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

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.10953.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.86
//
[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:

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