GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Chryseobacterium arthrosphaerae CC-VM-7

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_065401082.1 BBI00_RS22490 3-oxoadipyl-CoA thiolase

Query= metacyc::MONOMER-3207
         (400 letters)



>NCBI__GCF_001684965.1:WP_065401082.1
          Length = 401

 Score =  475 bits (1222), Expect = e-138
 Identities = 237/401 (59%), Positives = 307/401 (76%), Gaps = 1/401 (0%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           M +V+I D +RTPI +  G L+ VRADDLAA+ +K ++  NP V  +++++V FGCANQA
Sbjct: 1   MNNVYIIDYVRTPISKLQGGLSEVRADDLAAIVIKEVVARNPEVPVEEIEDVIFGCANQA 60

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           GEDNRNVARM LLLAGLP  I G T+NRLCASGM A+  AFR+IASGE E+ IAGGVE M
Sbjct: 61  GEDNRNVARMGLLLAGLPYKIGGETVNRLCASGMSAVANAFRSIASGEGEIYIAGGVEHM 120

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           +R+P+VM K  + + R+ ++ DTT GWRFINP MK  YGVD M ETA+N+AD + +SR D
Sbjct: 121 TRSPYVMSKPGAAFGRDSQMFDTTFGWRFINPKMKEMYGVDGMGETAENLADMHHISRED 180

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIV-ERDEHLRPETTLEALTKLKP 239
           QD FAL SQQKA  AQ +G  AEEIV V I  +KGE ++ E+DE ++P +++E L KL+P
Sbjct: 181 QDKFALWSQQKATKAQESGRLAEEIVKVEIPQRKGEPVIFEKDEFIKPGSSMEGLGKLRP 240

Query: 240 VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPV 299
               + TVTAGNASG+NDGAAALILAS EAVKK+GL P+AR+LG +  GV PR+MGIGPV
Sbjct: 241 AFRKEGTVTAGNASGMNDGAAALILASEEAVKKYGLKPKARILGSSVAGVEPRIMGIGPV 300

Query: 300 PAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLG 359
            A +KL +RL +++ D D+IELNEAFA+Q LAV R LG+ DD  ++NPNGGAIA+GHPLG
Sbjct: 301 EATQKLLKRLDLSLEDMDIIELNEAFAAQALAVTRTLGLKDDDSRINPNGGAIAIGHPLG 360

Query: 360 MSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           +SGAR++ +A  +L+K   +  L T+C+GVGQG A+ IE+V
Sbjct: 361 VSGARIIGSAAMELQKQNKKYALCTLCIGVGQGYAMVIEKV 401


Lambda     K      H
   0.318    0.134    0.383 

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: 451
Number of extensions: 12
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: 400
Length of database: 401
Length adjustment: 31
Effective length of query: 369
Effective length of database: 370
Effective search space:   136530
Effective search space used:   136530
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: 50 (23.9 bits)

Align candidate WP_065401082.1 BBI00_RS22490 (3-oxoadipyl-CoA thiolase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

# 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/TIGR01930.hmm
# target sequence database:        /tmp/gapView.1913766.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01930  [M=385]
Accession:   TIGR01930
Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.8e-144  466.7   0.3   3.2e-144  466.5   0.3    1.0  1  NCBI__GCF_001684965.1:WP_065401082.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001684965.1:WP_065401082.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  466.5   0.3  3.2e-144  3.2e-144       1     385 []       6     399 ..       6     399 .. 0.94

  Alignments for each domain:
  == domain 1  score: 466.5 bits;  conditional E-value: 3.2e-144
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaaglp 71 
                                           i+d+vRtpi kl+g l+e++a+dL+a vike+++r+ ++  e+i++vi+G++ qage+  n+aR+ +l aglp
  NCBI__GCF_001684965.1:WP_065401082.1   6 IIDYVRTPISKLQGGLSEVRADDLAAIVIKEVVARNpEVPVEEIEDVIFGCANQAGEDnRNVARMGLLLAGLP 78 
                                           89********************************************************9************** PP

                             TIGR01930  72 esvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl 144
                                           +++ + tvnr+CaSg+ Ava+a ++i++Ge ++++aGGvE+m+r+p+++++  ++ + +   +++ d+     
  NCBI__GCF_001684965.1:WP_065401082.1  79 YKIGGETVNRLCASGMSAVANAFRSIASGEGEIYIAGGVEHMTRSPYVMSKPGAAFGRD---SQMFDT----T 144
                                           ***********************************************999974333333...333331....1 PP

                             TIGR01930 145 ............vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...k 202
                                                        +    mgetAenla+ ++isRe+qD++al S+qka+kA+e+g++++eiv ve++++   +
  NCBI__GCF_001684965.1:WP_065401082.1 145 fgwrfinpkmkeMYGVDGMGETAENLADMHHISREDQDKFALWSQQKATKAQESGRLAEEIVKVEIPQRkgeP 217
                                           234456777787666778*************************************************999*9* PP

                             TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaava 275
                                           ++++kDe i+p++++e L+kL+paf++ +g tvtAgN+s++nDGAaal+l+see++k++gl+p+ari + +va
  NCBI__GCF_001684965.1:WP_065401082.1 218 VIFEKDEFIKPGSSMEGLGKLRPAFRK-EG-TVTAGNASGMNDGAAALILASEEAVKKYGLKPKARILGSSVA 288
                                           *************************95.8*.6***************************************** PP

                             TIGR01930 276 gvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld.lekvNvnGGAiAlGHPlGa 347
                                           gv+p++mg+gpv+A++k+Lk+ +ls++d+d++E+nEAFAaq+lav++ lg++d ++++N nGGAiA+GHPlG+
  NCBI__GCF_001684965.1:WP_065401082.1 289 GVEPRIMGIGPVEATQKLLKRLDLSLEDMDIIELNEAFAAQALAVTRTLGLKDdDSRINPNGGAIAIGHPLGV 361
                                           **************************************************8667******************* PP

                             TIGR01930 348 sGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                           sGari+ + + eL++++kky+l tlC+g GqG A+++e
  NCBI__GCF_001684965.1:WP_065401082.1 362 SGARIIGSAAMELQKQNKKYALCTLCIGVGQGYAMVIE 399
                                           ************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (401 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.32
//
[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