Alignments for a candidate for fadA in Rhodobacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Rhodobacter sphaeroides ATCC 17029

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_011840657.1 RSPH17029_RS04440 acetyl-CoA acetyltransferase

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



>NCBI__GCF_000015985.1:WP_011840657.1
          Length = 403

 Score =  267 bits (682), Expect = 5e-76
 Identities = 177/424 (41%), Positives = 242/424 (57%), Gaps = 45/424 (10%)

Query: 1   MRDVFICDAIRTPIG--RFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCAN 58
           M + +I DA+RTP G  R  GAL  V +  L+A  L A+ E N  +    V++V +G A 
Sbjct: 1   MTEAYIYDALRTPRGKGRPDGALHEVTSVALSAKVLNAVKERNH-LDGAAVEDVIWGNAT 59

Query: 59  QAGEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVE 118
           Q GE    +AR A+LL+ L ESIPG+++NR CASGM+A+  A   + +G  E  IAGGVE
Sbjct: 60  QVGEQGGCLARSAVLLSDLDESIPGLSINRFCASGMEAVNLAANQVRAGAGEAYIAGGVE 119

Query: 119 SMSRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSR 178
            MSR    MG   +  + +  L             MK+ +    +  +AD +A  Y  SR
Sbjct: 120 MMSRV--AMGSDGAAVAADPSLA------------MKTYFVPQGI--SADIIATRYGFSR 163

Query: 179 ADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLK 238
            + DA A+ SQ++AAAA A G FA  +VPVR   + G TI+ERDE+LRP T +++L  LK
Sbjct: 164 DEADALAVESQKRAAAAWAEGRFARSVVPVR--DQNGVTILERDEYLRPGTDMQSLGALK 221

Query: 239 P--------VNGPDKTVT--------------AGNASGVNDGAAALILASAEAVKKHGLT 276
           P        + G DK                 AGN+SG+ DGAAA+++ S    + HGL 
Sbjct: 222 PAFKEMGEQMPGFDKLALMKYPELERVEHIHHAGNSSGIVDGAAAVLIGSRAFGEAHGLR 281

Query: 277 PRARVLGMASGGVAPRVMGIGPVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLREL 336
           PRAR+   A  G  P +M  GPVP  +K+    G+ +SD D+ E+NEAFA+  L   +  
Sbjct: 282 PRARIRATAKIGTDPTIMLTGPVPVTQKILREAGMQISDIDLFEVNEAFAAVVLRFQQAF 341

Query: 337 GVADDAPQVNPNGGAIALGHPLGMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALA 396
           GV  D  +VNPNGGAIA+GHPLG +GA ++ T L +LE++    GLAT+CV  G G A  
Sbjct: 342 GV--DPARVNPNGGAIAMGHPLGATGAIIIGTLLDELERTDRSVGLATLCVASGMGAATI 399

Query: 397 IERV 400
           IERV
Sbjct: 400 IERV 403


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: 408
Number of extensions: 15
Number of successful extensions: 6
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: 403
Length adjustment: 31
Effective length of query: 369
Effective length of database: 372
Effective search space:   137268
Effective search space used:   137268
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_011840657.1 RSPH17029_RS04440 (acetyl-CoA 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.12860.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.1e-130  419.1   2.9   9.5e-130  418.9   2.9    1.0  1  lcl|NCBI__GCF_000015985.1:WP_011840657.1  RSPH17029_RS04440 acetyl-CoA ace


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015985.1:WP_011840657.1  RSPH17029_RS04440 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.9   2.9  9.5e-130  9.5e-130       1     385 []       6     401 ..       6     401 .. 0.95

  Alignments for each domain:
  == domain 1  score: 418.9 bits;  conditional E-value: 9.5e-130
                                 TIGR01930   1 ivdavRtpig..klggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaal 66 
                                               i+da+Rtp g  +  g+l+e++++ L+a+v++++ er++ld +++++vi+Gn++q geq   +aR a+l
  lcl|NCBI__GCF_000015985.1:WP_011840657.1   6 IYDALRTPRGkgRPDGALHEVTSVALSAKVLNAVKERNHLDGAAVEDVIWGNATQVGEQgGCLARSAVL 74 
                                               89********99899****************************************************** PP

                                 TIGR01930  67 aaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkak 135
                                                ++l+es+p+l++nr+CaSg++Av+laa++++aG+ ++++aGGvE+mSrv ++++ +  +  +++  a 
  lcl|NCBI__GCF_000015985.1:WP_011840657.1  75 LSDLDESIPGLSINRFCASGMEAVNLAANQVRAGAGEAYIAGGVEMMSRVAMGSDGA--AVAADPSLA- 140
                                               ****************************************************99997..455555222. PP

                                 TIGR01930 136 ledqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgkkkv 204
                                                ++       +  +++g++A+ +a++yg+sR+e D++a++S+++aa+A++eg+f++++vpv+ ++  ++
  lcl|NCBI__GCF_000015985.1:WP_011840657.1 141 -MK-------TYFVPQGISADIIATRYGFSRDEADALAVESQKRAAAAWAEGRFARSVVPVRDQNGVTI 201
                                               .22.......4579***********************************************999889** PP

                                 TIGR01930 205 vskDegirpnttlekLakLkpafkekkgs.....................tvtAgNssqlnDGAaalll 252
                                               +++De +rp+t +++L+ Lkpafke  g+                     +++AgNss++ DGAaa+l+
  lcl|NCBI__GCF_000015985.1:WP_011840657.1 202 LERDEYLRPGTDMQSLGALKPAFKE-MGEqmpgfdklalmkypelervehIHHAGNSSGIVDGAAAVLI 269
                                               ************************8.3444556667777777788888889****************** PP

                                 TIGR01930 253 mseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlave 321
                                                s+++ +++gl+p ari+++a +g dp++m++gpvp ++k+L++ag++isdidl+E+nEAFAa+vl ++
  lcl|NCBI__GCF_000015985.1:WP_011840657.1 270 GSRAFGEAHGLRPRARIRATAKIGTDPTIMLTGPVPVTQKILREAGMQISDIDLFEVNEAFAAVVLRFQ 338
                                               ********************************************************************* PP

                                 TIGR01930 322 kelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               +++g  d+++vN nGGAiA+GHPlGa+Ga+i+ tll+eL++ +  +GlatlCv+ G+GaA+i+e
  lcl|NCBI__GCF_000015985.1:WP_011840657.1 339 QAFG-VDPARVNPNGGAIAMGHPLGATGAIIIGTLLDELERTDRSVGLATLCVASGMGAATIIE 401
                                               ****.88*******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (403 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.78
//
[ok]

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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 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