GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ald-dh-CoA in Paraburkholderia bryophila 376MFSha3.1

Align Acetaldehyde dehydrogenase; Acetaldehyde dehydrogenase [acetylating]; EC 1.2.1.10 (characterized)
to candidate H281DRAFT_01665 H281DRAFT_01665 acetaldehyde dehydrogenase

Query= SwissProt::Q52060
         (312 letters)



>FitnessBrowser__Burk376:H281DRAFT_01665
          Length = 320

 Score =  432 bits (1110), Expect = e-126
 Identities = 221/312 (70%), Positives = 261/312 (83%), Gaps = 3/312 (0%)

Query: 1   MNQKLKVAIIGSGNIGTDLMIKVLRNAKYLEMGAMVGIDAASDGLARAQRMGVTTTYAGV 60
           MN+K+KVAIIG GNIGTDLMIKV+RN+++LEM AMVG+D  SDGLARA+RMGV TT  G+
Sbjct: 1   MNEKVKVAIIGPGNIGTDLMIKVMRNSQHLEMAAMVGVDPKSDGLARAERMGVATTAEGI 60

Query: 61  EGLIKLPEFADIDFVFDATSASAHVQNEALLRQAKPGIRLIDLTPAAIGPYCVPVVNLEE 120
           +GL+KL  F +ID VFDATSASAH  +  +L+  K G+++IDLTPAA+GPY +P +NLE 
Sbjct: 61  DGLLKLDVFKNIDIVFDATSASAHKHHNDVLQ--KHGVQVIDLTPAAVGPYVIPAINLEA 118

Query: 121 HLGKLNVNMVTCGGQATIPMVAAVSRVAKVHYAEIVASISSKSAGPGTRANIDEFTETTS 180
                N+NMVTCGGQATIP+VAAVSRVAKVHYAEIVASISS+SAGPGTRANIDEFTETT 
Sbjct: 119 ENAS-NMNMVTCGGQATIPIVAAVSRVAKVHYAEIVASISSRSAGPGTRANIDEFTETTR 177

Query: 181 KAIEVIGGAAKGKAIIIMNPAEPPLIMRDTVYVLSAAADQAAVAASVAEMVQAVQAYVPG 240
            AIE +GGA +GKAII++NPAEPPLIMRDTV+VLS   D  AV  SVA+M+ +VQAYVPG
Sbjct: 178 SAIETLGGATRGKAIIVLNPAEPPLIMRDTVFVLSDLVDVNAVEDSVAQMITSVQAYVPG 237

Query: 241 YRLKQQVQFDVIPESAPLNIPGLGRFSGLKTSVFLEVEGAAHYLPAYAGNLDIMTSAALA 300
           YRLKQ++QFD++    PLN+PGLG   GLKTSVFLEVEGAAHYLP+YAGNLDIMTSAALA
Sbjct: 238 YRLKQKIQFDIVSPEKPLNVPGLGVKHGLKTSVFLEVEGAAHYLPSYAGNLDIMTSAALA 297

Query: 301 TAERMAQSMLNA 312
             + MA+  L A
Sbjct: 298 CGDMMARRRLAA 309


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: 339
Number of extensions: 5
Number of successful extensions: 3
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: 320
Length adjustment: 27
Effective length of query: 285
Effective length of database: 293
Effective search space:    83505
Effective search space used:    83505
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 H281DRAFT_01665 H281DRAFT_01665 (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.23051.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   3.5e-146  471.9   5.7     4e-146  471.7   5.7    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_01665  H281DRAFT_01665 acetaldehyde deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_01665  H281DRAFT_01665 acetaldehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  471.7   5.7    4e-146    4e-146       1     284 [.       4     307 ..       4     308 .. 0.99

  Alignments for each domain:
  == domain 1  score: 471.7 bits;  conditional E-value: 4e-146
                                    TIGR03215   1 kvkvaiiGsGnigtdllikllr.sevlelallvGidpesdGlararelgvetsaeGvdalleee.. 63 
                                                  kvkvaiiG+Gnigtdl+ik++r s++le+a++vG+dp+sdGlara+++gv+t+aeG+d+ll+ +  
  lcl|FitnessBrowser__Burk376:H281DRAFT_01665   4 KVKVAIIGPGNIGTDLMIKVMRnSQHLEMAAMVGVDPKSDGLARAERMGVATTAEGIDGLLKLDvf 69 
                                                  79********************9***************************************9889 PP

                                    TIGR03215  64 .didivfdatsakahaenaklleelgkividltPaavGpyvvPavnleevldaknvnlvtCgGqat 128
                                                   +idivfdatsa+ah++++++l+++g++vidltPaavGpyv+Pa+nle+ ++a+n+n+vtCgGqat
  lcl|FitnessBrowser__Burk376:H281DRAFT_01665  70 kNIDIVFDATSASAHKHHNDVLQKHGVQVIDLTPAAVGPYVIPAINLEA-ENASNMNMVTCGGQAT 134
                                                  9**********************************************98.8899************ PP

                                    TIGR03215 129 iPivaavsrvakvkyaeivasiasksaGpgtranideftettskaleqvgGakkgkaiiilnPaeP 194
                                                  iPivaavsrvakv+yaeivasi+s+saGpgtranideftett+ a+e++gGa++gkaii+lnPaeP
  lcl|FitnessBrowser__Burk376:H281DRAFT_01665 135 IPIVAAVSRVAKVHYAEIVASISSRSAGPGTRANIDEFTETTRSAIETLGGATRGKAIIVLNPAEP 200
                                                  ****************************************************************** PP

                                    TIGR03215 195 pllmrdtvyalveeadeeaieasveemveevqkyvpGyrlkqevvld.................ge 243
                                                  pl+mrdtv++l++ +d +a+e+sv++m+++vq+yvpGyrlkq++++d                 g 
  lcl|FitnessBrowser__Burk376:H281DRAFT_01665 201 PLIMRDTVFVLSDLVDVNAVEDSVAQMITSVQAYVPGYRLKQKIQFDivspekplnvpglgvkhGL 266
                                                  ****************************************************************** PP

                                    TIGR03215 244 kvsvlleveGagdylPkyaGnldiltaaalavaeklaeell 284
                                                  k+sv+leveGa++ylP+yaGnldi+t+aala+++++a+++l
  lcl|FitnessBrowser__Burk376:H281DRAFT_01665 267 KTSVFLEVEGAAHYLPSYAGNLDIMTSAALACGDMMARRRL 307
                                                  *************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (320 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.17
//
[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