GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Sinorhizobium fredii NGR234

Align acetyl-CoA acetyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_012709751.1 NGR_RS27475 acetyl-CoA C-acetyltransferase

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



>NCBI__GCF_000018545.1:WP_012709751.1
          Length = 393

 Score =  616 bits (1588), Expect = 0.0
 Identities = 302/388 (77%), Positives = 342/388 (88%)

Query: 3   NVVIVSAARTAVGSFNGAFASTPAHDLGAAVIEAVVARAGIDKADVSETILGQVLTAGQG 62
           ++VI SAARTAVGSFNGAF +TPAH+LGA VI+AV+ RAG+D A+V E ILGQVL AG+G
Sbjct: 5   SIVIASAARTAVGSFNGAFGNTPAHELGATVIKAVLERAGVDAAEVDEVILGQVLPAGEG 64

Query: 63  QNPARQAHIKAGLPQESAAWSINQVCGSGLRAVALAAQHVQLGDASIVVAGGQENMSLSP 122
           QNPARQA IKAG+PQE  AW +NQ+CGSGLRAVAL  Q +  GDASI+VAGG E+MS++P
Sbjct: 65  QNPARQAAIKAGVPQEKTAWGMNQLCGSGLRAVALGMQQIATGDASIIVAGGMESMSMAP 124

Query: 123 HVAHLRAGQKMGDLSFIDSMIKDGLWDAFNGYHMGQTAENVAAKWQISRDMQDEFAVASQ 182
           H AHLR G KMGD   ID+MIKDGL DAF GYHMG TAENVA KWQ++R+ QDEFA+ SQ
Sbjct: 125 HCAHLRGGVKMGDYKMIDTMIKDGLTDAFYGYHMGTTAENVARKWQLTREEQDEFALRSQ 184

Query: 183 NKAEAAQKAGRFADEIVPFVIKTRKGDVTVDADEYIRHGATLDAMAKLRPAFIKDGTVTA 242
           NKAEAAQKAGRFADEIVPF++KTRKGDVTVD DEYIRHGATL+++AKLRPAF K+GTVTA
Sbjct: 185 NKAEAAQKAGRFADEIVPFIVKTRKGDVTVDQDEYIRHGATLESIAKLRPAFDKEGTVTA 244

Query: 243 ANASGINDGAAAVLVMSAEEAEKRGLSPLARIASYATAGLDPSIMGVGPIHASRKALEKA 302
            NASG+NDGAAA L+M+  EA KRG+ PLARI S+ATAG+DP IMG GPI ASRKALEKA
Sbjct: 245 GNASGLNDGAAATLLMTEAEAAKRGIQPLARIVSWATAGVDPQIMGTGPIPASRKALEKA 304

Query: 303 GWKVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARVLNTLLF 362
           GW +GD++LVEANEAFAAQACAVNKD+GWDPSIVNVNGGAIAIGHPIGASGARVLNTLLF
Sbjct: 305 GWPIGDVELVEANEAFAAQACAVNKDLGWDPSIVNVNGGAIAIGHPIGASGARVLNTLLF 364

Query: 363 EMQRRNAKKGLATLCIGGGMGVAMCLER 390
           EM+RR   KGLATLCIGGGMGVAMC+ER
Sbjct: 365 EMKRRGVSKGLATLCIGGGMGVAMCVER 392


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: 542
Number of extensions: 11
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: 393
Length adjustment: 31
Effective length of query: 360
Effective length of database: 362
Effective search space:   130320
Effective search space used:   130320
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_012709751.1 NGR_RS27475 (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.1040369.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.7e-148  480.0   8.1   3.1e-148  479.7   8.1    1.0  1  NCBI__GCF_000018545.1:WP_012709751.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000018545.1:WP_012709751.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.7   8.1  3.1e-148  3.1e-148       1     385 []       8     391 ..       8     391 .. 0.98

  Alignments for each domain:
  == domain 1  score: 479.7 bits;  conditional E-value: 3.1e-148
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 
                                           i +a+Rt++g+++g++ +++a++L+a+vik++lerag+d++++devilG+vl+age++n+aR+aa++ag+p++
  NCBI__GCF_000018545.1:WP_012709751.1   8 IASAARTAVGSFNGAFGNTPAHELGATVIKAVLERAGVDAAEVDEVILGQVLPAGEGQNPARQAAIKAGVPQE 80 
                                           789********************************************************************** PP

                             TIGR01930  74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144
                                             a+ +n++C+Sgl+Aval++q+i++G+a+++vaGG+EsmS +p+  +    r ++k+g++k+ d+++kd+  
  NCBI__GCF_000018545.1:WP_012709751.1  81 KTAWGMNQLCGSGLRAVALGMQQIATGDASIIVAGGMESMSMAPHCAHL---RGGVKMGDYKMIDTMIKDGlt 150
                                           ********************************************97776...69*****************99 PP

                             TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214
                                            +  +++mg+tAen+a+k++++ReeqDe+alrS++ka++A+++g+f+deivp+ vk++  +++v++De ir +
  NCBI__GCF_000018545.1:WP_012709751.1 151 dAFYGYHMGTTAENVARKWQLTREEQDEFALRSQNKAEAAQKAGRFADEIVPFIVKTRkgDVTVDQDEYIRHG 223
                                           98899************************************************99999999************ PP

                             TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287
                                            tle++akL+paf++ +g tvtAgN+s+lnDGAaa+llm+e+ a++ g++plarivs+a+agvdp++mg+gp+
  NCBI__GCF_000018545.1:WP_012709751.1 224 ATLESIAKLRPAFDK-EG-TVTAGNASGLNDGAAATLLMTEAEAAKRGIQPLARIVSWATAGVDPQIMGTGPI 294
                                           *************95.8*.6***************************************************** PP

                             TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360
                                           pA++kaL+kag+ i d++lvE nEAFAaq+ av+k+lg  d++ vNvnGGAiA+GHP+GasGar++ tll e+
  NCBI__GCF_000018545.1:WP_012709751.1 295 PASRKALEKAGWPIGDVELVEANEAFAAQACAVNKDLG-WDPSIVNVNGGAIAIGHPIGASGARVLNTLLFEM 366
                                           **************************************.88******************************** PP

                             TIGR01930 361 kergkkyGlatlCvggGqGaAvile 385
                                           k+rg+  GlatlC+ggG+G+A+ +e
  NCBI__GCF_000018545.1:WP_012709751.1 367 KRRGVSKGLATLCIGGGMGVAMCVE 391
                                           **********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (393 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: 00:00:00.00
# Mc/sec: 26.47
//
[ok]

This GapMind analysis is from Apr 09 2024. 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