Alignments for a candidate for treC in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for treC in Klebsiella michiganensis M5al

Align trehalose-6-phosphate hydrolase (TreC;KP1_0530) (EC 3.2.1.93) (characterized)
to candidate BWI76_RS02960 BWI76_RS02960 glucohydrolase

Query= CAZy::BAG86620.1
         (551 letters)



>FitnessBrowser__Koxy:BWI76_RS02960
          Length = 551

 Score = 1038 bits (2683), Expect = 0.0
 Identities = 482/550 (87%), Positives = 507/550 (92%)

Query: 1   MNHLPHWWQNGVIYQIYPKSFQDTTGSGTGDLRGVTARLDYLQKLGVDAIWLTPFYVSPQ 60
           MN LP WWQNGVIYQIYPKSFQDTTG+GTGDLRGVT+RLDYLQKLGVDAIWLTPFYVSPQ
Sbjct: 1   MNTLPLWWQNGVIYQIYPKSFQDTTGTGTGDLRGVTSRLDYLQKLGVDAIWLTPFYVSPQ 60

Query: 61  VDNGYDVANYTAIDPSYGTMADFDALVAEAKARGIRIVLDMVLNHTSTEHEWFRQSLNKE 120
           VDNGYDVANYTAIDP+YGT+ DFD LVA+A ARGIRIVLDMVLNHTSTEH WFR++LNKE
Sbjct: 61  VDNGYDVANYTAIDPTYGTLDDFDELVAQAHARGIRIVLDMVLNHTSTEHAWFREALNKE 120

Query: 121 SPYRQFYIWRDGEPDALPNNWRSKFGGNAWQWHADSGQYYLHLFAIEQADLNWENPAVRA 180
           SPYRQFYIWRDGEP   PNNWRSKFGGNAWQWHA+S QYYLHLFA+EQADLNWENPAVRA
Sbjct: 121 SPYRQFYIWRDGEPTTPPNNWRSKFGGNAWQWHAESEQYYLHLFAVEQADLNWENPAVRA 180

Query: 181 ELKKVCEFWADRGVDGLRLDVVNLISKDQTFPCDLDGDGRRFYTDGPRVHEFLQEMSRDV 240
           ELKKVCEFWADRGVDGLRLDVVNLISKDQTFP D DGDGRRFYTDGPR HEFLQEMSRDV
Sbjct: 181 ELKKVCEFWADRGVDGLRLDVVNLISKDQTFPSDTDGDGRRFYTDGPRAHEFLQEMSRDV 240

Query: 241 FTPRNLMTVGEMSSTSLEHCQQYAALDGRELSMTFNFHHLKVDYPGGEKWTLARPDYVAL 300
           FTPR LMTVGEMSST+L HCQQYAALDG ELSMTFNFHHLKVDYPGGEKWTLARPD+VAL
Sbjct: 241 FTPRGLMTVGEMSSTTLAHCQQYAALDGGELSMTFNFHHLKVDYPGGEKWTLARPDFVAL 300

Query: 301 KALFRHWQQGMHNRAWNALFWCNHDQPRIVSRFGDEGEYRVTAAKMLAMVLHGMQGTPYI 360
           K+LFRHWQQGMHNRAWNALFWCNHDQPRIVSRFGDEGEYRV AAKMLAMVLHGMQGTPYI
Sbjct: 301 KSLFRHWQQGMHNRAWNALFWCNHDQPRIVSRFGDEGEYRVPAAKMLAMVLHGMQGTPYI 360

Query: 361 YQGEEIGMTNPHFSSISDYRDVESHNMFIERAAQGQSPDELLAILASKSRDNSRTPMPWH 420
           YQGEEIGMTNPHF  I+DYRDVESHNMFIERAAQGQ PDELLAILASKSRDNSRTPM W+
Sbjct: 361 YQGEEIGMTNPHFMRITDYRDVESHNMFIERAAQGQDPDELLAILASKSRDNSRTPMQWN 420

Query: 421 AGENGGFSDGEPWIGLGDNYQEINVEAALADPDSVFYTYQQLITLRKTLPLLTWGDYEDL 480
             ++GGFS GEPWI L DNY+EIN EAA ADP+SVFYTYQQLI LRK+ P+LTWGDY+DL
Sbjct: 421 NADHGGFSAGEPWIALCDNYREINAEAAQADPESVFYTYQQLIALRKSAPVLTWGDYQDL 480

Query: 481 LPEHPSLWCYRRQWQGQTLVVAANLSRELQAWQPAEAPGEWKMIISNYAETTPRPTGLTL 540
           LPEHPSLWCYRRQWQGQTLVV ANLSRE Q WQP    GEW M++SNYAE   RP  +TL
Sbjct: 481 LPEHPSLWCYRRQWQGQTLVVVANLSREFQRWQPEAMSGEWGMLMSNYAEAANRPAAMTL 540

Query: 541 RPFEAIWWLQ 550
           RPFEA+WWLQ
Sbjct: 541 RPFEAVWWLQ 550


Lambda     K      H
   0.320    0.136    0.446 

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: 1392
Number of extensions: 55
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 BWI76_RS02960 BWI76_RS02960 (glucohydrolase)
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.11828.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   6.4e-262  856.0   0.0   7.2e-262  855.8   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS02960  BWI76_RS02960 glucohydrolase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS02960  BWI76_RS02960 glucohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  855.8   0.0  7.2e-262  7.2e-262       1     542 [.       7     548 ..       7     550 .. 0.99

  Alignments for each domain:
  == domain 1  score: 855.8 bits;  conditional E-value: 7.2e-262
                               TIGR02403   1 klkkkviyqiyPksfkdskgkgvGdlkGiiekldylkkLgvdviWltPiyksPqkDnGyDvsdylaidpef 71 
                                             ++++ viyqiyPksf+d++g+g+Gdl+G++++ldyl+kLgvd+iWltP+y+sPq DnGyDv++y+aidp++
  lcl|FitnessBrowser__Koxy:BWI76_RS02960   7 WWQNGVIYQIYPKSFQDTTGTGTGDLRGVTSRLDYLQKLGVDAIWLTPFYVSPQVDNGYDVANYTAIDPTY 77 
                                             79********************************************************************* PP

                               TIGR02403  72 GtledfeeLvkeakkrnikimlDlvlnhtsteheWfkkalagdekyrdfyilrdek.gklPtnWeskfGGs 141
                                             Gtl+df+eLv++a++r+i+i+lD+vlnhtsteh+Wf++al+++++yr+fyi+rd + +++P+nW+skfGG+
  lcl|FitnessBrowser__Koxy:BWI76_RS02960  78 GTLDDFDELVAQAHARGIRIVLDMVLNHTSTEHAWFREALNKESPYRQFYIWRDGEpTTPPNNWRSKFGGN 148
                                             *******************************************************999************* PP

                               TIGR02403 142 aWeleeetekyyLhLfdktqaDLnWeneevreevadvvkfwldkGvkGfrlDvinliskdelfeddeegdg 212
                                             aW++++e+e+yyLhLf+++qaDLnWen++vr+e+++v++fw+d+Gv+G+rlDv+nliskd++f+ d++gdg
  lcl|FitnessBrowser__Koxy:BWI76_RS02960 149 AWQWHAESEQYYLHLFAVEQADLNWENPAVRAELKKVCEFWADRGVDGLRLDVVNLISKDQTFPSDTDGDG 219
                                             *********************************************************************** PP

                               TIGR02403 213 rkfytDgpkvheylkelneevfekdkdlltvGelssttiekcikyskleekeLsmvftfhhLkvDyengek 283
                                             r+fytDgp+ he+l+e++++vf+  + l+tvGe+sstt+ +c++y++l+  eLsm+f+fhhLkvDy+ gek
  lcl|FitnessBrowser__Koxy:BWI76_RS02960 220 RRFYTDGPRAHEFLQEMSRDVFT-PRGLMTVGEMSSTTLAHCQQYAALDGGELSMTFNFHHLKVDYPGGEK 289
                                             **********************8.*********************************************** PP

                               TIGR02403 284 wtkakfdfaklkeilkewqeelqkengwnalflnnhDqPravsrfgddeeyreesakmlaaaihllrGtpy 354
                                             wt+a++df++lk+++++wq++++ + +wnalf++nhDqPr+vsrfgd++eyr+ +akmla+++h ++Gtpy
  lcl|FitnessBrowser__Koxy:BWI76_RS02960 290 WTLARPDFVALKSLFRHWQQGMH-NRAWNALFWCNHDQPRIVSRFGDEGEYRVPAAKMLAMVLHGMQGTPY 359
                                             **********************9.89********************************************* PP

                               TIGR02403 355 iyqGeeiGmtnpkfekiedykDveslnaykalkkkgkseeevlailkaksrDnsrtpmqWdeeknaGfste 425
                                             iyqGeeiGmtnp+f +i+dy+Dves n++ +  ++g++ +e+lail++ksrDnsrtpmqW++ +++Gfs++
  lcl|FitnessBrowser__Koxy:BWI76_RS02960 360 IYQGEEIGMTNPHFMRITDYRDVESHNMFIERAAQGQDPDELLAILASKSRDNSRTPMQWNNADHGGFSAG 430
                                             *********************************************************************** PP

                               TIGR02403 426 kpwlkvaknykeinvekeledeesvfkfykkliklrkeeeviaeGeyealekddpkvlaylrelkkekllv 496
                                             +pw+++ +ny+ein+e++++d esvf++y++li+lrk+ +v+++G+y++l+ ++p++++y+r+++ ++l+v
  lcl|FitnessBrowser__Koxy:BWI76_RS02960 431 EPWIALCDNYREINAEAAQADPESVFYTYQQLIALRKSAPVLTWGDYQDLLPEHPSLWCYRRQWQGQTLVV 501
                                             *********************************************************************** PP

                               TIGR02403 497 lanfsgeekkvklpeelksakvllsnyeeaekk.aklelkPyeaivl 542
                                             +an+s e ++ + ++ + ++ +l+sny ea+++ a+++l+P+ea+++
  lcl|FitnessBrowser__Koxy:BWI76_RS02960 502 VANLSREFQRWQPEAMSGEWGMLMSNYAEAANRpAAMTLRPFEAVWW 548
                                             *****88777777777778***********9999**********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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.55
//
[ok]

This GapMind analysis is from Sep 17 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 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