GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Rhodobacter maris JA276

Align acetyl-CoA acetyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_097068496.1 CRO22_RS02395 acetyl-CoA C-acetyltransferase

Query= metacyc::MONOMER-13585
         (391 letters)



>NCBI__GCF_900217815.1:WP_097068496.1
          Length = 391

 Score =  674 bits (1738), Expect = 0.0
 Identities = 336/389 (86%), Positives = 361/389 (92%)

Query: 1   MTNVVIVSAARTAVGSFNGAFASTPAHDLGAAVIEAVVARAGIDKADVSETILGQVLTAG 60
           MTNVVIVSAARTAVGSFNGAFA+TPAHDLGAAVIEAVVARAGIDKA+VSETILGQVL+AG
Sbjct: 1   MTNVVIVSAARTAVGSFNGAFANTPAHDLGAAVIEAVVARAGIDKAEVSETILGQVLSAG 60

Query: 61  QGQNPARQAHIKAGLPQESAAWSINQVCGSGLRAVALAAQHVQLGDASIVVAGGQENMSL 120
           QGQNPARQAHIKAGLP ESAAW INQVCGSGLR VAL AQH+QLGDA IVVAGGQE+MSL
Sbjct: 61  QGQNPARQAHIKAGLPIESAAWGINQVCGSGLRTVALGAQHIQLGDADIVVAGGQESMSL 120

Query: 121 SPHVAHLRAGQKMGDLSFIDSMIKDGLWDAFNGYHMGQTAENVAAKWQISRDMQDEFAVA 180
           SPHVAHLRAG KMGD+  IDSMIKDGLWDAFNGYHMGQTAENVAA+WQISR+MQD  A+A
Sbjct: 121 SPHVAHLRAGTKMGDMKMIDSMIKDGLWDAFNGYHMGQTAENVAAQWQISREMQDALALA 180

Query: 181 SQNKAEAAQKAGRFADEIVPFVIKTRKGDVTVDADEYIRHGATLDAMAKLRPAFIKDGTV 240
           SQNKAEAAQKAG+F DEIVPF +KTRKGD+ VDADEYIRHGATL++M KL+PAFIKDGTV
Sbjct: 181 SQNKAEAAQKAGKFTDEIVPFTVKTRKGDIVVDADEYIRHGATLESMQKLKPAFIKDGTV 240

Query: 241 TAANASGINDGAAAVLVMSAEEAEKRGLSPLARIASYATAGLDPSIMGVGPIHASRKALE 300
           TA NASGINDGAA VL+M+ EEA KRGL+P+ARIAS+ATAGLDPSIMG GPI ASRKALE
Sbjct: 241 TAGNASGINDGAAVVLLMTEEEAAKRGLTPMARIASWATAGLDPSIMGCGPIPASRKALE 300

Query: 301 KAGWKVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARVLNTL 360
           KAGW   DLDL+EANEAFAAQACAVNKDMGWD + VNVNGGAIAIGHPIGASG R+LNTL
Sbjct: 301 KAGWTAADLDLIEANEAFAAQACAVNKDMGWDTAKVNVNGGAIAIGHPIGASGCRILNTL 360

Query: 361 LFEMQRRNAKKGLATLCIGGGMGVAMCLE 389
           +FEM+R  AKKGLATLCIGGGMGVAMCLE
Sbjct: 361 VFEMKRSGAKKGLATLCIGGGMGVAMCLE 389


Lambda     K      H
   0.317    0.130    0.375 

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: 595
Number of extensions: 18
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: 391
Length of database: 391
Length adjustment: 31
Effective length of query: 360
Effective length of database: 360
Effective search space:   129600
Effective search space used:   129600
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_097068496.1 CRO22_RS02395 (acetyl-CoA C-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.2862469.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.4e-146  473.5  12.8   2.7e-146  473.4  12.8    1.0  1  NCBI__GCF_900217815.1:WP_097068496.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900217815.1:WP_097068496.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  473.4  12.8  2.7e-146  2.7e-146       1     385 []       6     389 ..       6     389 .. 0.98

  Alignments for each domain:
  == domain 1  score: 473.4 bits;  conditional E-value: 2.7e-146
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 
                                           iv+a+Rt++g+++g++++++a+dL+aavi+++++rag+d++++ e ilG+vl+ag+++n+aR+a ++aglp +
  NCBI__GCF_900217815.1:WP_097068496.1   6 IVSAARTAVGSFNGAFANTPAHDLGAAVIEAVVARAGIDKAEVSETILGQVLSAGQGQNPARQAHIKAGLPIE 78 
                                           8************************************************************************ PP

                             TIGR01930  74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144
                                            +a+ +n+vC+Sgl++val+aq+i+ G+ad+vvaGG EsmS +p++ +    r++ k+g++k+ d+++kd+  
  NCBI__GCF_900217815.1:WP_097068496.1  79 SAAWGINQVCGSGLRTVALGAQHIQLGDADIVVAGGQESMSLSPHVAHL---RAGTKMGDMKMIDSMIKDGlw 148
                                           ********************************************97776...699****************** PP

                             TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214
                                            + ++++mg+tAen+a++++isRe+qD++al+S++ka++A+++gkf deivp++vk++  + vv+ De ir +
  NCBI__GCF_900217815.1:WP_097068496.1 149 dAFNGYHMGQTAENVAAQWQISREMQDALALASQNKAEAAQKAGKFTDEIVPFTVKTRkgDIVVDADEYIRHG 221
                                           *99*****************************************************999999*********** PP

                             TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287
                                            tle+++kLkpaf + +g tvtAgN+s++nDGAa++llm+ee a++ gltp+ari s+a+ag+dp++mg+gp+
  NCBI__GCF_900217815.1:WP_097068496.1 222 ATLESMQKLKPAFIK-DG-TVTAGNASGINDGAAVVLLMTEEEAAKRGLTPMARIASWATAGLDPSIMGCGPI 292
                                           *************95.9*.6***************************************************** PP

                             TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360
                                           pA++kaL+kag+++ d+dl+E nEAFAaq+ av+k++g  d++kvNvnGGAiA+GHP+GasG+ri+ tl+ e+
  NCBI__GCF_900217815.1:WP_097068496.1 293 PASRKALEKAGWTAADLDLIEANEAFAAQACAVNKDMG-WDTAKVNVNGGAIAIGHPIGASGCRILNTLVFEM 364
                                           **************************************.88******************************** PP

                             TIGR01930 361 kergkkyGlatlCvggGqGaAvile 385
                                           k+ g+k GlatlC+ggG+G+A+ le
  NCBI__GCF_900217815.1:WP_097068496.1 365 KRSGAKKGLATLCIGGGMGVAMCLE 389
                                           **********************987 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: 00:00:00.00
# Mc/sec: 18.81
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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