Alignments for a candidate for fadA in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Stenotrophomonas chelatiphaga DSM 21508

Align 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16) (characterized)
to candidate WP_057508008.1 ABB28_RS07330 acetyl-CoA C-acyltransferase

Query= reanno::MR1:200842
         (396 letters)



>NCBI__GCF_001431535.1:WP_057508008.1
          Length = 391

 Score =  466 bits (1198), Expect = e-136
 Identities = 238/387 (61%), Positives = 295/387 (76%)

Query: 10  IVIVAAKRTPMGSFQGSLSGITSLSLAATAIKALLADTQVAPDKVDEVLMGCVLPAGLGQ 69
           IVI AAKRT +GSF G  +G+ + +L ATAI A L  + V    V EV+MGCVLPA LGQ
Sbjct: 4   IVIAAAKRTAIGSFLGQFNGVPTPTLGATAIAAALEASGVPASDVTEVIMGCVLPANLGQ 63

Query: 70  APARQATLGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGGMESMSQAPY 129
           APARQA +  GLPLS GATT+NKVCGSGMK +ML HDLIKAGSA +V+AGGMESMS AP+
Sbjct: 64  APARQAAIAGGLPLSTGATTLNKVCGSGMKAIMLGHDLIKAGSASIVVAGGMESMSNAPH 123

Query: 130 LLDKARAGIRMGHGKVLDHMFLDGLEDAYTGGAMGTFAQKTADEFGITREQMDAFALSSL 189
           LL  +R G R G+ + +DHM  DGL +AY G AMG FA+   D++  +RE+ DA+A+ S+
Sbjct: 124 LLPNSRTGNRFGNFQAVDHMAHDGLVNAYDGKAMGEFAECAVDKYQFSREEQDAYAIESV 183

Query: 190 EKANAAINSGAFKTEIVPVTVSDRRGDVTIDTDEQPGNARPEKIPTLRPAFAKDGTITAA 249
           ++A AA  SGAF  EIV V V+ R+G+V I  DEQP  A   KIPTLRPAF KDG++TAA
Sbjct: 184 KRAQAAQASGAFADEIVAVKVASRKGEVEISIDEQPTRADIAKIPTLRPAFKKDGSVTAA 243

Query: 250 NSSSISDGAAALMLTTRANAEQLGLTVLATIKGHTTHAQEPALFTTAPVGAMAKLLSNVG 309
           +SSSISDGAAA++L +  +A+  GL  LA I  H TH+QEP  FTTAP+GA+ KLL   G
Sbjct: 244 SSSSISDGAAAVVLLSEEDAQARGLQPLARIVAHATHSQEPEWFTTAPIGAIHKLLDKAG 303

Query: 310 WSKDEVDLFEINEAFAMVTMLAVSELGLDMTKVNVNGGACALGHPIGCSGARLLVTLIHA 369
           W+  +VDLFE+NEAFA+V M  + ELG+   K+NVNGGACALGHPIG SGARL+VTL+HA
Sbjct: 304 WTLADVDLFEVNEAFAVVAMAPMRELGIAHDKLNVNGGACALGHPIGASGARLVVTLVHA 363

Query: 370 LKARGLKRGVASLCIGGGEATAMAIEV 396
           L++RG KRG+A+LCIGGGEATA+AIE+
Sbjct: 364 LRSRGGKRGIATLCIGGGEATAIAIEL 390


Lambda     K      H
   0.316    0.131    0.364 

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: 503
Number of extensions: 12
Number of successful extensions: 1
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: 396
Length of database: 391
Length adjustment: 31
Effective length of query: 365
Effective length of database: 360
Effective search space:   131400
Effective search space used:   131400
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_057508008.1 ABB28_RS07330 (acetyl-CoA C-acyltransferase)
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.25830.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.8e-128  412.3  10.6   1.2e-127  412.0  10.6    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057508008.1  ABB28_RS07330 acetyl-CoA C-acylt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057508008.1  ABB28_RS07330 acetyl-CoA C-acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.0  10.6  1.2e-127  1.2e-127       1     385 []       6     389 ..       6     389 .. 0.98

  Alignments for each domain:
  == domain 1  score: 412.0 bits;  conditional E-value: 1.2e-127
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 
                                               i +a Rt+ig++ g+++ ++  +L+a++i ++le +g+ ++++ evi+G+vl+a+ ++++aR+aa+a g
  lcl|NCBI__GCF_001431535.1:WP_057508008.1   6 IAAAKRTAIGSFLGQFNGVPTPTLGATAIAAALEASGVPASDVTEVIMGCVLPANLGQAPARQAAIAGG 74 
                                               7899***************************************************************** PP

                                 TIGR01930  70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138
                                               lp s+ a+t+n+vC+Sg++A++l+ + ikaG a++vvaGG+EsmS++p+ll++s  r + ++g+++  d
  lcl|NCBI__GCF_001431535.1:WP_057508008.1  75 LPLSTGATTLNKVCGSGMKAIMLGHDLIKAGSASIVVAGGMESMSNAPHLLPNS--RTGNRFGNFQAVD 141
                                               *****************************************************8..899********** PP

                                 TIGR01930 139 qllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..k 202
                                               ++++d+   ++++ +mge Ae   +ky++sReeqD+ya++S ++a++A+++g f+deiv v+v  +  +
  lcl|NCBI__GCF_001431535.1:WP_057508008.1 142 HMAHDGlvnAYDGKAMGEFAECAVDKYQFSREEQDAYAIESVKRAQAAQASGAFADEIVAVKVASRkgE 210
                                               ******999999***************************************************999988 PP

                                 TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivs 271
                                               + +s De++  +  ++k+ +L+pafk+ +gs vtA++ss+++DGAaa++l see a++ gl+plariv+
  lcl|NCBI__GCF_001431535.1:WP_057508008.1 211 VEISIDEQPT-RADIAKIPTLRPAFKK-DGS-VTAASSSSISDGAAAVVLLSEEDAQARGLQPLARIVA 276
                                               8888888886.899***********95.9*7.************************************* PP

                                 TIGR01930 272 aavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiA 340
                                               +a+ + +pe ++++p+ Ai+k+L+kag+++ d+dl+E+nEAFA++++a ++elg ++++k+NvnGGA A
  lcl|NCBI__GCF_001431535.1:WP_057508008.1 277 HATHSQEPEWFTTAPIGAIHKLLDKAGWTLADVDLFEVNEAFAVVAMAPMRELG-IAHDKLNVNGGACA 344
                                               ******************************************************.77************ PP

                                 TIGR01930 341 lGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               lGHP+GasGar+v+tl+++L+ rg+k+G+atlC+ggG ++A+ +e
  lcl|NCBI__GCF_001431535.1:WP_057508008.1 345 LGHPIGASGARLVVTLVHALRSRGGKRGIATLCIGGGEATAIAIE 389
                                               *****************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (391 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: 10.48
//
[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)
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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