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.1488910.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: 17.19
//
[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:

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