Alignments for a candidate for fadA in Pseudarthrobacter sulfonivorans Ar51

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Pseudarthrobacter sulfonivorans Ar51

Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_058929093.1 AU252_RS00785 acetyl-CoA acetyltransferase

Query= SwissProt::O32177
         (391 letters)



>NCBI__GCF_001484605.1:WP_058929093.1
          Length = 405

 Score =  314 bits (804), Expect = 3e-90
 Identities = 178/415 (42%), Positives = 245/415 (59%), Gaps = 39/415 (9%)

Query: 1   MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEG-NIDDLIIGCATP 59
           M EAVIVS AR+P+G+A KGSL  +RPDDL A  V+  L +    +  +I+DL++GC  P
Sbjct: 1   MTEAVIVSIARSPIGRAMKGSLVDMRPDDLAAQMVRAALDKVPALDPTDINDLLLGCGLP 60

Query: 60  EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119
             EQG NM RN+    G  + +P  T+ RYCSS LQ+   A   I  G  D  I+ G E+
Sbjct: 61  GGEQGYNMGRNVAVQLGYDF-MPGTTITRYCSSSLQTTRMALHAIKAGEGDVFISAGVET 119

Query: 120 MSQV-------------PMMGHVTRPNLALAEKAPEY------------YMSMGHTAEQV 154
           +S+              P+          LA+    +            Y++MG TAE V
Sbjct: 120 VSRFVKGNSDSLPDTHNPLYADAQTRTEKLAQGGQTWEDPRKVGLVADTYIAMGQTAENV 179

Query: 155 AKKYGVSREDQDAFAVRSHQNAAKALAEGKFKDEIVPVEVTVTEIGEDHKPMEKQFVFSQ 214
           A+  G+SRE+QD +AVRS   A KA+  G ++ EI PV             +    V S 
Sbjct: 180 AQMTGISREEQDRWAVRSQNRAEKAIINGFYEREITPVT------------LPDGTVVST 227

Query: 215 DEGVRPQTTADILSTLRPAFSVDGTVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKF 274
           D+G R  TT + +S L+P F  DGTVTAGN+   +DGAAA+++M   KA  LGL P+ + 
Sbjct: 228 DDGPRAGTTYEAVSQLKPIFRPDGTVTAGNACPLNDGAAALVIMSDTKAKELGLTPIARI 287

Query: 275 RSFAVGGVPPEVMGIGPVEAIPRALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEE 334
            S  V G+ PE+MG+GP+EA  RAL +AG+ + DI LFE+NEAFA Q +   RELGIDE+
Sbjct: 288 VSTGVSGLSPEIMGLGPIEASKRALAIAGMGIGDIDLFEINEAFAVQVLGSARELGIDED 347

Query: 335 KVNVNGGAIALGHPLGCTGTKLTLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389
           K+NV+GG IALGHP G TG ++T +L++ ++  ++QFG+ TMC+GGG G A V E
Sbjct: 348 KLNVSGGGIALGHPFGMTGARITATLLNNLQTYDKQFGLETMCVGGGQGMAMVLE 402


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: 418
Number of extensions: 21
Number of successful extensions: 5
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: 405
Length adjustment: 31
Effective length of query: 360
Effective length of database: 374
Effective search space:   134640
Effective search space used:   134640
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_058929093.1 AU252_RS00785 (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.3794937.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-137  445.1   0.1   1.2e-137  444.9   0.1    1.0  1  NCBI__GCF_001484605.1:WP_058929093.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001484605.1:WP_058929093.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  444.9   0.1  1.2e-137  1.2e-137       1     385 []       6     402 ..       6     402 .. 0.97

  Alignments for each domain:
  == domain 1  score: 444.9 bits;  conditional E-value: 1.2e-137
                             TIGR01930   1 ivdavRtpig.klggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaagl 70 
                                           iv+ +R+pig +++gsl +++++dL+a++++++l+++  ldp +i+++ lG+ l+ geq  n++R++a++ g 
  NCBI__GCF_001484605.1:WP_058929093.1   6 IVSIARSPIGrAMKGSLVDMRPDDLAAQMVRAALDKVpALDPTDINDLLLGCGLPGGEQgYNMGRNVAVQLGY 78 
                                           89*********99************************************************************ PP

                             TIGR01930  71 pesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkd 143
                                           +  +p++t++r+C+S+lq+ ++a ++ikaGe dv++++GvE++Sr   ++++s  ++++++  a+ + +++k 
  NCBI__GCF_001484605.1:WP_058929093.1  79 DF-MPGTTITRYCSSSLQTTRMALHAIKAGEGDVFISAGVETVSRFVKGNSDS-LPDTHNPLYADAQTRTEKL 149
                                           99.9********************************************99998.5777777666666655555 PP

                             TIGR01930 144 l...............vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk 201
                                           +               ++t ++mg+tAen+a+  gisReeqD++a+rS+++a+kAi +g+ ++ei+pv++++ 
  NCBI__GCF_001484605.1:WP_058929093.1 150 AqggqtwedprkvglvADTYIAMGQTAENVAQMTGISREEQDRWAVRSQNRAEKAIINGFYEREITPVTLPD- 221
                                           5779************99****************************************************98. PP

                             TIGR01930 202 kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaav 274
                                            +vvs+D+g+r++tt e++++Lkp+f+ ++g tvtAgN+++lnDGAaal++ms+++akelgltp+arivs++v
  NCBI__GCF_001484605.1:WP_058929093.1 222 GTVVSTDDGPRAGTTYEAVSQLKPIFR-PDG-TVTAGNACPLNDGAAALVIMSDTKAKELGLTPIARIVSTGV 292
                                           7999**********************9.69*.6**************************************** PP

                             TIGR01930 275 agvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGa 347
                                           +g++pe+mglgp++A+++aL+ ag+ i didl+EinEAFA+qvl +++elg +d++k+Nv GG iAlGHP+G+
  NCBI__GCF_001484605.1:WP_058929093.1 293 SGLSPEIMGLGPIEASKRALAIAGMGIGDIDLFEINEAFAVQVLGSARELG-IDEDKLNVSGGGIALGHPFGM 364
                                           ***************************************************.88******************* PP

                             TIGR01930 348 sGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                           +Gari++tll++L+  +k++Gl t+CvggGqG+A++le
  NCBI__GCF_001484605.1:WP_058929093.1 365 TGARITATLLNNLQTYDKQFGLETMCVGGGQGMAMVLE 402
                                           ************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (405 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 20.08
//
[ok]

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

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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