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.17699.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.45
//
[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:

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:

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:

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:

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