Alignments for a candidate for treC in Cronobacter condimenti 1330

GapMind for catabolism of small carbon sources

Alignments for a candidate for treC in Cronobacter condimenti 1330

Align trehalose-6-phosphate hydrolase (TreC) (EC 3.2.1.93) (characterized)
to candidate WP_007678620.1 BN137_RS04085 alpha,alpha-phosphotrehalase

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



>NCBI__GCF_000319285.1:WP_007678620.1
          Length = 551

 Score =  922 bits (2384), Expect = 0.0
 Identities = 426/544 (78%), Positives = 465/544 (85%)

Query: 7   WWQNGVIYQIYPKSFQDTTGSGTGDLRGVIQHLDYLHKLGVDAIWLTPFYVSPQVDNGYD 66
           WWQNGVIYQIYPKSFQDT+G+GTGDL GVIQ LDYLH LG+DAIWLTPFY+SPQVDNGYD
Sbjct: 7   WWQNGVIYQIYPKSFQDTSGNGTGDLAGVIQRLDYLHTLGIDAIWLTPFYLSPQVDNGYD 66

Query: 67  VANYTAIDPTYGTLDDFDELVTQAKSRGIRIILDMVFNHTSTQHAWFREALNKESPYRQF 126
           VANYTAIDP YGTLD+FD LV++A +RGIR++LDMVFNHTSTQHAWF +AL +ES +R F
Sbjct: 67  VANYTAIDPAYGTLDEFDTLVSEAHARGIRVVLDMVFNHTSTQHAWFHDALTRESAHRNF 126

Query: 127 YIWRDGEPETPPNNWRSKFGGSAWRWHAESEQYYLHLFAPEQADLNWENPAVRAELKKVC 186
           YIWRDG PE  PNNWRSKFGGSAWRWHAES QYYLHLFAPEQADLNWENP VR E+KKVC
Sbjct: 127 YIWRDGTPEEAPNNWRSKFGGSAWRWHAESGQYYLHLFAPEQADLNWENPQVRDEVKKVC 186

Query: 187 EFWADRGVDGLRLDVVNLISKDPRFPEDLDGDGRRFYTDGPRAHEFLHEMNRDVFTPRGL 246
           EFWADRGVDGLRLDV+NLISKD  FP D  GDGRRFYTDGPR H++L E++RDVF PRGL
Sbjct: 187 EFWADRGVDGLRLDVINLISKDQDFPADDRGDGRRFYTDGPRIHDYLQELSRDVFVPRGL 246

Query: 247 MTVGEMSSTSLEHCQRYAALTGSELSMTFNFHHLKVDYPGGEKWTLAKPDFVALKTLFRH 306
           MTVGEMSST+LE+CQRYAAL G ELSMTFNFHHLKVDYP G+KWTLA+PDFVALK +F H
Sbjct: 247 MTVGEMSSTTLENCQRYAALEGHELSMTFNFHHLKVDYPNGQKWTLAQPDFVALKAIFNH 306

Query: 307 WQQGMHNVAWNALFWCNHDQPRIVSRFGDEGEYRVPAAKMLAMVLHGMQGTPYIYQGEEI 366
           WQQGMHNVAWNALFWCNHDQPRIVSRFGDEG  RVPAAKMLAMVLHGMQGTPYIYQGEE+
Sbjct: 307 WQQGMHNVAWNALFWCNHDQPRIVSRFGDEGALRVPAAKMLAMVLHGMQGTPYIYQGEEL 366

Query: 367 GMTNPHFTRITDYRDVESLNMFAELRNDGRDADELLAILASKSRDNSRTPMQWSNGDNAG 426
           GMTNPHFTRI DYRDVES NMFAE R  G+  + LLAILASKSRDN RTPMQW + DN G
Sbjct: 367 GMTNPHFTRIVDYRDVESHNMFAERRAQGQSPETLLAILASKSRDNGRTPMQWDDSDNGG 426

Query: 427 FTAGEPWIGLGDNYQQINVEAALADDSSVFYTYQKLIALRKQEAILTWGNYQDLLPNSPV 486
           FT G PWIGL DNY++IN   AL D  SVFY YQKLIALRK   I TWG+YQDLL   P 
Sbjct: 427 FTTGTPWIGLCDNYREINAARALEDPDSVFYAYQKLIALRKAHPIFTWGDYQDLLAGHPY 486

Query: 487 LWCYRREWKGQTLLVIANLSREIQPWQAGQMRGNWQLVMHNYEEASPQPCAMNLRPFEAV 546
           LWCYRREW+GQ ++V+ANLSRE      G   G WQ +M NY +A+P P  +NLRPFEAV
Sbjct: 487 LWCYRREWQGQQMVVVANLSREAHWCTPGDFTGEWQTLMSNYPDAAPAPGEINLRPFEAV 546

Query: 547 WWLQ 550
            WLQ
Sbjct: 547 IWLQ 550


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: 1397
Number of extensions: 61
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 WP_007678620.1 BN137_RS04085 (alpha,alpha-phosphotrehalase)
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.61534.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-257  842.1   0.0   1.2e-257  841.9   0.0    1.0  1  NCBI__GCF_000319285.1:WP_007678620.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000319285.1:WP_007678620.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  841.9   0.0  1.2e-257  1.2e-257       1     542 [.       7     548 ..       7     550 .. 0.98

  Alignments for each domain:
  == domain 1  score: 841.9 bits;  conditional E-value: 1.2e-257
                             TIGR02403   1 klkkkviyqiyPksfkdskgkgvGdlkGiiekldylkkLgvdviWltPiyksPqkDnGyDvsdylaidpefGt 73 
                                           ++++ viyqiyPksf+d++g+g+Gdl G+i++ldyl++Lg+d+iWltP+y sPq DnGyDv++y+aidp +Gt
  NCBI__GCF_000319285.1:WP_007678620.1   7 WWQNGVIYQIYPKSFQDTSGNGTGDLAGVIQRLDYLHTLGIDAIWLTPFYLSPQVDNGYDVANYTAIDPAYGT 79 
                                           79*********************************************************************** PP

                             TIGR02403  74 ledfeeLvkeakkrnikimlDlvlnhtsteheWfkkalagdekyrdfyilrdek.gklPtnWeskfGGsaWel 145
                                           l++f++Lv+ea++r+i+++lD+v+nhtst+h+Wf++al+ ++ +r+fyi+rd + ++ P+nW+skfGGsaW++
  NCBI__GCF_000319285.1:WP_007678620.1  80 LDEFDTLVSEAHARGIRVVLDMVFNHTSTQHAWFHDALTRESAHRNFYIWRDGTpEEAPNNWRSKFGGSAWRW 152
                                           *****************************************************99****************** PP

                             TIGR02403 146 eeetekyyLhLfdktqaDLnWeneevreevadvvkfwldkGvkGfrlDvinliskdelfeddeegdgrkfytD 218
                                           ++e+++yyLhLf+++qaDLnWen++vr+ev++v++fw+d+Gv+G+rlDvinliskd++f+ d +gdgr+fytD
  NCBI__GCF_000319285.1:WP_007678620.1 153 HAESGQYYLHLFAPEQADLNWENPQVRDEVKKVCEFWADRGVDGLRLDVINLISKDQDFPADDRGDGRRFYTD 225
                                           ************************************************************************* PP

                             TIGR02403 219 gpkvheylkelneevfekdkdlltvGelssttiekcikyskleekeLsmvftfhhLkvDyengekwtkakfdf 291
                                           gp++h+yl+el+++vf   + l+tvGe+sstt+e+c++y++le +eLsm+f+fhhLkvDy+ng+kwt+a++df
  NCBI__GCF_000319285.1:WP_007678620.1 226 GPRIHDYLQELSRDVFV-PRGLMTVGEMSSTTLENCQRYAALEGHELSMTFNFHHLKVDYPNGQKWTLAQPDF 297
                                           ****************8.******************************************************* PP

                             TIGR02403 292 aklkeilkewqeelqkengwnalflnnhDqPravsrfgddeeyreesakmlaaaihllrGtpyiyqGeeiGmt 364
                                           ++lk+i+++wq++++ + +wnalf++nhDqPr+vsrfgd+++ r+ +akmla+++h ++GtpyiyqGee+Gmt
  NCBI__GCF_000319285.1:WP_007678620.1 298 VALKAIFNHWQQGMH-NVAWNALFWCNHDQPRIVSRFGDEGALRVPAAKMLAMVLHGMQGTPYIYQGEELGMT 369
                                           **************9.99******************************************************* PP

                             TIGR02403 365 npkfekiedykDveslnaykalkkkgkseeevlailkaksrDnsrtpmqWdeeknaGfstekpwlkvaknyke 437
                                           np+f++i dy+Dves n++++ +++g+s e +lail++ksrDn+rtpmqWd+++n+Gf+t++pw+ + +ny+e
  NCBI__GCF_000319285.1:WP_007678620.1 370 NPHFTRIVDYRDVESHNMFAERRAQGQSPETLLAILASKSRDNGRTPMQWDDSDNGGFTTGTPWIGLCDNYRE 442
                                           ************************************************************************* PP

                             TIGR02403 438 invekeledeesvfkfykkliklrkeeeviaeGeyealekddpkvlaylrelkkekllvlanfsgeekkvklp 510
                                           in+ ++led +svf++y+kli+lrk ++++++G+y++l+  +p +++y+re++ ++++v+an+s e + ++  
  NCBI__GCF_000319285.1:WP_007678620.1 443 INAARALEDPDSVFYAYQKLIALRKAHPIFTWGDYQDLLAGHPYLWCYRREWQGQQMVVVANLSREAHWCTPG 515
                                           ****************************************************************665555555 PP

                             TIGR02403 511 eelksakvllsnyeeaekk.aklelkPyeaivl 542
                                           + + ++++l+sny +a+ +  +++l+P+ea+++
  NCBI__GCF_000319285.1:WP_007678620.1 516 DFTGEWQTLMSNYPDAAPApGEINLRPFEAVIW 548
                                           55566***********99999*********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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 27.42
//
[ok]

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

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Candidates (tab-delimited)
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 2024 update 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