Alignments for a candidate for treC in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for treC in Pseudomonas simiae WCS417

Align Alpha,alpha-phosphotrehalase (EC 3.2.1.93) (characterized)
to candidate GFF4502 PS417_23045 trehalose-6-phosphate hydrolase

Query= reanno::WCS417:GFF4502
         (548 letters)



>FitnessBrowser__WCS417:GFF4502
          Length = 548

 Score = 1158 bits (2995), Expect = 0.0
 Identities = 548/548 (100%), Positives = 548/548 (100%)

Query: 1   MQDWQHSVIYQIYPKSFHSHAGNATGDLLGIVDKLDYLKWLGVDCLWITPFLRSPQRDNG 60
           MQDWQHSVIYQIYPKSFHSHAGNATGDLLGIVDKLDYLKWLGVDCLWITPFLRSPQRDNG
Sbjct: 1   MQDWQHSVIYQIYPKSFHSHAGNATGDLLGIVDKLDYLKWLGVDCLWITPFLRSPQRDNG 60

Query: 61  YDISDYYAIDPSYGTMADCDLLISEAAKRGIKLMLDIVVNHTSIEHEWFQQARSSLDNPY 120
           YDISDYYAIDPSYGTMADCDLLISEAAKRGIKLMLDIVVNHTSIEHEWFQQARSSLDNPY
Sbjct: 61  YDISDYYAIDPSYGTMADCDLLISEAAKRGIKLMLDIVVNHTSIEHEWFQQARSSLDNPY 120

Query: 121 RDFYIWRDQPNNWESKFGGSAWEYEAQTGQYFLHLFDHTQADLNWDNPKVRAEVFKLMRF 180
           RDFYIWRDQPNNWESKFGGSAWEYEAQTGQYFLHLFDHTQADLNWDNPKVRAEVFKLMRF
Sbjct: 121 RDFYIWRDQPNNWESKFGGSAWEYEAQTGQYFLHLFDHTQADLNWDNPKVRAEVFKLMRF 180

Query: 181 WRDKGVGGFRLDVINLISKPADFPEDNTDGRRFYTDGPNVHEYLQEMHREVFEGHDLINV 240
           WRDKGVGGFRLDVINLISKPADFPEDNTDGRRFYTDGPNVHEYLQEMHREVFEGHDLINV
Sbjct: 181 WRDKGVGGFRLDVINLISKPADFPEDNTDGRRFYTDGPNVHEYLQEMHREVFEGHDLINV 240

Query: 241 GEMSSTSLEHCIRYSRPESKELSMTFNFHHLKVDYPNLQKWVKADFDFLQLKQIFTDWQL 300
           GEMSSTSLEHCIRYSRPESKELSMTFNFHHLKVDYPNLQKWVKADFDFLQLKQIFTDWQL
Sbjct: 241 GEMSSTSLEHCIRYSRPESKELSMTFNFHHLKVDYPNLQKWVKADFDFLQLKQIFTDWQL 300

Query: 301 GMQAGGGWNALFWCNHDQPRVVSRFGNDGEHRVVSAKMLATALHFLQGTPYVYQGEELGM 360
           GMQAGGGWNALFWCNHDQPRVVSRFGNDGEHRVVSAKMLATALHFLQGTPYVYQGEELGM
Sbjct: 301 GMQAGGGWNALFWCNHDQPRVVSRFGNDGEHRVVSAKMLATALHFLQGTPYVYQGEELGM 360

Query: 361 TNPGFDRIEQYRDVESLNIFRLKRDAGEPEASSMAAIMQKSRDNGRTPMQWNAGENAGFS 420
           TNPGFDRIEQYRDVESLNIFRLKRDAGEPEASSMAAIMQKSRDNGRTPMQWNAGENAGFS
Sbjct: 361 TNPGFDRIEQYRDVESLNIFRLKRDAGEPEASSMAAIMQKSRDNGRTPMQWNAGENAGFS 420

Query: 421 TGEPWIGIPANAAQINVESQLDDPDSVLHHYRALIALRRHEPLIQEGVYRPLLQDHLRVW 480
           TGEPWIGIPANAAQINVESQLDDPDSVLHHYRALIALRRHEPLIQEGVYRPLLQDHLRVW
Sbjct: 421 TGEPWIGIPANAAQINVESQLDDPDSVLHHYRALIALRRHEPLIQEGVYRPLLQDHLRVW 480

Query: 481 AYLREGHGERLLVLNNFYGTPCEIQLPDNVINPAREQRVLISNYPDCPQRTATVTLRPYE 540
           AYLREGHGERLLVLNNFYGTPCEIQLPDNVINPAREQRVLISNYPDCPQRTATVTLRPYE
Sbjct: 481 AYLREGHGERLLVLNNFYGTPCEIQLPDNVINPAREQRVLISNYPDCPQRTATVTLRPYE 540

Query: 541 SFVLHLTD 548
           SFVLHLTD
Sbjct: 541 SFVLHLTD 548


Lambda     K      H
   0.321    0.138    0.443 

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: 1466
Number of extensions: 51
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: 548
Length of database: 548
Length adjustment: 36
Effective length of query: 512
Effective length of database: 512
Effective search space:   262144
Effective search space used:   262144
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 GFF4502 PS417_23045 (trehalose-6-phosphate hydrolase)
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.14557.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.1e-264  865.0   0.0   1.3e-264  864.8   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF4502  PS417_23045 trehalose-6-phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4502  PS417_23045 trehalose-6-phosphate hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  864.8   0.0  1.3e-264  1.3e-264       2     543 ..       4     545 ..       3     546 .. 0.99

  Alignments for each domain:
  == domain 1  score: 864.8 bits;  conditional E-value: 1.3e-264
                           TIGR02403   2 lkkkviyqiyPksfkdskgkgvGdlkGiiekldylkkLgvdviWltPiyksPqkDnGyDvsdylaidpefGtled 76 
                                         ++++viyqiyPksf+++ g+++Gdl Gi++kldylk+Lgvd++W+tP+++sPq+DnGyD+sdy+aidp++Gt++d
  lcl|FitnessBrowser__WCS417:GFF4502   4 WQHSVIYQIYPKSFHSHAGNATGDLLGIVDKLDYLKWLGVDCLWITPFLRSPQRDNGYDISDYYAIDPSYGTMAD 78 
                                         899************************************************************************ PP

                           TIGR02403  77 feeLvkeakkrnikimlDlvlnhtsteheWfkkalag.dekyrdfyilrdekgklPtnWeskfGGsaWeleeete 150
                                         ++ L++ea kr+ik+mlD+v+nhts+eheWf++a+++ d++yrdfyi+rd    +P+nWeskfGGsaWe+e++t+
  lcl|FitnessBrowser__WCS417:GFF4502  79 CDLLISEAAKRGIKLMLDIVVNHTSIEHEWFQQARSSlDNPYRDFYIWRD----QPNNWESKFGGSAWEYEAQTG 149
                                         *************************************************5....69******************* PP

                           TIGR02403 151 kyyLhLfdktqaDLnWeneevreevadvvkfwldkGvkGfrlDvinliskdelfeddeegdgrkfytDgpkvhey 225
                                         +y+LhLfd+tqaDLnW+n++vr+ev+++++fw+dkGv GfrlDvinlisk+++f++d+ +dgr+fytDgp+vhey
  lcl|FitnessBrowser__WCS417:GFF4502 150 QYFLHLFDHTQADLNWDNPKVRAEVFKLMRFWRDKGVGGFRLDVINLISKPADFPEDN-TDGRRFYTDGPNVHEY 223
                                         ********************************************************96.89************** PP

                           TIGR02403 226 lkelneevfekdkdlltvGelssttiekcikyskleekeLsmvftfhhLkvDyengekwtkakfdfaklkeilke 300
                                         l+e+++evfe  +dl++vGe+sst++e+ci+ys++e+keLsm+f+fhhLkvDy+n +kw+ka+fdf +lk+i+++
  lcl|FitnessBrowser__WCS417:GFF4502 224 LQEMHREVFE-GHDLINVGEMSSTSLEHCIRYSRPESKELSMTFNFHHLKVDYPNLQKWVKADFDFLQLKQIFTD 297
                                         *********8.**************************************************************** PP

                           TIGR02403 301 wqeelqkengwnalflnnhDqPravsrfgddeeyreesakmlaaaihllrGtpyiyqGeeiGmtnpkfekiedyk 375
                                         wq ++q+++gwnalf++nhDqPr+vsrfg+d+e+r+ sakmla+a+h+l+Gtpy+yqGee+Gmtnp f++ie+y+
  lcl|FitnessBrowser__WCS417:GFF4502 298 WQLGMQAGGGWNALFWCNHDQPRVVSRFGNDGEHRVVSAKMLATALHFLQGTPYVYQGEELGMTNPGFDRIEQYR 372
                                         *************************************************************************** PP

                           TIGR02403 376 DveslnaykalkkkgkseeevlailkaksrDnsrtpmqWdeeknaGfstekpwlkvaknykeinvekeledeesv 450
                                         Dvesln+++ ++++g+ e+  +a +++ksrDn+rtpmqW++ +naGfst++pw+ + +n+++inve++l+d +sv
  lcl|FitnessBrowser__WCS417:GFF4502 373 DVESLNIFRLKRDAGEPEASSMAAIMQKSRDNGRTPMQWNAGENAGFSTGEPWIGIPANAAQINVESQLDDPDSV 447
                                         *************************************************************************** PP

                           TIGR02403 451 fkfykkliklrkeeeviaeGeyealekddpkvlaylrelkkekllvlanfsgeekkvklpeelks....akvlls 521
                                         +++y+ li+lr++e++i+eG y+ l++d+ +v+aylre + e+llvl+nf+g+ ++++lp+++ +    ++vl+s
  lcl|FitnessBrowser__WCS417:GFF4502 448 LHHYRALIALRRHEPLIQEGVYRPLLQDHLRVWAYLREGHGERLLVLNNFYGTPCEIQLPDNVINpareQRVLIS 522
                                         **************************************************************99989989***** PP

                           TIGR02403 522 nyeeaekk.aklelkPyeaivle 543
                                         ny +  ++ a+++l+Pye++vl+
  lcl|FitnessBrowser__WCS417:GFF4502 523 NYPDCPQRtATVTLRPYESFVLH 545
                                         ***9988879*********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (544 nodes)
Target sequences:                          1  (548 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: 00:00:00.02
# Mc/sec: 11.06
//
[ok]

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

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Protein sequences (fasta format)
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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