GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Rhodobacter viridis JA737

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate WP_110804635.1 C8J30_RS05090 acetyl-CoA C-acyltransferase family protein

Query= SwissProt::Q0KBP1
         (394 letters)



>NCBI__GCF_003217355.1:WP_110804635.1
          Length = 391

 Score =  455 bits (1170), Expect = e-132
 Identities = 228/390 (58%), Positives = 288/390 (73%), Gaps = 2/390 (0%)

Query: 5   VVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTEPRD 64
           +V++SG RTAIG FGGSL   AP +LG +  R AL R+ ++ + +  VV G+++ TEPRD
Sbjct: 4   IVILSGARTAIGAFGGSLAGFAPVDLGTIAARAALERSGIAPEQINQVVMGHILNTEPRD 63

Query: 65  MYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMSRAP 124
           MY+ RVAA+  G+ +  PA+ VNRLCGSG+QAIVSAAQ ++LG+ D A+ GG + MSRAP
Sbjct: 64  MYVSRVAAIQAGIPVETPAMNVNRLCGSGVQAIVSAAQALMLGEGDFALAGGVDVMSRAP 123

Query: 125 YLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAALESH 184
           Y+ PAAR+G +MGDA ++DMM+GAL  PF   HMGVTAENVA E  ISR  QD  ALES 
Sbjct: 124 YILPAARFGQKMGDASVIDMMVGALSCPFGTGHMGVTAENVATECAISREDQDTFALESQ 183

Query: 185 RRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKENGTVT 244
            RA+AAI AG FKD+IVPV    RKG V FDTDEH +   T+D +  L+P F+K  G+VT
Sbjct: 184 TRAAAAIAAGAFKDEIVPVEIASRKGTVIFDTDEHPK-ATTLDKLAALKPAFLK-GGSVT 241

Query: 245 AGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKIALER 304
           AGNASG+ND A A+V+     A   GLKPLAR+  +  AGV P+ MG+GP+PA ++  E+
Sbjct: 242 AGNASGINDGAGALVIAREDAAVATGLKPLARIRGFAIAGVRPEVMGLGPIPAVRLLCEK 301

Query: 305 AGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALITVKAL 364
            GL+VSD DVIE+NEAFAAQA AV++AL LDP KVNPNG  I+LGHP+GATGA++TVK L
Sbjct: 302 TGLKVSDFDVIESNEAFAAQALAVSRALDLDPTKVNPNGGAIALGHPVGATGAILTVKTL 361

Query: 365 HELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           + L R  GR  L+TMCIGGGQGIA   ER+
Sbjct: 362 YHLRRTGGRLGLITMCIGGGQGIALAIERL 391


Lambda     K      H
   0.318    0.134    0.381 

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: 512
Number of extensions: 19
Number of successful extensions: 3
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: 394
Length of database: 391
Length adjustment: 31
Effective length of query: 363
Effective length of database: 360
Effective search space:   130680
Effective search space used:   130680
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 WP_110804635.1 C8J30_RS05090 (acetyl-CoA C-acyltransferase family protein)
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.2325385.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-136  441.5   6.6   1.4e-136  441.4   6.6    1.0  1  NCBI__GCF_003217355.1:WP_110804635.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003217355.1:WP_110804635.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  441.4   6.6  1.4e-136  1.4e-136       1     385 []       6     389 ..       6     389 .. 0.98

  Alignments for each domain:
  == domain 1  score: 441.4 bits;  conditional E-value: 1.4e-136
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaaglpe 72 
                                           i++++Rt+ig++ggsl+ + ++dL++ + +++ler+g+ pe+i++v++G+ l++    + + R aa++ag+p 
  NCBI__GCF_003217355.1:WP_110804635.1   6 ILSGARTAIGAFGGSLAGFAPVDLGTIAARAALERSGIAPEQINQVVMGHILNTEPRdMYVSRVAAIQAGIPV 78 
                                           899**************************************************99988*************** PP

                             TIGR01930  73 svpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl. 144
                                           ++pa++vnr+C+Sg+qA+ +aaq+++ Ge d ++aGGv+ mSr+p++l+a+  r + k+g+a++ d+++  l 
  NCBI__GCF_003217355.1:WP_110804635.1  79 ETPAMNVNRLCGSGVQAIVSAAQALMLGEGDFALAGGVDVMSRAPYILPAA--RFGQKMGDASVIDMMVGALs 149
                                           *************************************************98..89***********9998889 PP

                             TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214
                                            +    +mg+tAen+a++ +isRe+qD +al+S+++aa+Ai++g fkdeivpve+  +  ++++++De+++  
  NCBI__GCF_003217355.1:WP_110804635.1 150 cPFGTGHMGVTAENVATECAISREDQDTFALESQTRAAAAIAAGAFKDEIVPVEIASRkgTVIFDTDEHPK-A 221
                                           9999***************************************************999999999*****99.8 PP

                             TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287
                                           ttl+kLa Lkpaf +  gs vtAgN+s++nDGA+al+++ e++a + gl+plari+++a+agv pe+mglgp+
  NCBI__GCF_003217355.1:WP_110804635.1 222 TTLDKLAALKPAFLK-GGS-VTAGNASGINDGAGALVIAREDAAVATGLKPLARIRGFAIAGVRPEVMGLGPI 292
                                           9************95.796.***************************************************** PP

                             TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360
                                           pA++ + +k+gl++sd+d++E nEAFAaq+lav ++l+ ld+ kvN nGGAiAlGHP+Ga+Ga++++++l++L
  NCBI__GCF_003217355.1:WP_110804635.1 293 PAVRLLCEKTGLKVSDFDVIESNEAFAAQALAVSRALD-LDPTKVNPNGGAIALGHPVGATGAILTVKTLYHL 364
                                           **************************************.89******************************** PP

                             TIGR01930 361 kergkkyGlatlCvggGqGaAvile 385
                                           ++ g+++Gl+t+C+ggGqG+A+ +e
  NCBI__GCF_003217355.1:WP_110804635.1 365 RRTGGRLGLITMCIGGGQGIALAIE 389
                                           *********************9886 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 12.65
//
[ok]

This GapMind analysis is from Sep 24 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