GapMind for catabolism of small carbon sources

 

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

Align acylating aldehyde dehydrogenase (EC 1.2.1.10) (characterized)
to candidate WP_003943168.1 C1M55_RS29420 acetaldehyde dehydrogenase (acetylating)

Query= metacyc::MONOMER-11388
         (316 letters)



>NCBI__GCF_002893965.1:WP_003943168.1
          Length = 314

 Score =  402 bits (1032), Expect = e-117
 Identities = 212/309 (68%), Positives = 243/309 (78%), Gaps = 5/309 (1%)

Query: 4   KVKAAIIGSGNIGTDLMIKILRHGQHIEMGAMVGIDPASDGLARGERMGVAITHEGVEGL 63
           KVK AIIGSGNIGTDLMIK+LR+  ++EMGAMVGIDPASDGLAR  R+ V IT EGVEGL
Sbjct: 3   KVKVAIIGSGNIGTDLMIKVLRNSDYLEMGAMVGIDPASDGLARAARLNVPITAEGVEGL 62

Query: 64  TRLPVFNEIDVVFDATSAGAHVKNEALLRERKPGLRMIDLTPAAIAPYCIPVVNGDDHLD 123
             LP F+EI++VFDATSA AHV N A L     G RMIDLTPAAI PY +P VN D+HLD
Sbjct: 63  VGLPNFDEIEIVFDATSAKAHVANNARLAPL--GKRMIDLTPAAIGPYVVPAVNADEHLD 120

Query: 124 ATNVNMVTCGGQATIPMVAAVSRVAKVHYAEIIASISSKSAGPGTRANIDEFTETTSKAI 183
           A NVNMVTCGGQATIPMVAAVSRV  V YAEI+ASI+SKSAGPGTRANIDEFTETTS+AI
Sbjct: 121 APNVNMVTCGGQATIPMVAAVSRVVPVAYAEIVASIASKSAGPGTRANIDEFTETTSEAI 180

Query: 184 EVVGGAAKGKAIIVLNPAEPPLMMRDAVYTLSDFAD---IDQIEESVQRMADAVQAYVPG 240
             VGGA +GKAII+LNPAEPPL+MRD V+ L D  D    D+I +S+++M   V AYVPG
Sbjct: 181 VAVGGARRGKAIIILNPAEPPLIMRDTVFCLVDAPDPAVHDEIRQSIEKMVGDVSAYVPG 240

Query: 241 YRLKQRVQFDRIEADCPIRIPGVGDRMNGLKTSIFLEVEGAAHYLPAYAGNLDIMTSAAL 300
           YRLKQ VQ   I AD P+    V       + S+FLEVEGAAHYLPAYAGNLDIMTSA +
Sbjct: 241 YRLKQEVQITEIPADQPVETLLVDGNRPTHQVSVFLEVEGAAHYLPAYAGNLDIMTSAGM 300

Query: 301 RTAEKLAER 309
           + AE++A++
Sbjct: 301 QIAERIAQQ 309


Lambda     K      H
   0.319    0.135    0.379 

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: 357
Number of extensions: 10
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: 316
Length of database: 314
Length adjustment: 27
Effective length of query: 289
Effective length of database: 287
Effective search space:    82943
Effective search space used:    82943
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate WP_003943168.1 C1M55_RS29420 (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.1560564.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.4e-143  462.1   5.7   3.9e-143  461.9   5.7    1.0  1  NCBI__GCF_002893965.1:WP_003943168.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002893965.1:WP_003943168.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  461.9   5.7  3.9e-143  3.9e-143       1     283 [.       3     310 ..       3     312 .. 0.98

  Alignments for each domain:
  == domain 1  score: 461.9 bits;  conditional E-value: 3.9e-143
                             TIGR03215   1 kvkvaiiGsGnigtdllikllr.sevlelallvGidpesdGlararelgvetsaeGvdalleee...didivf 69 
                                           kvkvaiiGsGnigtdl+ik+lr s+ le+ ++vGidp+sdGlara++l+v ++aeGv++l+  +   +i+ivf
  NCBI__GCF_002893965.1:WP_003943168.1   3 KVKVAIIGSGNIGTDLMIKVLRnSDYLEMGAMVGIDPASDGLARAARLNVPITAEGVEGLVGLPnfdEIEIVF 75 
                                           79********************99*************************************9988889***** PP

                             TIGR03215  70 datsakahaenaklleelgkividltPaavGpyvvPavnleevldaknvnlvtCgGqatiPivaavsrvakvk 142
                                           datsakah++n+++l+ lgk++idltPaa+GpyvvPavn++e+lda+nvn+vtCgGqatiP+vaavsrv++v+
  NCBI__GCF_002893965.1:WP_003943168.1  76 DATSAKAHVANNARLAPLGKRMIDLTPAAIGPYVVPAVNADEHLDAPNVNMVTCGGQATIPMVAAVSRVVPVA 148
                                           ************************************************************************* PP

                             TIGR03215 143 yaeivasiasksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtvyalveead...ee 212
                                           yaeivasiasksaGpgtranideftetts+a+ +vgGa++gkaiiilnPaePpl+mrdtv++lv+++d   ++
  NCBI__GCF_002893965.1:WP_003943168.1 149 YAEIVASIASKSAGPGTRANIDEFTETTSEAIVAVGGARRGKAIIILNPAEPPLIMRDTVFCLVDAPDpavHD 221
                                           ****************************************************************999977789 PP

                             TIGR03215 213 aieasveemveevqkyvpGyrlkqevvld..................gekvsvlleveGagdylPkyaGnldi 267
                                           +i++s+e+mv +v +yvpGyrlkqev+++                   ++vsv+leveGa++ylP+yaGnldi
  NCBI__GCF_002893965.1:WP_003943168.1 222 EIRQSIEKMVGDVSAYVPGYRLKQEVQITeipadqpvetllvdgnrpTHQVSVFLEVEGAAHYLPAYAGNLDI 294
                                           ****************************99*************9998888*********************** PP

                             TIGR03215 268 ltaaalavaeklaeel 283
                                           +t+a +++ae++a++ 
  NCBI__GCF_002893965.1:WP_003943168.1 295 MTSAGMQIAERIAQQK 310
                                           *************986 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: 12.55
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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