Alignments for a candidate for tpi in Rhizobium freirei PRF 81

GapMind for catabolism of small carbon sources

Alignments for a candidate for tpi in Rhizobium freirei PRF 81

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_004111324.1 RHSP_RS07025 triose-phosphate isomerase

Query= SwissProt::Q8L1Z5
         (254 letters)



>NCBI__GCF_000359745.1:WP_004111324.1
          Length = 245

 Score =  239 bits (610), Expect = 4e-68
 Identities = 120/243 (49%), Positives = 159/243 (65%), Gaps = 3/243 (1%)

Query: 5   IRPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGGENIL 64
           +R  IAGNWKMNG   SL E+ A+  G++ +     + ++C P TL+ +A +   G  I 
Sbjct: 1   MRKLIAGNWKMNGLASSLAEIEALK-GLTGEAA--CDIVVCPPFTLVEKAVECTKGAAIA 57

Query: 65  LGGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAAWRAG 124
           +G Q+CH    G YTGD+SA ML E GA  VI+GHSERR  Y+E DA V  K  A   AG
Sbjct: 58  VGAQDCHAQAAGAYTGDVSAGMLAEIGARFVILGHSERRLAYKEMDAAVAGKAAAVHEAG 117

Query: 125 LVALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTATSAD 184
           L ++ICVGET  ER   + +DV+  QLEGS+PD AT+ N+ IAYEPVWA+GTG   T   
Sbjct: 118 LTSIICVGETRAERDEGRAIDVVRAQLEGSIPDTATSSNMTIAYEPVWAIGTGLVPTLEQ 177

Query: 185 VAEVHAFIHHKMHSRFGDEGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLKAIDF 244
           + EVH+ I H +  R GD+G ++R+LYGGSVK  NA  +   ++V+GAL+GGASLKA +F
Sbjct: 178 IGEVHSSIRHMLEERLGDDGRRVRILYGGSVKAQNAKAIFGVSNVDGALVGGASLKASEF 237

Query: 245 LTI 247
             I
Sbjct: 238 AGI 240


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: 217
Number of extensions: 7
Number of successful extensions: 2
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: 245
Length adjustment: 24
Effective length of query: 230
Effective length of database: 221
Effective search space:    50830
Effective search space used:    50830
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 WP_004111324.1 RHSP_RS07025 (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.3512873.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    4.1e-58  182.9   3.7    4.7e-58  182.7   3.7    1.0  1  NCBI__GCF_000359745.1:WP_004111324.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000359745.1:WP_004111324.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.7   3.7   4.7e-58   4.7e-58       1     227 [.       4     234 ..       4     235 .. 0.93

  Alignments for each domain:
  == domain 1  score: 182.7 bits;  conditional E-value: 4.7e-58
                             TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 
                                           l+ +n+K+n+  ++ +++   l + +++ea + ++v ppf  ++ +++  + + i v+Aq+++a+ +Ga+tG+
  NCBI__GCF_000359745.1:WP_004111324.1   4 LIAGNWKMNGLASSLAEI-EAL-KGLTGEAACDIVVCPPFTLVEKAVECTKgAAIAVGAQDCHAQAAGAYTGD 74 
                                           689*******98887654.444.579*********************999989******************** PP

                             TIGR00419  73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaaa 145
                                           +sA ml+++Ga++v++gHsErR   ke d  ++ k a ++e gl+s++Cvget +er+ +r i++v  + +  
  NCBI__GCF_000359745.1:WP_004111324.1  75 VSAGMLAEIGARFVILGHSERRLAYKEMDAAVAGKAAAVHEAGLTSIICVGETRAERDEGRAIDVVRAQLEGS 147
                                           ******************************************************************9886543 PP

                             TIGR00419 146 A.....lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaql 213
                                                  ++  +A+EPv++iGtG + +  +  +v++s+r  l++   +  + vr+lyG+sv+a++++  +   
  NCBI__GCF_000359745.1:WP_004111324.1 148 IpdtatSSNMTIAYEPVWAIGTGLVPTLEQIGEVHSSIRHMLEERLGDDGRRVRILYGGSVKAQNAKAIFGVS 220
                                           2244449999*****************************99999999999*********************** PP

                             TIGR00419 214 dvdGvLlasavlka 227
                                           +vdG+L+++a+lka
  NCBI__GCF_000359745.1:WP_004111324.1 221 NVDGALVGGASLKA 234
                                           *************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (245 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: 21.43
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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