GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ald-dh-CoA in Shewanella halifaxensis HAW-EB4

Align Acetaldehyde dehydrogenase 2; EC 1.2.1.10; Acetaldehyde dehydrogenase [acetylating] 2 (uncharacterized)
to candidate WP_012277178.1 SHAL_RS10915 acetaldehyde dehydrogenase (acetylating)

Query= curated2:Q396N9
         (299 letters)



>NCBI__GCF_000019185.1:WP_012277178.1
          Length = 307

 Score =  459 bits (1182), Expect = e-134
 Identities = 230/290 (79%), Positives = 253/290 (87%), Gaps = 1/290 (0%)

Query: 3   KIKCALIGPGNIGTDLLYKLRRSTVLEPVWMVGVDPASDGLARAREFGLKTTDKGVDGLL 62
           KIKCALIG GNIGTDLLYKL RS VLEPVWMVG+DP SDGLARA+  GLK T  G++GLL
Sbjct: 4   KIKCALIGSGNIGTDLLYKLMRSDVLEPVWMVGIDPESDGLARAKAAGLKVTADGINGLL 63

Query: 63  PHVAADEIRIAFDATSAYVHRDNSDKLTALGVKMIDLTPAAIGPYCVPPVNLDAHLDSAQ 122
           P V ADEI+IAFDATSAYVH +NS KL  LGV MIDLTPAAIGP+CVPPVNL + LD   
Sbjct: 64  PFVEADEIKIAFDATSAYVHAENSRKLNELGVVMIDLTPAAIGPFCVPPVNL-SQLDENV 122

Query: 123 TNVNMVTCGGQATIPMVYAVSRVQPVAYGEIVATVSSRSVGPGTRKNIDEFTRTTSGAIE 182
            N+NMVTCGGQATIPMV AVSRVQ V YGEIVATVSSRSVGPGTR+NIDEFTRTT+GA+E
Sbjct: 123 KNINMVTCGGQATIPMVAAVSRVQAVEYGEIVATVSSRSVGPGTRQNIDEFTRTTAGAVE 182

Query: 183 QVGGARKGKAIIVINPAEPPLIMRDTIHCLTDGPPDVDAITASVHAMVKEVQRYVPGYTL 242
           Q+GGA KGKAIIVINPAEPPL+MRDTIHCLT   PD  AITASVH M+++VQ+YVPGYTL
Sbjct: 183 QIGGAEKGKAIIVINPAEPPLLMRDTIHCLTKEQPDEQAITASVHEMIEQVQQYVPGYTL 242

Query: 243 KNGPVFDGNRVSVFMEVEGLGDYLPKYAGNLDIMTAAAAATAERFAEQML 292
           KNGPVFDG +V++F+EVEGLGDYLPKYAGNLDIMTAAAA TAE  A +ML
Sbjct: 243 KNGPVFDGRKVTIFLEVEGLGDYLPKYAGNLDIMTAAAARTAEMLASKML 292


Lambda     K      H
   0.318    0.134    0.391 

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: 349
Number of extensions: 11
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: 299
Length of database: 307
Length adjustment: 27
Effective length of query: 272
Effective length of database: 280
Effective search space:    76160
Effective search space used:    76160
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 WP_012277178.1 SHAL_RS10915 (acetaldehyde dehydrogenase (acetylating))
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.2320232.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.7e-148  478.8   1.4   3.1e-148  478.7   1.4    1.0  1  NCBI__GCF_000019185.1:WP_012277178.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000019185.1:WP_012277178.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  478.7   1.4  3.1e-148  3.1e-148       1     284 [.       4     292 ..       4     293 .. 0.97

  Alignments for each domain:
  == domain 1  score: 478.7 bits;  conditional E-value: 3.1e-148
                             TIGR03215   1 kvkvaiiGsGnigtdllikllrsevlelallvGidpesdGlararelgvetsaeGvdalleee...didivfd 70 
                                           k+k+a+iGsGnigtdll+kl+rs+vle++++vGidpesdGlara+ +g++++a+G+++ll      +i+i+fd
  NCBI__GCF_000019185.1:WP_012277178.1   4 KIKCALIGSGNIGTDLLYKLMRSDVLEPVWMVGIDPESDGLARAKAAGLKVTADGINGLLPFVeadEIKIAFD 76 
                                           79********************************************************987555559****** PP

                             TIGR03215  71 atsakahaenaklleelgkividltPaavGpyvvPavnleevldak.nvnlvtCgGqatiPivaavsrvakvk 142
                                           atsa++haen+++l+elg+++idltPaa+Gp++vP+vnl++  ++  n+n+vtCgGqatiP+vaavsrv+ v+
  NCBI__GCF_000019185.1:WP_012277178.1  77 ATSAYVHAENSRKLNELGVVMIDLTPAAIGPFCVPPVNLSQLDENVkNINMVTCGGQATIPMVAAVSRVQAVE 149
                                           ****************************************9876544************************** PP

                             TIGR03215 143 yaeivasiasksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtvyalv.eeadeeai 214
                                           y+eiva+++s+s+Gpgtr+nideft+tt+ a+eq+gGa+kgkaii++nPaePpllmrdt+++l+ e++de+ai
  NCBI__GCF_000019185.1:WP_012277178.1 150 YGEIVATVSSRSVGPGTRQNIDEFTRTTAGAVEQIGGAEKGKAIIVINPAEPPLLMRDTIHCLTkEQPDEQAI 222
                                           ***************************************************************9899****** PP

                             TIGR03215 215 easveemveevqkyvpGyrlkqevvldgekvsvlleveGagdylPkyaGnldiltaaalavaeklaeell 284
                                           +asv+em+e+vq+yvpGy+lk+ +v+dg+kv+++leveG gdylPkyaGnldi+taaa+++ae+la+++l
  NCBI__GCF_000019185.1:WP_012277178.1 223 TASVHEMIEQVQQYVPGYTLKNGPVFDGRKVTIFLEVEGLGDYLPKYAGNLDIMTAAAARTAEMLASKML 292
                                           ******************************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (307 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: 8.78
//
[ok]

This GapMind analysis is from Sep 24 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