GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gloB in Paraburkholderia bryophila 376MFSha3.1

Align hydroxyacylglutathione hydrolase (EC 3.1.2.6) (characterized)
to candidate H281DRAFT_04399 H281DRAFT_04399 hydroxyacylglutathione hydrolase

Query= BRENDA::Q8ZRM2
         (251 letters)



>FitnessBrowser__Burk376:H281DRAFT_04399
          Length = 263

 Score =  205 bits (522), Expect = 7e-58
 Identities = 113/256 (44%), Positives = 151/256 (58%), Gaps = 12/256 (4%)

Query: 6   IPAFQDNYIWVLTNDEGRCVIVDPGEAAPVLKAIAEHKWMPEAIFLTHHHHDHVGGVKEL 65
           +PAF+DNYIWV++ D    V+VDPGEAAPV   +A   W   AI LTHHH DHVGGV +L
Sbjct: 9   VPAFEDNYIWVVS-DGYHAVVVDPGEAAPVRAYLARRGWRLSAILLTHHHQDHVGGVADL 67

Query: 66  LQHFPQMTVYGPAETQDKGATHLVGDGDTIRVLGEKFTL--FATPGHTLGHVCYFSR--- 120
           L     + VYGPA       TH +  GD + +      L     PGHT GH+ YF     
Sbjct: 68  LNG-QAVPVYGPAGEAIGHLTHRLKHGDRVTIAAPALDLSVLEVPGHTSGHIAYFQAADP 126

Query: 121 ---PYLFCGDTLFSGGCGRLFEGTPSQMYQSLMKINSLPDDTLICCAHEYTLANIKFALS 177
              P++FCGDTLF+ GCGRLFEGTPSQM  SL  + +LP  T + CAHEYTL+NI+FAL+
Sbjct: 127 GGTPHVFCGDTLFACGCGRLFEGTPSQMLASLDSLAALPGATEVHCAHEYTLSNIRFALA 186

Query: 178 ILPHDSFINEYYRKVKELRVKKQMTLPVILKNERKINLFLRTEDIDLINEINKETILQQP 237
             P +  +  +  K  +LR +K  TLP  + +ER +N FLR ++  +   + ++     P
Sbjct: 187 CDPDNDELLAWRDKASDLRARKVPTLPTTIAHERAVNPFLRADNPAIQTTLREQLHADVP 246

Query: 238 E--ARFAWLRSKKDTF 251
           +  A F  +R  K+ F
Sbjct: 247 DRLASFTLMREWKNRF 262


Lambda     K      H
   0.323    0.140    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: 249
Number of extensions: 15
Number of successful extensions: 5
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: 251
Length of database: 263
Length adjustment: 24
Effective length of query: 227
Effective length of database: 239
Effective search space:    54253
Effective search space used:    54253
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate H281DRAFT_04399 H281DRAFT_04399 (hydroxyacylglutathione hydrolase)
to HMM TIGR03413 (gloB: hydroxyacylglutathione hydrolase (EC 3.1.2.6))

# 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/TIGR03413.hmm
# target sequence database:        /tmp/gapView.30577.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03413  [M=248]
Accession:   TIGR03413
Description: GSH_gloB: hydroxyacylglutathione hydrolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
     6e-102  326.2   0.0   6.8e-102  326.1   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_04399  H281DRAFT_04399 hydroxyacylgluta


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_04399  H281DRAFT_04399 hydroxyacylglutathione hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  326.1   0.0  6.8e-102  6.8e-102       2     248 .]       7     262 ..       6     262 .. 0.97

  Alignments for each domain:
  == domain 1  score: 326.1 bits;  conditional E-value: 6.8e-102
                                    TIGR03413   2 iaipalsdNyiwllkdekseavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaellekf 67 
                                                  +++pa++dNyiw+++d   +avvvDpgea+pv ++l+++g++l+aillTHhH+DHvggva+ll+  
  lcl|FitnessBrowser__Burk376:H281DRAFT_04399   7 VPVPAFEDNYIWVVSDGY-HAVVVDPGEAAPVRAYLARRGWRLSAILLTHHHQDHVGGVADLLNGQ 71 
                                                  589*************99.*********************************************** PP

                                    TIGR03413  68 pvkvvgpaeeripgltkevkegdevel..lelevevlevpGHtlgHiayyleee....kvlFcgDt 127
                                                   v+v+gpa e+i +lt+++k+gd+v++   +l+++vlevpGHt+gHiay+++++    +++FcgDt
  lcl|FitnessBrowser__Burk376:H281DRAFT_04399  72 AVPVYGPAGEAIGHLTHRLKHGDRVTIaaPALDLSVLEVPGHTSGHIAYFQAADpggtPHVFCGDT 137
                                                  **************************955578899****************98899999******* PP

                                    TIGR03413 128 LfsaGCGrlfegtaeqmleslqklaaLpeetkvycaHEYtlsNlrFalavepenealkerlkevea 193
                                                  Lf++GCGrlfegt++qml+sl+ laaLp +t+v+caHEYtlsN+rFala++p+n++l ++ +++++
  lcl|FitnessBrowser__Burk376:H281DRAFT_04399 138 LFACGCGRLFEGTPSQMLASLDSLAALPGATEVHCAHEYTLSNIRFALACDPDNDELLAWRDKASD 203
                                                  ****************************************************************** PP

                                    TIGR03413 194 lrakgkptlPstlaeekatNpFLraeeaevkaalee....ekaeevevfaelRekkdkf 248
                                                  lra++ ptlP+t+a+e+a+NpFLra++++++++l+e    +  ++++ f+ +Re+k++f
  lcl|FitnessBrowser__Burk376:H281DRAFT_04399 204 LRARKVPTLPTTIAHERAVNPFLRADNPAIQTTLREqlhaDVPDRLASFTLMREWKNRF 262
                                                  *******************************9999977767778999**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (263 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 6.77
//
[ok]

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

Links

Downloads

Related tools

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:

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:

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:

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:

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