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_037153750.1 RHSP_RS21965 triose-phosphate isomerase

Query= SwissProt::Q8L1Z5
         (254 letters)



>NCBI__GCF_000359745.1:WP_037153750.1
          Length = 256

 Score =  268 bits (684), Expect = 1e-76
 Identities = 131/253 (51%), Positives = 174/253 (68%)

Query: 1   MSPNIRPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGG 60
           M+  +RP +AGNWKMNGT  SL +++AIA G+ + L    + L+C PATLL  A  +   
Sbjct: 1   MTKTVRPLLAGNWKMNGTRASLDQIKAIADGVKAPLSEKIDTLLCPPATLLYVATALCDD 60

Query: 61  ENILLGGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAA 120
             + +G Q+CH    G +TGDISA M+ +   +HVI+GHSERR  + ESD +VRAK QAA
Sbjct: 61  SPLAIGAQDCHQQVSGAHTGDISAEMIADCFGTHVIVGHSERRRNHAESDMLVRAKAQAA 120

Query: 121 WRAGLVALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTA 180
             AGL+A+IC+GET  ER S + LDVL R+L GS+PDG++A+  ++AYEPVWA+GTG   
Sbjct: 121 HDAGLIAIICIGETAYERNSGQTLDVLKRELIGSIPDGSSAQTTVVAYEPVWAIGTGVVP 180

Query: 181 TSADVAEVHAFIHHKMHSRFGDEGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLK 240
           T  +V E HAFI  ++  RFG EGA +R+LYGGSV  +NA +LL   HVNG L+GG SLK
Sbjct: 181 TQENVEEAHAFIRAELIQRFGKEGANMRILYGGSVSGANARDLLEVPHVNGVLVGGQSLK 240

Query: 241 AIDFLTICDVYRK 253
           A DFL I   + +
Sbjct: 241 AADFLAIYAAFER 253


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: 231
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 WP_037153750.1 RHSP_RS21965 (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.208152.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.2e-51  161.7   0.4    1.5e-51  161.5   0.4    1.0  1  NCBI__GCF_000359745.1:WP_037153750.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000359745.1:WP_037153750.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.5   0.4   1.5e-51   1.5e-51       2     227 ..       9     241 ..       8     242 .. 0.87

  Alignments for each domain:
  == domain 1  score: 161.5 bits;  conditional E-value: 1.5e-51
                             TIGR00419   2 viinfKlnesvgkvelevaklaeevase..agvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftG 71 
                                           + +n+K+n+++ + ++ +  +a+ v  +  +++   + pp   l v++   + s + ++Aq+++ + sGa+tG
  NCBI__GCF_000359745.1:WP_037153750.1   9 LAGNWKMNGTRASLDQ-IKAIADGVKAPlsEKIDTLLCPPATLLYVATALCDdSPLAIGAQDCHQQVSGAHTG 80 
                                           679******9988765.56666666554113455567888888887777777789****************** PP

                             TIGR00419  72 eisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaa 144
                                           +isAem++d+   +v++gHsErR  ++e+d l+ +k   +++ gl +++C+get  er++++t+++++++   
  NCBI__GCF_000359745.1:WP_037153750.1  81 DISAEMIADCFGTHVIVGHSERRRNHAESDMLVRAKAQAAHDAGLIAIICIGETAYERNSGQTLDVLKRELIG 153
                                           *****************************************************************99876543 PP

                             TIGR00419 145 aA.....lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaq 212
                                                   +  vvA+EPv++iGtG++ ++ + e+ ++++r  l +   +   ++r+lyG+sv++a++ +l   
  NCBI__GCF_000359745.1:WP_037153750.1 154 SIpdgssAQTTVVAYEPVWAIGTGVVPTQENVEEAHAFIRAELIQRFGKEGANMRILYGGSVSGANARDLLEV 226
                                           33467668999*****************************88877555557789******************* PP

                             TIGR00419 213 ldvdGvLlasavlka 227
                                           + v+GvL+++ +lka
  NCBI__GCF_000359745.1:WP_037153750.1 227 PHVNGVLVGGQSLKA 241
                                           **************8 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: 00:00:00.01
# Mc/sec: 4.62
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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