Alignments for a candidate for treC in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for treC in Escherichia coli BW25113

Align trehalose-6-phosphate hydrolase (TreC) (EC 3.2.1.93) (characterized)
to candidate 18264 b4239 trehalose-6-P hydrolase (NCBI)

Query= CAZy::AAC77196.1
         (551 letters)



>FitnessBrowser__Keio:18264
          Length = 551

 Score = 1176 bits (3042), Expect = 0.0
 Identities = 551/551 (100%), Positives = 551/551 (100%)

Query: 1   MTHLPHWWQNGVIYQIYPKSFQDTTGSGTGDLRGVIQHLDYLHKLGVDAIWLTPFYVSPQ 60
           MTHLPHWWQNGVIYQIYPKSFQDTTGSGTGDLRGVIQHLDYLHKLGVDAIWLTPFYVSPQ
Sbjct: 1   MTHLPHWWQNGVIYQIYPKSFQDTTGSGTGDLRGVIQHLDYLHKLGVDAIWLTPFYVSPQ 60

Query: 61  VDNGYDVANYTAIDPTYGTLDDFDELVTQAKSRGIRIILDMVFNHTSTQHAWFREALNKE 120
           VDNGYDVANYTAIDPTYGTLDDFDELVTQAKSRGIRIILDMVFNHTSTQHAWFREALNKE
Sbjct: 61  VDNGYDVANYTAIDPTYGTLDDFDELVTQAKSRGIRIILDMVFNHTSTQHAWFREALNKE 120

Query: 121 SPYRQFYIWRDGEPETPPNNWRSKFGGSAWRWHAESEQYYLHLFAPEQADLNWENPAVRA 180
           SPYRQFYIWRDGEPETPPNNWRSKFGGSAWRWHAESEQYYLHLFAPEQADLNWENPAVRA
Sbjct: 121 SPYRQFYIWRDGEPETPPNNWRSKFGGSAWRWHAESEQYYLHLFAPEQADLNWENPAVRA 180

Query: 181 ELKKVCEFWADRGVDGLRLDVVNLISKDPRFPEDLDGDGRRFYTDGPRAHEFLHEMNRDV 240
           ELKKVCEFWADRGVDGLRLDVVNLISKDPRFPEDLDGDGRRFYTDGPRAHEFLHEMNRDV
Sbjct: 181 ELKKVCEFWADRGVDGLRLDVVNLISKDPRFPEDLDGDGRRFYTDGPRAHEFLHEMNRDV 240

Query: 241 FTPRGLMTVGEMSSTSLEHCQRYAALTGSELSMTFNFHHLKVDYPGGEKWTLAKPDFVAL 300
           FTPRGLMTVGEMSSTSLEHCQRYAALTGSELSMTFNFHHLKVDYPGGEKWTLAKPDFVAL
Sbjct: 241 FTPRGLMTVGEMSSTSLEHCQRYAALTGSELSMTFNFHHLKVDYPGGEKWTLAKPDFVAL 300

Query: 301 KTLFRHWQQGMHNVAWNALFWCNHDQPRIVSRFGDEGEYRVPAAKMLAMVLHGMQGTPYI 360
           KTLFRHWQQGMHNVAWNALFWCNHDQPRIVSRFGDEGEYRVPAAKMLAMVLHGMQGTPYI
Sbjct: 301 KTLFRHWQQGMHNVAWNALFWCNHDQPRIVSRFGDEGEYRVPAAKMLAMVLHGMQGTPYI 360

Query: 361 YQGEEIGMTNPHFTRITDYRDVESLNMFAELRNDGRDADELLAILASKSRDNSRTPMQWS 420
           YQGEEIGMTNPHFTRITDYRDVESLNMFAELRNDGRDADELLAILASKSRDNSRTPMQWS
Sbjct: 361 YQGEEIGMTNPHFTRITDYRDVESLNMFAELRNDGRDADELLAILASKSRDNSRTPMQWS 420

Query: 421 NGDNAGFTAGEPWIGLGDNYQQINVEAALADDSSVFYTYQKLIALRKQEAILTWGNYQDL 480
           NGDNAGFTAGEPWIGLGDNYQQINVEAALADDSSVFYTYQKLIALRKQEAILTWGNYQDL
Sbjct: 421 NGDNAGFTAGEPWIGLGDNYQQINVEAALADDSSVFYTYQKLIALRKQEAILTWGNYQDL 480

Query: 481 LPNSPVLWCYRREWKGQTLLVIANLSREIQPWQAGQMRGNWQLVMHNYEEASPQPCAMNL 540
           LPNSPVLWCYRREWKGQTLLVIANLSREIQPWQAGQMRGNWQLVMHNYEEASPQPCAMNL
Sbjct: 481 LPNSPVLWCYRREWKGQTLLVIANLSREIQPWQAGQMRGNWQLVMHNYEEASPQPCAMNL 540

Query: 541 RPFEAVWWLQK 551
           RPFEAVWWLQK
Sbjct: 541 RPFEAVWWLQK 551


Lambda     K      H
   0.320    0.136    0.448 

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: 1499
Number of extensions: 59
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: 551
Length of database: 551
Length adjustment: 36
Effective length of query: 515
Effective length of database: 515
Effective search space:   265225
Effective search space used:   265225
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: 53 (25.0 bits)

Align candidate 18264 b4239 (trehalose-6-P hydrolase (NCBI))
to HMM TIGR02403 (treC: alpha,alpha-phosphotrehalase (EC 3.2.1.93))

# 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/TIGR02403.hmm
# target sequence database:        /tmp/gapView.25493.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02403  [M=544]
Accession:   TIGR02403
Description: trehalose_treC: alpha,alpha-phosphotrehalase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.3e-269  881.4   0.0   1.4e-269  881.2   0.0    1.0  1  lcl|FitnessBrowser__Keio:18264  b4239 trehalose-6-P hydrolase (N


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:18264  b4239 trehalose-6-P hydrolase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  881.2   0.0  1.4e-269  1.4e-269       1     542 [.       7     548 ..       7     550 .. 0.99

  Alignments for each domain:
  == domain 1  score: 881.2 bits;  conditional E-value: 1.4e-269
                       TIGR02403   1 klkkkviyqiyPksfkdskgkgvGdlkGiiekldylkkLgvdviWltPiyksPqkDnGyDvsdylaidpefGtledfee 79 
                                     ++++ viyqiyPksf+d++g+g+Gdl+G+i++ldyl+kLgvd+iWltP+y+sPq DnGyDv++y+aidp++Gtl+df+e
  lcl|FitnessBrowser__Keio:18264   7 WWQNGVIYQIYPKSFQDTTGSGTGDLRGVIQHLDYLHKLGVDAIWLTPFYVSPQVDNGYDVANYTAIDPTYGTLDDFDE 85 
                                     79***************************************************************************** PP

                       TIGR02403  80 LvkeakkrnikimlDlvlnhtsteheWfkkalagdekyrdfyilrdek.gklPtnWeskfGGsaWeleeetekyyLhLf 157
                                     Lv++ak+r+i+i+lD+v+nhtst+h+Wf++al+++++yr+fyi+rd + +++P+nW+skfGGsaW++++e+e+yyLhLf
  lcl|FitnessBrowser__Keio:18264  86 LVTQAKSRGIRIILDMVFNHTSTQHAWFREALNKESPYRQFYIWRDGEpETPPNNWRSKFGGSAWRWHAESEQYYLHLF 164
                                     ***********************************************99****************************** PP

                       TIGR02403 158 dktqaDLnWeneevreevadvvkfwldkGvkGfrlDvinliskdelfeddeegdgrkfytDgpkvheylkelneevfek 236
                                     +++qaDLnWen++vr+e+++v++fw+d+Gv+G+rlDv+nliskd +f++d +gdgr+fytDgp+ he+l+e+n++vf+ 
  lcl|FitnessBrowser__Keio:18264 165 APEQADLNWENPAVRAELKKVCEFWADRGVDGLRLDVVNLISKDPRFPEDLDGDGRRFYTDGPRAHEFLHEMNRDVFT- 242
                                     *****************************************************************************8. PP

                       TIGR02403 237 dkdlltvGelssttiekcikyskleekeLsmvftfhhLkvDyengekwtkakfdfaklkeilkewqeelqkengwnalf 315
                                      + l+tvGe+sst++e+c++y++l+ +eLsm+f+fhhLkvDy+ gekwt+ak+df++lk+++++wq++++ + +wnalf
  lcl|FitnessBrowser__Keio:18264 243 PRGLMTVGEMSSTSLEHCQRYAALTGSELSMTFNFHHLKVDYPGGEKWTLAKPDFVALKTLFRHWQQGMH-NVAWNALF 320
                                     *********************************************************************9.99****** PP

                       TIGR02403 316 lnnhDqPravsrfgddeeyreesakmlaaaihllrGtpyiyqGeeiGmtnpkfekiedykDveslnaykalkkkgksee 394
                                     ++nhDqPr+vsrfgd++eyr+ +akmla+++h ++GtpyiyqGeeiGmtnp+f++i+dy+Dvesln++++l+++g++++
  lcl|FitnessBrowser__Keio:18264 321 WCNHDQPRIVSRFGDEGEYRVPAAKMLAMVLHGMQGTPYIYQGEEIGMTNPHFTRITDYRDVESLNMFAELRNDGRDAD 399
                                     ******************************************************************************* PP

                       TIGR02403 395 evlailkaksrDnsrtpmqWdeeknaGfstekpwlkvaknykeinvekeledeesvfkfykkliklrkeeeviaeGeye 473
                                     e+lail++ksrDnsrtpmqW++ +naGf++++pw+ +++ny++inve++l+d++svf++y+kli+lrk+e+++++G+y+
  lcl|FitnessBrowser__Keio:18264 400 ELLAILASKSRDNSRTPMQWSNGDNAGFTAGEPWIGLGDNYQQINVEAALADDSSVFYTYQKLIALRKQEAILTWGNYQ 478
                                     ******************************************************************************* PP

                       TIGR02403 474 alekddpkvlaylrelkkekllvlanfsgeekkvklpeelksakvllsnyeeaekk.aklelkPyeaivl 542
                                     +l+ ++p +++y+re+k ++llv+an+s e +  +  +   +++++++nyeea+ + ++++l+P+ea+++
  lcl|FitnessBrowser__Keio:18264 479 DLLPNSPVLWCYRREWKGQTLLVIANLSREIQPWQAGQMRGNWQLVMHNYEEASPQpCAMNLRPFEAVWW 548
                                     ****************************98888888888888**************9**********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (544 nodes)
Target sequences:                          1  (551 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.36
//
[ok]

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 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