GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ald-dh-CoA in Rhodococcus qingshengii djl-6-2

Align Acetaldehyde dehydrogenase 1; EC 1.2.1.10; Acetaldehyde dehydrogenase [acetylating] 1 (uncharacterized)
to candidate WP_050655875.1 C1M55_RS04080 acetaldehyde dehydrogenase (acetylating)

Query= curated2:A1UM81
         (310 letters)



>NCBI__GCF_002893965.1:WP_050655875.1
          Length = 300

 Score =  498 bits (1283), Expect = e-146
 Identities = 252/301 (83%), Positives = 272/301 (90%), Gaps = 5/301 (1%)

Query: 4   KLQVAIVGSGNISTDLLYKLQRSEYLEPRWMIGIDPESEGLARARKLGLETSHEGVDWLL 63
           K  VAIVGSGNISTDLLYKLQRSE+LEPRWMIGIDPESEGLARARK+GLETS EGVDWLL
Sbjct: 3   KASVAIVGSGNISTDLLYKLQRSEWLEPRWMIGIDPESEGLARARKMGLETSAEGVDWLL 62

Query: 64  AQDDKPDLVFEATSAYVHRAAAPRYEEAGIRAIDLTPAAVGPAVIPPANLREHLDAPNVN 123
           +Q +KPDLVFEATSAYVHR AAPRYE AGIRAIDLTPAAVGPAV+PPANLREHLDAPNVN
Sbjct: 63  SQAEKPDLVFEATSAYVHREAAPRYEAAGIRAIDLTPAAVGPAVVPPANLREHLDAPNVN 122

Query: 124 MITCGGQATIPIVYAVTRAVTEQGGTVPYAEIVASVSSSSAGPGTRANIDEFTKTTSKGV 183
           MITCGGQATIPIVYAV+R V      V YAEIVASV+S SAGPGTRANIDEFTKTTS+G+
Sbjct: 123 MITCGGQATIPIVYAVSRVV-----DVAYAEIVASVASLSAGPGTRANIDEFTKTTSRGI 177

Query: 184 QTIGGAARGKAIIILNPADPPMIMRDTIFCAIPEDVDRDAIAQSIRDVVAEVQTYVPGYR 243
           +TIGGA RGKAIIILNPADPPMIMRDTIFCAIPED D+ AI  SI  VV ++Q YVPGYR
Sbjct: 178 ETIGGAQRGKAIIILNPADPPMIMRDTIFCAIPEDADQAAITDSIHRVVKDIQQYVPGYR 237

Query: 244 LLNDPQFDDPSINSGGQAVVTTFVEVEGAGDYLPPYAGNLDIMTAAAAKVGEEIAKESLS 303
           LLN+PQFD+PS+ SGG A VTTFVEVEGAGD+LPPYAGNLDIMTAAA KVGEEIA++ LS
Sbjct: 238 LLNEPQFDEPSVVSGGYATVTTFVEVEGAGDFLPPYAGNLDIMTAAATKVGEEIAQKLLS 297

Query: 304 L 304
           +
Sbjct: 298 V 298


Lambda     K      H
   0.315    0.133    0.381 

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: 394
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: 310
Length of database: 300
Length adjustment: 27
Effective length of query: 283
Effective length of database: 273
Effective search space:    77259
Effective search space used:    77259
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: 42 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate WP_050655875.1 C1M55_RS04080 (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.1564389.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-141  456.9   0.2   1.5e-141  456.7   0.2    1.0  1  NCBI__GCF_002893965.1:WP_050655875.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002893965.1:WP_050655875.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.7   0.2  1.5e-141  1.5e-141       1     284 [.       3     296 ..       3     297 .. 0.98

  Alignments for each domain:
  == domain 1  score: 456.7 bits;  conditional E-value: 1.5e-141
                             TIGR03215   1 kvkvaiiGsGnigtdllikllrsevlelallvGidpesdGlararelgvetsaeGvdalleeedi.divfdat 72 
                                           k+ vai+GsGni+tdll+kl+rse le+++++Gidpes+Glarar++g+etsaeGvd+ll++ +  d+vf+at
  NCBI__GCF_002893965.1:WP_050655875.1   3 KASVAIVGSGNISTDLLYKLQRSEWLEPRWMIGIDPESEGLARARKMGLETSAEGVDWLLSQAEKpDLVFEAT 75 
                                           5789**********************************************************9877******* PP

                             TIGR03215  73 sakahaenaklleelgkividltPaavGpyvvPavnleevldaknvnlvtCgGqatiPivaavsrvakvkyae 145
                                           sa++h+e+a ++e++g+++idltPaavGp vvP+ nl+e+lda+nvn++tCgGqatiPiv+avsrv++v+yae
  NCBI__GCF_002893965.1:WP_050655875.1  76 SAYVHREAAPRYEAAGIRAIDLTPAAVGPAVVPPANLREHLDAPNVNMITCGGQATIPIVYAVSRVVDVAYAE 148
                                           ************************************************************************* PP

                             TIGR03215 146 ivasiasksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtvyalv.eeadeeaieas 217
                                           ivas+as saGpgtranideft+tts+++e++gGa++gkaiiilnPa+Pp++mrdt+++++ e+ad++ai++s
  NCBI__GCF_002893965.1:WP_050655875.1 149 IVASVASLSAGPGTRANIDEFTKTTSRGIETIGGAQRGKAIIILNPADPPMIMRDTIFCAIpEDADQAAITDS 221
                                           ************************************************************99*********** PP

                             TIGR03215 218 veemveevqkyvpGyrlkqevvld........gekvsvlleveGagdylPkyaGnldiltaaalavaeklaee 282
                                           ++++v+++q+yvpGyrl +e+++d           v++++eveGagd+lP yaGnldi+taaa++v+e++a++
  NCBI__GCF_002893965.1:WP_050655875.1 222 IHRVVKDIQQYVPGYRLLNEPQFDepsvvsggYATVTTFVEVEGAGDFLPPYAGNLDIMTAAATKVGEEIAQK 294
                                           *****************************985567************************************99 PP

                             TIGR03215 283 ll 284
                                           ll
  NCBI__GCF_002893965.1:WP_050655875.1 295 LL 296
                                           86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (300 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: 11.46
//
[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