GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Phyllobacterium brassicacearum STM 196

Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_106711729.1 CU102_RS14130 acetyl-CoA C-acetyltransferase

Query= SwissProt::O32177
         (391 letters)



>NCBI__GCF_003010955.1:WP_106711729.1
          Length = 402

 Score =  256 bits (653), Expect = 1e-72
 Identities = 154/411 (37%), Positives = 223/411 (54%), Gaps = 33/411 (8%)

Query: 1   MKEAVIVSGARTPVGKAKK-GSLATVRPDDLGAICVKETLKRAGGYEGNIDDLIIGCATP 59
           M EA I    RTP G+ KK GSL  V    LGA  ++    R G   G +DD+I GC  P
Sbjct: 1   MTEAYIYDHVRTPRGRGKKDGSLHEVPAVRLGAHVLEALRDRNGLDTGLVDDIIYGCVDP 60

Query: 60  EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119
             E G  + R+    AG  +  P + ++R+C+SGL ++ +AA KI+ GA D  IAGG ES
Sbjct: 61  VGEAGAVIPRSSAFEAGYDFKAPGMQISRFCASGLDAVNFAAAKIVQGADDIVIAGGVES 120

Query: 120 MSQVPMMGHVTRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAKA 179
           MS+V M        +  +   P Y+M  G +A+ +A KYG SR+D DA+AV S + A +A
Sbjct: 121 MSRVGMGMSGGAWYMDPSVGLPGYFMPQGVSADLIATKYGFSRDDVDAYAVESQKRAGEA 180

Query: 180 LAEGKFKDEIVPVEVTVTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSVDGT 239
             +G FK+ ++ +           K      +   DE +RP T    L++L P+F + G 
Sbjct: 181 WKKGYFKNSVLEI-----------KDQNGLTILDHDEHMRPTTDMQALASLNPSFVMPGE 229

Query: 240 VT---------------------AGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFA 278
           +                      AGNSS   DGAA V+L  +    A+G  P  + R+FA
Sbjct: 230 MGGFNAVGIQAHPEVETINHVHHAGNSSGIVDGAAGVLLGSKSAGKAIGTKPRARIRAFA 289

Query: 279 VGGVPPEVMGIGPVEAIPRALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNV 338
             G  P +M  GPV+   + LK A +++ DI LFELNEAFA+  ++ ++   I  +K+NV
Sbjct: 290 NIGSDPALMLTGPVDVTEKLLKRAKMKISDIDLFELNEAFAAVVLRYMQAFDIPRDKINV 349

Query: 339 NGGAIALGHPLGCTGTKLTLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389
           NGGAIA+GHPLG TG  +  +++ E++RR+    +VT+CIG GMG A + E
Sbjct: 350 NGGAIAMGHPLGATGAMILGTVLDELERRDLNVALVTLCIGAGMGTATIIE 400


Lambda     K      H
   0.316    0.133    0.377 

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: 428
Number of extensions: 15
Number of successful extensions: 4
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: 391
Length of database: 402
Length adjustment: 31
Effective length of query: 360
Effective length of database: 371
Effective search space:   133560
Effective search space used:   133560
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_106711729.1 CU102_RS14130 (acetyl-CoA C-acetyltransferase)
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.3458480.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-124  401.7   0.1     2e-124  401.4   0.1    1.1  1  NCBI__GCF_003010955.1:WP_106711729.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010955.1:WP_106711729.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  401.4   0.1    2e-124    2e-124       1     385 []       6     400 ..       6     400 .. 0.95

  Alignments for each domain:
  == domain 1  score: 401.4 bits;  conditional E-value: 2e-124
                             TIGR01930   1 ivdavRtpig..klggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaagl 70 
                                           i+d vRtp g  k  gsl+e++a+ L+a+v+++l +r+gld   +d++i+G+v + ge  a i R  a++ag 
  NCBI__GCF_003010955.1:WP_106711729.1   6 IYDHVRTPRGrgKKDGSLHEVPAVRLGAHVLEALRDRNGLDTGLVDDIIYGCVDPVGEAgAVIPRSSAFEAGY 78 
                                           7899*******988*********************************************************** PP

                             TIGR01930  71 pesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkd 143
                                           + + p+++++r+CaSgl+Av+ aa+ki  G+ d+v+aGGvEsmSrv ++++    ++ +++            
  NCBI__GCF_003010955.1:WP_106711729.1  79 DFKAPGMQISRFCASGLDAVNFAAAKIVQGADDIVIAGGVESMSRVGMGMSGG--AWYMDPS--VG------- 140
                                           ************************************************99997..6777772..22....... PP

                             TIGR01930 144 lvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgkkkvvskDegirpntt 216
                                           l+   +++g++A+ +a+kyg+sR+++D+ya++S+++a +A+++g+fk++++ ++ ++  +++++De++rp+t 
  NCBI__GCF_003010955.1:WP_106711729.1 141 LPGYFMPQGVSADLIATKYGFSRDDVDAYAVESQKRAGEAWKKGYFKNSVLEIKDQNGLTILDHDEHMRPTTD 213
                                           245689**********************************************99998899************* PP

                             TIGR01930 217 lekLakLkpafkekkgs....................tvtAgNssqlnDGAaalllmseevakelgltplari 269
                                           +++La+L+p f    g+                    +++AgNss++ DGAa +ll s+++ k++g +p ari
  NCBI__GCF_003010955.1:WP_106711729.1 214 MQALASLNPSFVM-PGEmggfnavgiqahpevetinhVHHAGNSSGIVDGAAGVLLGSKSAGKAIGTKPRARI 285
                                           ***********98.244455666667777788888889*********************************** PP

                             TIGR01930 270 vsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlG 342
                                           +++a++g+dp+ m++gpv  +ek+Lk+a+++isdidl+E+nEAFAa+vl  +++++ + ++k+NvnGGAiA+G
  NCBI__GCF_003010955.1:WP_106711729.1 286 RAFANIGSDPALMLTGPVDVTEKLLKRAKMKISDIDLFELNEAFAAVVLRYMQAFD-IPRDKINVNGGAIAMG 357
                                           ********************************************************.88************** PP

                             TIGR01930 343 HPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                           HPlGa+Ga+i+ t+l+eL++r+ +++l+tlC+g G+G+A+i+e
  NCBI__GCF_003010955.1:WP_106711729.1 358 HPLGATGAMILGTVLDELERRDLNVALVTLCIGAGMGTATIIE 400
                                           *****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (402 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: 25.35
//
[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