GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Caulobacter crescentus NA1000

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate CCNA_01970 CCNA_01970 triosephosphate isomerase

Query= SwissProt::Q8L1Z5
         (254 letters)



>FitnessBrowser__Caulo:CCNA_01970
          Length = 253

 Score =  223 bits (569), Expect = 2e-63
 Identities = 117/242 (48%), Positives = 158/242 (65%), Gaps = 1/242 (0%)

Query: 6   RPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGGENILL 65
           RP IAGNWKMNG   +L E RA+AA + +       A+   PATLL R    + G ++L 
Sbjct: 9   RPLIAGNWKMNGLSVALDEARAVAAALEAKPPAARVAIF-PPATLLHRLSQAVEGAHLLT 67

Query: 66  GGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAAWRAGL 125
           GGQ+CH    G +TGD+SA M+ +AG S VI GHSERRT + E+ A V  K +AA  AGL
Sbjct: 68  GGQDCHGKSSGAHTGDVSAEMVADAGGSLVICGHSERRTDHGETSAQVAGKAEAAAAAGL 127

Query: 126 VALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTATSADV 185
             ++CVGETLE R++ + +  +  Q+  SLP     +   +AYEP+WA+GTG TA+  ++
Sbjct: 128 EPIVCVGETLETREAGQAVSFVVSQVRDSLPTSLAGKAFSVAYEPLWAIGTGRTASVDNI 187

Query: 186 AEVHAFIHHKMHSRFGDEGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLKAIDFL 245
            E+HA I  ++ SRF ++G  + +LYGGSVKP NA E+L+   V GAL+GGASLKA DFL
Sbjct: 188 VEMHAAIRAELVSRFCEQGRTVLILYGGSVKPENAREILAAPEVGGALVGGASLKAKDFL 247

Query: 246 TI 247
            I
Sbjct: 248 AI 249


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: 218
Number of extensions: 8
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: 253
Length adjustment: 24
Effective length of query: 230
Effective length of database: 229
Effective search space:    52670
Effective search space used:    52670
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 CCNA_01970 CCNA_01970 (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.carbon/TIGR00419.hmm
# target sequence database:        /tmp/gapView.5958.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.9e-51  160.5   1.5    3.3e-51  160.3   1.5    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_01970  CCNA_01970 triosephosphate isome


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_01970  CCNA_01970 triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.3   1.5   3.3e-51   3.3e-51       1     228 []      11     244 ..      11     244 .. 0.92

  Alignments for each domain:
  == domain 1  score: 160.3 bits;  conditional E-value: 3.3e-51
                             TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 
                                           l+ +n+K+n+     ++  a  a+  a++    va+ pp   l++++++ve +++  + q+++ ++sGa+tG+
  lcl|FitnessBrowser__Caulo:CCNA_01970  11 LIAGNWKMNGLSVALDEARAVAAALEAKPPAARVAIFPPATLLHRLSQAVEgAHLLTGGQDCHGKSSGAHTGD 83 
                                           689******98888887777777777999**********************99******************** PP

                             TIGR00419  73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaa.. 143
                                           +sAem++d+G   v+ gHsErR+ + e++  ++ k   + + gl+++vCvgetle rea++ +  v  +    
  lcl|FitnessBrowser__Caulo:CCNA_01970  84 VSAEMVADAGGSLVICGHSERRTDHGETSAQVAGKAEAAAAAGLEPIVCVGETLETREAGQAVSFVVSQVRds 156
                                           ***********************************************************99999888775411 PP

                             TIGR00419 144 ...aaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaql 213
                                                A +   vA+EP ++iGtG+++s  +  ++++ +r  l     e  + v +lyG+sv+ +++ e  a +
  lcl|FitnessBrowser__Caulo:CCNA_01970 157 lptSLAGKAFSVAYEPLWAIGTGRTASVDNIVEMHAAIRAELVSRFCEQGRTVLILYGGSVKPENAREILAAP 229
                                           11144566678****************************9998888899999********************* PP

                             TIGR00419 214 dvdGvLlasavlkae 228
                                           +v G+L+++a+lka+
  lcl|FitnessBrowser__Caulo:CCNA_01970 230 EVGGALVGGASLKAK 244
                                           *************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (253 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: 8.36
//
[ok]

This GapMind analysis is from Sep 17 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