GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Phaeobacter inhibens BS107

Align 3-ketoacyl-CoA thiolase (EC 2.3.1.16) (characterized)
to candidate GFF3267 PGA1_c33180 acetyl-CoA acetyltransferase

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



>FitnessBrowser__Phaeo:GFF3267
          Length = 390

 Score =  487 bits (1253), Expect = e-142
 Identities = 247/387 (63%), Positives = 292/387 (75%), Gaps = 2/387 (0%)

Query: 9   IVIVGAARTPMGSLQGDFSSLAAHDLGGAAIKAAIERAGVSPDAVGEVLFGNCLMAGQGQ 68
           +VI GAARTPMG  QG +  +AA +LGG+AI+AA+  AG +   V E+L G  L AGQGQ
Sbjct: 4   VVIAGAARTPMGGFQGMYDGVAAAELGGSAIRAALAGAGAT--TVDEILMGCVLPAGQGQ 61

Query: 69  APARQAAFKGGLPKGAGAVTLSKMCGSGMKAAMMAHDMLLAGSHDVMVAGGMESMTNAPY 128
           APARQA F  GL +   A TL+KMCGSGMKAAMMA+D +  G  D M+AGGMESMTNAPY
Sbjct: 62  APARQAGFAAGLGEEVPATTLNKMCGSGMKAAMMAYDQIALGQADTMIAGGMESMTNAPY 121

Query: 129 LLQKGRGGYRLGHDRIFDHMMLDGLEDAYEAGRSMGTFGEDCAAKYSFTREQQDAFATAS 188
           LL K R G RLGH ++ DHM LDGLEDAY+ GR MGTF EDCA  Y FTRE QD +A  S
Sbjct: 122 LLPKMRNGARLGHGQVVDHMFLDGLEDAYDKGRLMGTFAEDCAETYQFTREAQDEYALTS 181

Query: 189 VQRAKAATESGAFAAEIVPVTVKTRAGETVVSVDEGPGKVKLEKIATLKPAFKKDGTITA 248
           +  A AA ESGAF AEI PVTVKTR GETV + DE P   + +KI TLKPAF+KDGT+TA
Sbjct: 182 LSNALAAQESGAFDAEIAPVTVKTRKGETVTNADEQPKSARPDKIPTLKPAFRKDGTVTA 241

Query: 249 ASSSSINDGAAALVMMRESTAKKLGAKPLARIVSHATHAQEPEWFATAPLGATQKALAKA 308
           A++SSI+DGAAALV+  E  A+  G    ARI+ HA+HAQ P  F TAP+ A +K +A+ 
Sbjct: 242 ANASSISDGAAALVLASEDAAEAQGLTVRARIMGHASHAQAPGLFTTAPVPAAKKLMAQL 301

Query: 309 GWQVGDVQLWEINEAFAVVPMALMKELDLPHDKVNVNGGACALGHPIGASGARIMVTLIH 368
           GW V DV LWE+NEAFAVVPMA M E+ LP DKVNVNGGACALGHPIGASGARIMVTL++
Sbjct: 302 GWTVSDVDLWEVNEAFAVVPMAFMHEMGLPRDKVNVNGGACALGHPIGASGARIMVTLLN 361

Query: 369 ALKARGLTKGLATLCIGGGEATAVALE 395
           AL+ R L +G+A +CIGGGE TA+A+E
Sbjct: 362 ALEKRNLKRGIAAICIGGGEGTAIAIE 388


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: 510
Number of extensions: 18
Number of successful extensions: 2
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: 390
Length adjustment: 31
Effective length of query: 366
Effective length of database: 359
Effective search space:   131394
Effective search space used:   131394
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 GFF3267 PGA1_c33180 (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.16090.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   5.2e-129  416.4  10.6   6.1e-129  416.2  10.6    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3267  PGA1_c33180 acetyl-CoA acetyltra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3267  PGA1_c33180 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  416.2  10.6  6.1e-129  6.1e-129       1     385 []       6     388 ..       6     388 .. 0.96

  Alignments for each domain:
  == domain 1  score: 416.2 bits;  conditional E-value: 6.1e-129
                          TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesvpa 76 
                                        i +a+Rtp+g ++g +  + a++L+  +i+++l+ ag     +de+ +G+vl+ag+++++aR+a +aagl+e+vpa
  lcl|FitnessBrowser__Phaeo:GFF3267   6 IAGAARTPMGGFQGMYDGVAAAELGGSAIRAALAGAGA--TTVDEILMGCVLPAGQGQAPARQAGFAAGLGEEVPA 79 
                                        7899******99*********************99855..58********************************** PP

                          TIGR01930  77 ltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl....vktk 148
                                        +t+n++C+Sg++A ++a+++i+ G+ad+++aGG+Esm+++p+ll++   r++++lg+ ++ d++  d+     +++
  lcl|FitnessBrowser__Phaeo:GFF3267  80 TTLNKMCGSGMKAAMMAYDQIALGQADTMIAGGMESMTNAPYLLPKM--RNGARLGHGQVVDHMFLDGledaYDKG 153
                                        *********************************************97..899999999999999988889988899 PP

                          TIGR01930 149 lsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpnttlekLak 222
                                          mg+ Ae +a++y+++Re qDeyal S ++a +A+e+g f++ei pv+vk++  ++v++ De+++     +k+ +
  lcl|FitnessBrowser__Phaeo:GFF3267 154 RLMGTFAEDCAETYQFTREAQDEYALTSLSNALAAQESGAFDAEIAPVTVKTRkgETVTNADEQPK-SARPDKIPT 228
                                        9**************************************************999766667777776.899****** PP

                          TIGR01930 223 LkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkag 298
                                        Lkpaf++ +g tvtA+N+s+++DGAaal+l+se++a++ glt+ ari+++a  +  p  ++++pvpA +k++++ g
  lcl|FitnessBrowser__Phaeo:GFF3267 229 LKPAFRK-DG-TVTAANASSISDGAAALVLASEDAAEAQGLTVRARIMGHASHAQAPGLFTTAPVPAAKKLMAQLG 302
                                        *****95.9*.6**************************************************************** PP

                          TIGR01930 299 lsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCv 374
                                        +++sd+dl+E+nEAFA++ +a+++e+g l ++kvNvnGGA AlGHP+GasGari++tll++L++r+ k+G+a++C+
  lcl|FitnessBrowser__Phaeo:GFF3267 303 WTVSDVDLWEVNEAFAVVPMAFMHEMG-LPRDKVNVNGGACALGHPIGASGARIMVTLLNALEKRNLKRGIAAICI 377
                                        ***************************.88********************************************** PP

                          TIGR01930 375 ggGqGaAvile 385
                                        ggG G+A+ +e
  lcl|FitnessBrowser__Phaeo:GFF3267 378 GGGEGTAIAIE 388
                                        *******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (390 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: 12.17
//
[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