Alignments for a candidate for treC in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for treC in Pseudomonas fluorescens FW300-N2E3

Align Alpha,alpha-phosphotrehalase (EC 3.2.1.93) (characterized)
to candidate AO353_15985 AO353_15985 trehalose-6-phosphate hydrolase

Query= reanno::pseudo3_N2E3:AO353_15985
         (549 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_15985
          Length = 549

 Score = 1152 bits (2980), Expect = 0.0
 Identities = 549/549 (100%), Positives = 549/549 (100%)

Query: 1   MQDWQRSVIYQIYPKSFHSHAGNPTGDLLGVVAKLDYLQWLGVDCLWITPFLRSPQRDNG 60
           MQDWQRSVIYQIYPKSFHSHAGNPTGDLLGVVAKLDYLQWLGVDCLWITPFLRSPQRDNG
Sbjct: 1   MQDWQRSVIYQIYPKSFHSHAGNPTGDLLGVVAKLDYLQWLGVDCLWITPFLRSPQRDNG 60

Query: 61  YDISDYYAIDPSYGTMADCELLIAEAGKRGIKLMLDIVVNHTSIEHSWFQQARSSLDNPY 120
           YDISDYYAIDPSYGTMADCELLIAEAGKRGIKLMLDIVVNHTSIEHSWFQQARSSLDNPY
Sbjct: 61  YDISDYYAIDPSYGTMADCELLIAEAGKRGIKLMLDIVVNHTSIEHSWFQQARSSLDNPY 120

Query: 121 RDFYIWRDQPNNWESKFGGSAWEYEAQTGQYFLHLFDHTQADLNWDNPQVRAEVFKLMRF 180
           RDFYIWRDQPNNWESKFGGSAWEYEAQTGQYFLHLFDHTQADLNWDNPQVRAEVFKLMRF
Sbjct: 121 RDFYIWRDQPNNWESKFGGSAWEYEAQTGQYFLHLFDHTQADLNWDNPQVRAEVFKLMRF 180

Query: 181 WRDKGVGGFRLDVINLISKPADFPEDHTDGRRFYTDGPNVHEYLQEMHREVFEGHDLINV 240
           WRDKGVGGFRLDVINLISKPADFPEDHTDGRRFYTDGPNVHEYLQEMHREVFEGHDLINV
Sbjct: 181 WRDKGVGGFRLDVINLISKPADFPEDHTDGRRFYTDGPNVHEYLQEMHREVFEGHDLINV 240

Query: 241 GEMSSTSLEHCIRYSRPDSKELSMTFNFHHLKVDYPNMQKWVRADFDFLELKRILSDWQT 300
           GEMSSTSLEHCIRYSRPDSKELSMTFNFHHLKVDYPNMQKWVRADFDFLELKRILSDWQT
Sbjct: 241 GEMSSTSLEHCIRYSRPDSKELSMTFNFHHLKVDYPNMQKWVRADFDFLELKRILSDWQT 300

Query: 301 GMQAGGGWNALFWCNHDQPRVVSRFGDDGEHRVVSAKMLGTALHFLQGTPFIYQGEELGM 360
           GMQAGGGWNALFWCNHDQPRVVSRFGDDGEHRVVSAKMLGTALHFLQGTPFIYQGEELGM
Sbjct: 301 GMQAGGGWNALFWCNHDQPRVVSRFGDDGEHRVVSAKMLGTALHFLQGTPFIYQGEELGM 360

Query: 361 TNPGFERIEQYRDVETLNIYRLKREAGESEASSMAAIMQKSRDNSRTPMQWSALPNAGFS 420
           TNPGFERIEQYRDVETLNIYRLKREAGESEASSMAAIMQKSRDNSRTPMQWSALPNAGFS
Sbjct: 361 TNPGFERIEQYRDVETLNIYRLKREAGESEASSMAAIMQKSRDNSRTPMQWSALPNAGFS 420

Query: 421 SSEPWIGVPANAMQINVENQLDDTTSVLHHYRQLIALRRSEPLIQDGVYRQLLPTHKQVW 480
           SSEPWIGVPANAMQINVENQLDDTTSVLHHYRQLIALRRSEPLIQDGVYRQLLPTHKQVW
Sbjct: 421 SSEPWIGVPANAMQINVENQLDDTTSVLHHYRQLIALRRSEPLIQDGVYRQLLPTHKQVW 480

Query: 481 VYLREGEGERLLVVNNFYGTACEVELPERVITDCMLQRLVISNYPDSEVRKQQLFLRPYE 540
           VYLREGEGERLLVVNNFYGTACEVELPERVITDCMLQRLVISNYPDSEVRKQQLFLRPYE
Sbjct: 481 VYLREGEGERLLVVNNFYGTACEVELPERVITDCMLQRLVISNYPDSEVRKQQLFLRPYE 540

Query: 541 SFVLHLTDH 549
           SFVLHLTDH
Sbjct: 541 SFVLHLTDH 549


Lambda     K      H
   0.321    0.137    0.436 

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: 1426
Number of extensions: 50
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: 549
Length of database: 549
Length adjustment: 36
Effective length of query: 513
Effective length of database: 513
Effective search space:   263169
Effective search space used:   263169
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 (21.9 bits)
S2: 53 (25.0 bits)

Align candidate AO353_15985 AO353_15985 (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.7949.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-264  864.8   0.0   1.5e-264  864.6   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_15985  AO353_15985 trehalose-6-phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_15985  AO353_15985 trehalose-6-phosphate hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  864.6   0.0  1.5e-264  1.5e-264       2     543 ..       4     545 ..       3     546 .. 0.99

  Alignments for each domain:
  == domain 1  score: 864.6 bits;  conditional E-value: 1.5e-264
                                     TIGR02403   2 lkkkviyqiyPksfkdskgkgvGdlkGiiekldylkkLgvdviWltPiyksPqkDnGyDvsdyla 66 
                                                   ++++viyqiyPksf+++ g+ +Gdl G++ kldyl++Lgvd++W+tP+++sPq+DnGyD+sdy+a
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_15985   4 WQRSVIYQIYPKSFHSHAGNPTGDLLGVVAKLDYLQWLGVDCLWITPFLRSPQRDNGYDISDYYA 68 
                                                   99*************************************************************** PP

                                     TIGR02403  67 idpefGtledfeeLvkeakkrnikimlDlvlnhtsteheWfkkalag.dekyrdfyilrdekgkl 130
                                                   idp++Gt++d+e L++ea kr+ik+mlD+v+nhts+eh+Wf++a+++ d++yrdfyi+rd    +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_15985  69 IDPSYGTMADCELLIAEAGKRGIKLMLDIVVNHTSIEHSWFQQARSSlDNPYRDFYIWRD----Q 129
                                                   ***********************************************************5....6 PP

                                     TIGR02403 131 PtnWeskfGGsaWeleeetekyyLhLfdktqaDLnWeneevreevadvvkfwldkGvkGfrlDvi 195
                                                   P+nWeskfGGsaWe+e++t++y+LhLfd+tqaDLnW+n++vr+ev+++++fw+dkGv GfrlDvi
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_15985 130 PNNWESKFGGSAWEYEAQTGQYFLHLFDHTQADLNWDNPQVRAEVFKLMRFWRDKGVGGFRLDVI 194
                                                   9**************************************************************** PP

                                     TIGR02403 196 nliskdelfeddeegdgrkfytDgpkvheylkelneevfekdkdlltvGelssttiekcikyskl 260
                                                   nlisk+++f++d+ +dgr+fytDgp+vheyl+e+++evfe  +dl++vGe+sst++e+ci+ys++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_15985 195 NLISKPADFPEDH-TDGRRFYTDGPNVHEYLQEMHREVFE-GHDLINVGEMSSTSLEHCIRYSRP 257
                                                   ************7.88***********************8.************************ PP

                                     TIGR02403 261 eekeLsmvftfhhLkvDyengekwtkakfdfaklkeilkewqeelqkengwnalflnnhDqPrav 325
                                                   ++keLsm+f+fhhLkvDy+n +kw++a+fdf +lk+il++wq+++q+++gwnalf++nhDqPr+v
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_15985 258 DSKELSMTFNFHHLKVDYPNMQKWVRADFDFLELKRILSDWQTGMQAGGGWNALFWCNHDQPRVV 322
                                                   ***************************************************************** PP

                                     TIGR02403 326 srfgddeeyreesakmlaaaihllrGtpyiyqGeeiGmtnpkfekiedykDveslnaykalkkkg 390
                                                   srfgdd+e+r+ sakml++a+h+l+Gtp+iyqGee+Gmtnp fe+ie+y+Dve+ln+y+ ++++g
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_15985 323 SRFGDDGEHRVVSAKMLGTALHFLQGTPFIYQGEELGMTNPGFERIEQYRDVETLNIYRLKREAG 387
                                                   ***************************************************************** PP

                                     TIGR02403 391 kseeevlailkaksrDnsrtpmqWdeeknaGfstekpwlkvaknykeinvekeledeesvfkfyk 455
                                                   +se+  +a +++ksrDnsrtpmqW++  naGfs+++pw+ v +n+ +inve++l+d++sv+++y+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_15985 388 ESEASSMAAIMQKSRDNSRTPMQWSALPNAGFSSSEPWIGVPANAMQINVENQLDDTTSVLHHYR 452
                                                   ***************************************************************** PP

                                     TIGR02403 456 kliklrkeeeviaeGeyealekddpkvlaylrelkkekllvlanfsgeekkvklpeelks....a 516
                                                   +li+lr++e++i++G y++l+  +++v+ ylre + e+llv++nf+g+ ++v+lpe++ +    +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_15985 453 QLIALRRSEPLIQDGVYRQLLPTHKQVWVYLREGEGERLLVVNNFYGTACEVELPERVITdcmlQ 517
                                                   *********************************************************99889999 PP

                                     TIGR02403 517 kvllsnyeeaekk.aklelkPyeaivle 543
                                                   ++++sny ++e++ ++l l+Pye++vl+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_15985 518 RLVISNYPDSEVRkQQLFLRPYESFVLH 545
                                                   **********999899********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (544 nodes)
Target sequences:                          1  (549 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: 11.35
//
[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