GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Rhodococcus qingshengii djl-6-2

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_050656343.1 C1M55_RS15105 triose-phosphate isomerase

Query= BRENDA::P9WG43
         (261 letters)



>NCBI__GCF_002893965.1:WP_050656343.1
          Length = 261

 Score =  398 bits (1023), Expect = e-116
 Identities = 196/261 (75%), Positives = 226/261 (86%)

Query: 1   MSRKPLIAGNWKMNLNHYEAIALVQKIAFSLPDKYYDRVDVAVIPPFTDLRSVQTLVDGD 60
           M RKPLIAGNWKMNLNH EAIALVQKIAFSLP KY+D+VDV VIPPFTD+RSVQTL++GD
Sbjct: 1   MVRKPLIAGNWKMNLNHLEAIALVQKIAFSLPAKYFDKVDVTVIPPFTDIRSVQTLIEGD 60

Query: 61  KLRLTYGAQDLSPHDSGAYTGDVSGAFLAKLGCSYVVVGHSERRTYHNEDDALVAAKAAT 120
           KL LTYGAQD+S HDSGA+TG++SG+ LAKLGC++VVVGHSERRT H E +  V AK   
Sbjct: 61  KLLLTYGAQDVSAHDSGAFTGEISGSMLAKLGCTFVVVGHSERRTLHGETNETVLAKTKA 120

Query: 121 ALKHGLTPIVCIGEHLDVREAGNHVAHNIEQLRGSLAGLLAEQIGSVVIAYEPVWAIGTG 180
           ALK+GLTPIVCIGE L++REAG HVA+N++QL+GSLAGL AE+I  +VIAYEPVWAIGTG
Sbjct: 121 ALKNGLTPIVCIGEGLEIREAGEHVAYNVDQLKGSLAGLSAEEISKIVIAYEPVWAIGTG 180

Query: 181 RVASAADAQEVCAAIRKELASLASPRIADTVRVLYGGSVNAKNVGDIVAQDDVDGGLVGG 240
           RVASAADAQEVCAA+R  +A LA   +A  VRVLYGGSV++KNVG+IV Q DVDG LVGG
Sbjct: 181 RVASAADAQEVCAAVRATVAELADAEVAAGVRVLYGGSVSSKNVGEIVGQADVDGALVGG 240

Query: 241 ASLDGEHFATLAAIAAGGPLP 261
           ASL  + FATL+AIAAGGPLP
Sbjct: 241 ASLKADEFATLSAIAAGGPLP 261


Lambda     K      H
   0.318    0.135    0.393 

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: 284
Number of extensions: 5
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: 261
Length of database: 261
Length adjustment: 25
Effective length of query: 236
Effective length of database: 236
Effective search space:    55696
Effective search space used:    55696
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate WP_050656343.1 C1M55_RS15105 (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.2004555.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-61  194.4   4.0    1.4e-61  194.2   4.0    1.0  1  NCBI__GCF_002893965.1:WP_050656343.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002893965.1:WP_050656343.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.2   4.0   1.4e-61   1.4e-61       1     228 []       6     246 ..       6     246 .. 0.94

  Alignments for each domain:
  == domain 1  score: 194.2 bits;  conditional E-value: 1.4e-61
                             TIGR00419   1 lviinfKlnesvgkvelevaklaeevase..agvevavappfvdldvvkdeve.se..iqvaAqnvdavksGa 68 
                                           l+ +n+K+n    +   +v+k+a  +  +  ++v v+v ppf d++ v+  +e  +  ++ +Aq+v a++sGa
  NCBI__GCF_002893965.1:WP_050656343.1   6 LIAGNWKMNLNHLEAIALVQKIAFSLPAKyfDKVDVTVIPPFTDIRSVQTLIEgDKllLTYGAQDVSAHDSGA 78 
                                           689********99**********98876534799****************999544225668*********** PP

                             TIGR00419  69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartin.nvat 140
                                           ftGeis  ml+ lG+ +v++gHsErR+l+ e++e + +k   + + gl+++vC+ge le rea++++  nv +
  NCBI__GCF_002893965.1:WP_050656343.1  79 FTGEISGSMLAKLGCTFVVVGHSERRTLHGETNETVLAKTKAALKNGLTPIVCIGEGLEIREAGEHVAyNVDQ 151
                                           **************************************************************99987438999 PP

                             TIGR00419 141 taaaaA......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaaed 206
                                            ++  A      +++ v+A+EPv++iGtG+++s A+a++v + vr  +++ +++eva  vrvlyG+sv++++ 
  NCBI__GCF_002893965.1:WP_050656343.1 152 LKGSLAglsaeeISKIVIAYEPVWAIGTGRVASAADAQEVCAAVRATVAElADAEVAAGVRVLYGGSVSSKNV 224
                                           99999999999999***********************************99********************** PP

                             TIGR00419 207 aelaaqldvdGvLlasavlkae 228
                                            e + q dvdG+L+++a+lka+
  NCBI__GCF_002893965.1:WP_050656343.1 225 GEIVGQADVDGALVGGASLKAD 246
                                           ********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (261 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.77
//
[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