GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadA in Pseudomonas fluorescens FW300-N1B4

Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate Pf1N1B4_3904 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= BRENDA::P28790
         (391 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3904 3-ketoacyl-CoA
           thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase
           (EC 2.3.1.9)
          Length = 383

 Score =  732 bits (1889), Expect = 0.0
 Identities = 362/383 (94%), Positives = 376/383 (98%)

Query: 9   VIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKVLERNSKVDPGEVEDVIWGCVNQTLEQ 68
           VIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISK+LERN KVDP EVEDVIWGCVNQTLEQ
Sbjct: 1   VIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNVKVDPSEVEDVIWGCVNQTLEQ 60

Query: 69  GWNIARMASLMTQIPHTSAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMGHV 128
           GWNIARMASLMTQIPHT+A QTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMGHV
Sbjct: 61  GWNIARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMGHV 120

Query: 129 SMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGISREQQDAFAVRSHQLAHKATVEGK 188
           SMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGI+REQQDAF VRSHQLAHKAT+EGK
Sbjct: 121 SMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGITREQQDAFGVRSHQLAHKATLEGK 180

Query: 189 FKDEIIPMQGYDENGFLKIFDYDETIRPDTTLESLAALKPAFNPKGGTVTAGTSSQITDG 248
           FKDEIIPMQGYDENGFLK+FDYDETIRP+TTLESLAALKPAFNPKGGTVTAGTSSQITDG
Sbjct: 181 FKDEIIPMQGYDENGFLKLFDYDETIRPETTLESLAALKPAFNPKGGTVTAGTSSQITDG 240

Query: 249 ASCMIVMSAQRAKDLGLEPLAVIRSMAVAGVDPAIMGYGPVPATQKALKRAGLNMADIDF 308
           ASCMIVMSAQRA+DLG++P+AVIRSMAVAGVDPAIMGYGPVPATQKALKRAGL + DIDF
Sbjct: 241 ASCMIVMSAQRAQDLGIQPMAVIRSMAVAGVDPAIMGYGPVPATQKALKRAGLGINDIDF 300

Query: 309 IELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTLLNVMKQNG 368
            ELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTLLNVMKQNG
Sbjct: 301 FELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTLLNVMKQNG 360

Query: 369 GTFGLSTMCIGLGQGIATVFERV 391
           GTFG++TMCIGLGQGI+TVFERV
Sbjct: 361 GTFGVATMCIGLGQGISTVFERV 383


Lambda     K      H
   0.318    0.133    0.386 

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: 662
Number of extensions: 15
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: 383
Length adjustment: 30
Effective length of query: 361
Effective length of database: 353
Effective search space:   127433
Effective search space used:   127433
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 Pf1N1B4_3904 (3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9))
to HMM TIGR02445 (fadA: acetyl-CoA C-acyltransferase FadA (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/TIGR02445.hmm
# target sequence database:        /tmp/gapView.27011.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02445  [M=385]
Accession:   TIGR02445
Description: fadA: acetyl-CoA C-acyltransferase FadA
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.3e-238  777.3   8.0   1.4e-238  777.1   8.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3904  3-ketoacyl-CoA thiolase (EC 2.3.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3904  3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  777.1   8.0  1.4e-238  1.4e-238       3     385 .]       1     383 []       1     383 [] 1.00

  Alignments for each domain:
  == domain 1  score: 777.1 bits;  conditional E-value: 1.4e-238
                                      TIGR02445   3 vivdalrtpmgrskggafrntraedlsahllkkllarnpkveaaevediywgcvqqtleqgfni 66 
                                                    vivd++rtpmgrskgg++rntraed+sahl++kll+rn kv+++eved++wgcv+qtleqg+ni
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3904   1 VIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNVKVDPSEVEDVIWGCVNQTLEQGWNI 64 
                                                    8*************************************************************** PP

                                      TIGR02445  67 arnaallaevphevaavtvnrlcgssmqalhdaaraimtgdaevcliggvehmghvsmshgvdf 130
                                                    ar+a+l++++ph+ a +tv+rlcgssm+alh+aa+aimtg+++v+++ggvehmghvsm+hgvd+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3904  65 ARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMGHVSMMHGVDP 128
                                                    **************************************************************** PP

                                      TIGR02445 131 hpglskhvakaagmmgltaemlgklhgisreqqdafaarsharahaatlegkfkneiiptegyd 194
                                                    +p++s  +aka+gmmgltaemlgk+hgi+reqqdaf++rsh++ah+atlegkfk+eiip++gyd
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3904 129 NPHMSLYAAKASGMMGLTAEMLGKMHGITREQQDAFGVRSHQLAHKATLEGKFKDEIIPMQGYD 192
                                                    **************************************************************** PP

                                      TIGR02445 195 adgvlkvldydevirpettvealaalrpafdpkngtvtagtssalsdgasamlvmseeraqelg 258
                                                    ++g+lk +dyde+irpett+e+laal+paf+pk+gtvtagtss+++dgas+m+vms++raq+lg
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3904 193 ENGFLKLFDYDETIRPETTLESLAALKPAFNPKGGTVTAGTSSQITDGASCMIVMSAQRAQDLG 256
                                                    **************************************************************** PP

                                      TIGR02445 259 vkprarirsmavagvdpsimgygpvpatkkalkraglsisdidvlelneafaaqalpvlkdlgl 322
                                                    ++p+a+irsmavagvdp+imgygpvpat+kalkragl i+did++elneafaaqalpvlkdl++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3904 257 IQPMAVIRSMAVAGVDPAIMGYGPVPATQKALKRAGLGINDIDFFELNEAFAAQALPVLKDLKV 320
                                                    **************************************************************** PP

                                      TIGR02445 323 ldkldekvnlnggaialghplgcsgaristtllnlmerkdakfglatmciglgqgiatvferv 385
                                                    ldk++ekvnl+ggaialghp+gcsgaris+tlln+m++++++fg+atmciglgqgi+tvferv
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3904 321 LDKMNEKVNLHGGAIALGHPFGCSGARISGTLLNVMKQNGGTFGVATMCIGLGQGISTVFERV 383
                                                    **************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (383 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: 10.57
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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