GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ald-dh-CoA in Cupriavidus basilensis 4G11

Align Acetaldehyde dehydrogenase; Acetaldehyde dehydrogenase [acetylating]; EC 1.2.1.10 (characterized)
to candidate RR42_RS32630 RR42_RS32630 acetaldehyde dehydrogenase

Query= SwissProt::Q52060
         (312 letters)



>FitnessBrowser__Cup4G11:RR42_RS32630
          Length = 314

 Score =  456 bits (1172), Expect = e-133
 Identities = 237/309 (76%), Positives = 267/309 (86%), Gaps = 2/309 (0%)

Query: 4   KLKVAIIGSGNIGTDLMIKVLRNAKYLEMGAMVGIDAASDGLARAQRMGVTTTYAGVEGL 63
           K KVAIIGSGNIGTDLMIKV+RN + LEMGAMVGIDAASDGLARA R+GV TT  G+EGL
Sbjct: 8   KHKVAIIGSGNIGTDLMIKVMRNGRQLEMGAMVGIDAASDGLARAARLGVPTTAEGIEGL 67

Query: 64  IKLPEFADIDFVFDATSASAHVQNEALLRQAKPGIRLIDLTPAAIGPYCVPVVNLEEHLG 123
           +++  F DI   FDATSA AH  +  +L+Q   GI++IDLTPAAIGPY VPVVNL++ LG
Sbjct: 68  VRMAGFGDIRIAFDATSAGAHAHHNQILQQH--GIQVIDLTPAAIGPYVVPVVNLDQQLG 125

Query: 124 KLNVNMVTCGGQATIPMVAAVSRVAKVHYAEIVASISSKSAGPGTRANIDEFTETTSKAI 183
             N+NMVTCGGQATIPMVAAVSRVAKVHYAEIVASISSKSAGPGTRANIDEFTETTS+AI
Sbjct: 126 ASNINMVTCGGQATIPMVAAVSRVAKVHYAEIVASISSKSAGPGTRANIDEFTETTSQAI 185

Query: 184 EVIGGAAKGKAIIIMNPAEPPLIMRDTVYVLSAAADQAAVAASVAEMVQAVQAYVPGYRL 243
             +GGAA+GKAII++NPAEPPL+MRDTV+ LS  AD+AA+ ASV  M +AVQAYVPGYRL
Sbjct: 186 CSVGGAARGKAIIVLNPAEPPLMMRDTVFTLSEDADEAAIEASVQAMAKAVQAYVPGYRL 245

Query: 244 KQQVQFDVIPESAPLNIPGLGRFSGLKTSVFLEVEGAAHYLPAYAGNLDIMTSAALATAE 303
           KQ+VQF+ I  SAPLNIPGLG  SGLKTS+FLEVEGAAHYLPAYAGNLDIMTSAALA AE
Sbjct: 246 KQRVQFERIDPSAPLNIPGLGLMSGLKTSIFLEVEGAAHYLPAYAGNLDIMTSAALACAE 305

Query: 304 RMAQSMLNA 312
           R+AQ+ L A
Sbjct: 306 RLAQTRLAA 314


Lambda     K      H
   0.317    0.132    0.362 

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: 320
Number of extensions: 3
Number of successful extensions: 2
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: 312
Length of database: 314
Length adjustment: 27
Effective length of query: 285
Effective length of database: 287
Effective search space:    81795
Effective search space used:    81795
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate RR42_RS32630 RR42_RS32630 (acetaldehyde dehydrogenase)
to HMM TIGR03215 (acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10))

# 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/TIGR03215.hmm
# target sequence database:        /tmp/gapView.2683877.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03215  [M=285]
Accession:   TIGR03215
Description: ac_ald_DH_ac: acetaldehyde dehydrogenase (acetylating)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-145  469.9   5.9   1.6e-145  469.7   5.9    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS32630  RR42_RS32630 acetaldehyde dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS32630  RR42_RS32630 acetaldehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.7   5.9  1.6e-145  1.6e-145       1     284 [.       8     312 ..       8     313 .. 0.99

  Alignments for each domain:
  == domain 1  score: 469.7 bits;  conditional E-value: 1.6e-145
                                 TIGR03215   1 kvkvaiiGsGnigtdllikllr.sevlelallvGidpesdGlararelgvetsaeGvdalleee...di 65 
                                               k kvaiiGsGnigtdl+ik++r +++le+ ++vGid++sdGlara++lgv t+aeG+++l+++    di
  lcl|FitnessBrowser__Cup4G11:RR42_RS32630   8 KHKVAIIGSGNIGTDLMIKVMRnGRQLEMGAMVGIDAASDGLARAARLGVPTTAEGIEGLVRMAgfgDI 76 
                                               689*******************999**************************************9999** PP

                                 TIGR03215  66 divfdatsakahaenaklleelgkividltPaavGpyvvPavnleevldaknvnlvtCgGqatiPivaa 134
                                               +i+fdatsa aha+++++l+++g++vidltPaa+GpyvvP+vnl+++l a+n+n+vtCgGqatiP+vaa
  lcl|FitnessBrowser__Cup4G11:RR42_RS32630  77 RIAFDATSAGAHAHHNQILQQHGIQVIDLTPAAIGPYVVPVVNLDQQLGASNINMVTCGGQATIPMVAA 145
                                               ********************************************************************* PP

                                 TIGR03215 135 vsrvakvkyaeivasiasksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtvy 203
                                               vsrvakv+yaeivasi+sksaGpgtranideftetts+a+ +vgGa++gkaii+lnPaePpl+mrdtv+
  lcl|FitnessBrowser__Cup4G11:RR42_RS32630 146 VSRVAKVHYAEIVASISSKSAGPGTRANIDEFTETTSQAICSVGGAARGKAIIVLNPAEPPLMMRDTVF 214
                                               ********************************************************************* PP

                                 TIGR03215 204 alveeadeeaieasveemveevqkyvpGyrlkqevvld.................gekvsvlleveGag 255
                                               +l+e+ade+aieasv++m ++vq+yvpGyrlkq+v+++                 g k+s++leveGa+
  lcl|FitnessBrowser__Cup4G11:RR42_RS32630 215 TLSEDADEAAIEASVQAMAKAVQAYVPGYRLKQRVQFEridpsaplnipglglmsGLKTSIFLEVEGAA 283
                                               ********************************************************************* PP

                                 TIGR03215 256 dylPkyaGnldiltaaalavaeklaeell 284
                                               +ylP+yaGnldi+t+aala+ae+la+++l
  lcl|FitnessBrowser__Cup4G11:RR42_RS32630 284 HYLPAYAGNLDIMTSAALACAERLAQTRL 312
                                               *************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (314 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 23.03
//
[ok]

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

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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:

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