1   8 LVAGNWKMNGTRASLDQIKAMAEGvKGALSAKVETLICPPATLLYVATALCDdSPLMIGAQDCHQKQSG 76 
                                               799*********999876554444556778999999*****99999998888899************** PP

                                 TIGR00419  68 aftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartin 136
                                               a+tGeisAem++d+   +v++gHsErR+ ++e+d l+ +k   +++  l ++vC+get+eer++++t++
  lcl|NCBI__GCF_000018545.1:YP_002825810.1  77 AHTGEISAEMIADCFGTHVIVGHSERRTDHAETDALVRAKTEAAHAAALVAIVCIGETEEERKSGKTLD 145
                                               ********************************************************************* PP

                                 TIGR00419 137 nvattaa.....aaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGas 200
                                               +++++ a     aa  e+ v+A+EPv++iGtG + +  + e+ ++++r  l         ++r+lyG+s
  lcl|NCBI__GCF_000018545.1:YP_002825810.1 146 VLKRQLAeslpdAATAENTVIAYEPVWAIGTGLTPTVGDVEEAHAFMRRELVSRFGSEGGKMRILYGGS 214
                                               9998865333336779********************************87777666667889******* PP

                                 TIGR00419 201 vtaaedaelaaqldvdGvLlasavlkae 228
                                               v+ ++++el+   +vdG+L+++a+lkae
  lcl|NCBI__GCF_000018545.1:YP_002825810.1 215 VKPSNATELMGVANVDGALIGGASLKAE 242
                                               **************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (256 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: 7.91
//
[ok]

This GapMind analysis is from Apr 10 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:

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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis