Alignments for a candidate for fadA in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Sphingomonas koreensis DSMZ 15582

Align 3-ketoacyl-CoA thiolase (EC 2.3.1.16) (characterized)
to candidate Ga0059261_1483 Ga0059261_1483 acetyl-CoA acetyltransferases

Query= reanno::acidovorax_3H11:Ac3H11_2994
         (397 letters)



>FitnessBrowser__Korea:Ga0059261_1483
          Length = 395

 Score =  479 bits (1234), Expect = e-140
 Identities = 244/391 (62%), Positives = 295/391 (75%)

Query: 7   DPIVIVGAARTPMGSLQGDFSSLAAHDLGGAAIKAAIERAGVSPDAVGEVLFGNCLMAGQ 66
           DP+VI+  ARTPMGS+QG  S   A +LG AA+ AA+ERAG+  +AV  +  G  L AG 
Sbjct: 4   DPVVIISYARTPMGSMQGVLSDATATELGAAAVGAAVERAGLKGEAVERIYMGCVLPAGL 63

Query: 67  GQAPARQAAFKGGLPKGAGAVTLSKMCGSGMKAAMMAHDMLLAGSHDVMVAGGMESMTNA 126
           GQAPARQAA K GLP    A T++KMCGSGM+AA+M  + L AGS D++VAGG+ESMTNA
Sbjct: 64  GQAPARQAARKAGLPDHVEATTVNKMCGSGMQAAIMGAEALAAGSVDLLVAGGLESMTNA 123

Query: 127 PYLLQKGRGGYRLGHDRIFDHMMLDGLEDAYEAGRSMGTFGEDCAAKYSFTREQQDAFAT 186
           PYL  K R G R+GHDR+FDHM LDGLEDAYE GR+MGTF E+ A +Y FTRE QD FA 
Sbjct: 124 PYLSMKHRSGARIGHDRLFDHMFLDGLEDAYEPGRAMGTFAEEIATEYQFTREAQDEFAI 183

Query: 187 ASVQRAKAATESGAFAAEIVPVTVKTRAGETVVSVDEGPGKVKLEKIATLKPAFKKDGTI 246
           AS+ RA+ A ++G F  EI PV +KTR G   V  DE P K    KI TLKPAF KDGTI
Sbjct: 184 ASLMRAQKAQQTGGFDREITPVEIKTRKGVVTVDKDEQPAKADPSKIPTLKPAFAKDGTI 243

Query: 247 TAASSSSINDGAAALVMMRESTAKKLGAKPLARIVSHATHAQEPEWFATAPLGATQKALA 306
           TAA++SSI+DGAAALV+ R S A++LG  P+ARIVSHA HA  P  F TAP+ A QKAL 
Sbjct: 244 TAANASSISDGAAALVLTRASVAERLGLDPVARIVSHAAHAHLPARFTTAPVFAMQKALG 303

Query: 307 KAGWQVGDVQLWEINEAFAVVPMALMKELDLPHDKVNVNGGACALGHPIGASGARIMVTL 366
           KAGW +GDV L+E+NEAFAVV M  M++L + HD +NVNGGACALGHP+GASGARI+ TL
Sbjct: 304 KAGWGIGDVDLFEVNEAFAVVAMIAMRDLSISHDVLNVNGGACALGHPVGASGARILATL 363

Query: 367 IHALKARGLTKGLATLCIGGGEATAVALELV 397
           + AL+  G  +GLA+LCIGGGEATA+A+EL+
Sbjct: 364 LAALQNSGQKRGLASLCIGGGEATAMAVELM 394


Lambda     K      H
   0.317    0.131    0.376 

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: 22
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: 397
Length of database: 395
Length adjustment: 31
Effective length of query: 366
Effective length of database: 364
Effective search space:   133224
Effective search space used:   133224
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 Ga0059261_1483 Ga0059261_1483 (acetyl-CoA acetyltransferases)
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.24403.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.9e-129  416.9  10.9   4.4e-129  416.7  10.9    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_1483  Ga0059261_1483 acetyl-CoA acetyl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_1483  Ga0059261_1483 acetyl-CoA acetyltransferases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  416.7  10.9  4.4e-129  4.4e-129       1     385 []       8     392 ..       8     392 .. 0.97

  Alignments for each domain:
  == domain 1  score: 416.7 bits;  conditional E-value: 4.4e-129
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 
                                               i++++Rtp+g+++g+l++++a +L+aa++ +++eragl+ e+++ +++G+vl+ag ++++aR+aa +ag
  lcl|FitnessBrowser__Korea:Ga0059261_1483   8 IISYARTPMGSMQGVLSDATATELGAAAVGAAVERAGLKGEAVERIYMGCVLPAGLGQAPARQAARKAG 76 
                                               899****************************************************************** PP

                                 TIGR01930  70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138
                                               lp++v+a+tvn++C+Sg+qA +++a++++aG  d++vaGG+Esm+++p+l++++  r+++++g+ +l d
  lcl|FitnessBrowser__Korea:Ga0059261_1483  77 LPDHVEATTVNKMCGSGMQAAIMGAEALAAGSVDLLVAGGLESMTNAPYLSMKH--RSGARIGHDRLFD 143
                                               *************************************************99997..8999********* PP

                                 TIGR01930 139 qllkdl....vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk.. 201
                                               ++  d+     + + +mg+ Ae++a++y+++Re qDe+a++S ++a+kA++ g f++ei+pve+k++  
  lcl|FitnessBrowser__Korea:Ga0059261_1483 144 HMFLDGledaYEPGRAMGTFAEEIATEYQFTREAQDEFAIASLMRAQKAQQTGGFDREITPVEIKTRkg 212
                                               999988999888999**************************************************9998 PP

                                 TIGR01930 202 kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplariv 270
                                                ++v+kDe++  +    k+ +Lkpaf++ +g t+tA+N+s+++DGAaal+l+  +va++lgl+p+ariv
  lcl|FitnessBrowser__Korea:Ga0059261_1483 213 VVTVDKDEQPA-KADPSKIPTLKPAFAK-DG-TITAANASSISDGAAALVLTRASVAERLGLDPVARIV 278
                                               78888888876.8899**********95.9*.6************************************ PP

                                 TIGR01930 271 saavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAi 339
                                               s+a  ++ p++++++pv A++kaL kag+ i d+dl+E+nEAFA+++++++++l  ++++ +NvnGGA 
  lcl|FitnessBrowser__Korea:Ga0059261_1483 279 SHAAHAHLPARFTTAPVFAMQKALGKAGWGIGDVDLFEVNEAFAVVAMIAMRDLS-ISHDVLNVNGGAC 346
                                               *******************************************************.779********** PP

                                 TIGR01930 340 AlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               AlGHP+GasGari++tll +L++ g+k+Gla+lC+ggG ++A+ +e
  lcl|FitnessBrowser__Korea:Ga0059261_1483 347 ALGHPVGASGARILATLLAALQNSGQKRGLASLCIGGGEATAMAVE 392
                                               *******************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (395 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: 00:00:00.01
# Mc/sec: 12.31
//
[ok]

This GapMind analysis is from Sep 17 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:

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