Alignments for a candidate for fadA in Sinorhizobium fredii NGR234

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Sinorhizobium fredii NGR234

Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_012706753.1 NGR_RS12215 acetyl-CoA C-acetyltransferase

Query= SwissProt::O32177
         (391 letters)



>NCBI__GCF_000018545.1:WP_012706753.1
          Length = 402

 Score =  249 bits (635), Expect = 1e-70
 Identities = 149/411 (36%), Positives = 222/411 (54%), Gaps = 33/411 (8%)

Query: 1   MKEAVIVSGARTPVGKAKK-GSLATVRPDDLGAICVKETLKRAGGYEGNIDDLIIGCATP 59
           M +  +    RTP G+ KK GSL  V    L A  ++    R G     +DD+++GC  P
Sbjct: 1   MTKVFVYDHVRTPRGRGKKDGSLHEVPSVRLAAKVLEAVRDRNGLDTATVDDIVMGCVDP 60

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

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

Query: 180 LAEGKFKDEIVPVEVTVTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSVDGT 239
             +G F++ +VPV           K      +  +DE +RP T    L++L P+F + G 
Sbjct: 181 WEKGYFENSVVPV-----------KDQNGLTILDRDEHMRPGTDMQALASLNPSFQMPGE 229

Query: 240 VT---------------------AGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFA 278
           +                      AGNSS   DGAAAV+L  +   +A+GL P  + R+FA
Sbjct: 230 MGGFEAVAIQAHPEIERINYVHHAGNSSGIVDGAAAVLLGSKAGGEAMGLKPRARIRAFA 289

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

Query: 339 NGGAIALGHPLGCTGTKLTLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389
           NGGAIA+GHPLG TG  +  +++ E++RR+    +VT+CIG GMG A + E
Sbjct: 350 NGGAIAMGHPLGATGAMILGTVLDELERRDLNTALVTLCIGAGMGTATIIE 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: 420
Number of extensions: 21
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_012706753.1 NGR_RS12215 (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.3102517.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.2e-126  406.6   0.3   6.1e-126  406.4   0.3    1.0  1  NCBI__GCF_000018545.1:WP_012706753.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000018545.1:WP_012706753.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.4   0.3  6.1e-126  6.1e-126       1     385 []       6     400 ..       6     400 .. 0.95

  Alignments for each domain:
  == domain 1  score: 406.4 bits;  conditional E-value: 6.1e-126
                             TIGR01930   1 ivdavRtpig..klggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaagl 70 
                                           ++d vRtp g  k  gsl+e++++ L+a+v++++ +r+gld + +d++++G+v +  +  + i + aa++ag 
  NCBI__GCF_000018545.1:WP_012706753.1   6 VYDHVRTPRGrgKKDGSLHEVPSVRLAAKVLEAVRDRNGLDTATVDDIVMGCVDPVMDAgSVIPKAAAFEAGY 78 
                                           6799*******988********************************************99************* PP

                             TIGR01930  71 pesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkd 143
                                           +++ p+++++r+CaSgl+Av+ +a+ki+ G+ d+v+aGGvEsmSrv ++++    ++ +++  + l       
  NCBI__GCF_000018545.1:WP_012706753.1  79 STRAPGMQISRFCASGLDAVNFGAAKIAQGADDIVIAGGVESMSRVGLGMSGG--SWFMDPSVS-L------- 141
                                           **********************************************9999987..788888322.2....... PP

                             TIGR01930 144 lvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgkkkvvskDegirpntt 216
                                            +   +++g++A+ +a+kyg+sR+++D+ya++S+++aa+A+e+g+f++++vpv+ ++  +++++De++rp+t 
  NCBI__GCF_000018545.1:WP_012706753.1 142 -PAYFMPQGVSADLIATKYGFSRDDVDAYAVESQKRAAHAWEKGYFENSVVPVKDQNGLTILDRDEHMRPGTD 213
                                           .34689************************************************998899************* PP

                             TIGR01930 217 lekLakLkpafkekkgs....................tvtAgNssqlnDGAaalllmseevakelgltplari 269
                                           +++La+L+p f+   g+                    +++AgNss++ DGAaa+ll s++  +++gl+p ari
  NCBI__GCF_000018545.1:WP_012706753.1 214 MQALASLNPSFQM-PGEmggfeavaiqahpeierinyVHHAGNSSGIVDGAAAVLLGSKAGGEAMGLKPRARI 285
                                           ***********98.344455666777777888888889*********************************** PP

                             TIGR01930 270 vsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlG 342
                                           +++a++g+dp+ m++gpv  +ek+Lk+a++++sdidl+E+nEAFAa+vl ++++++ + ++++NvnGGAiA+G
  NCBI__GCF_000018545.1:WP_012706753.1 286 RAFANIGSDPALMLTGPVDVTEKLLKRADMKLSDIDLFELNEAFAAVVLRFMQAFD-IPHDQINVNGGAIAMG 357
                                           ********************************************************.88************** PP

                             TIGR01930 343 HPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                           HPlGa+Ga+i+ t+l+eL++r+ + +l+tlC+g G+G+A+i+e
  NCBI__GCF_000018545.1:WP_012706753.1 358 HPLGATGAMILGTVLDELERRDLNTALVTLCIGAGMGTATIIE 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: 15.81
//
[ok]

This GapMind analysis is from Apr 09 2024. 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources