GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Pseudomonas fluorescens FW300-N2E2

Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate Pf6N2E2_2289 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= BRENDA::P28790
         (391 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2289
          Length = 383

 Score =  738 bits (1904), Expect = 0.0
 Identities = 366/383 (95%), Positives = 377/383 (98%)

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

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

Query: 129 SMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGISREQQDAFAVRSHQLAHKATVEGK 188
           SMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGI+REQQDAF VRSHQLAHKATVEGK
Sbjct: 121 SMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGITREQQDAFGVRSHQLAHKATVEGK 180

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

Query: 249 ASCMIVMSAQRAKDLGLEPLAVIRSMAVAGVDPAIMGYGPVPATQKALKRAGLNMADIDF 308
           ASCMIVMSAQRA+DLG++P+AVIRSMAVAGVDPAIMGYGPVPATQKALKRAGL +ADIDF
Sbjct: 241 ASCMIVMSAQRAQDLGIQPMAVIRSMAVAGVDPAIMGYGPVPATQKALKRAGLGIADIDF 300

Query: 309 IELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTLLNVMKQNG 368
            ELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTLLNVMKQNG
Sbjct: 301 FELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTLLNVMKQNG 360

Query: 369 GTFGLSTMCIGLGQGIATVFERV 391
           GTFG+STMCIGLGQGIATVFERV
Sbjct: 361 GTFGVSTMCIGLGQGIATVFERV 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: 670
Number of extensions: 13
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 Pf6N2E2_2289 (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.32538.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   3.3e-238  775.9   8.5   3.7e-238  775.8   8.5    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2289  3-ketoacyl-CoA thiolase (EC 2.3.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2289  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 !  775.8   8.5  3.7e-238  3.7e-238       3     385 .]       1     383 []       1     383 [] 1.00

  Alignments for each domain:
  == domain 1  score: 775.8 bits;  conditional E-value: 3.7e-238
                                      TIGR02445   3 vivdalrtpmgrskggafrntraedlsahllkkllarnpkveaaevediywgcvqqtleqgfni 66 
                                                    vivd++rtpmgrskgg++rntraed+sahl++kll+rn kv++ eved++wgcv+qtleqg+ni
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2289   1 VIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNVKVDPNEVEDVIWGCVNQTLEQGWNI 64 
                                                    8*************************************************************** PP

                                      TIGR02445  67 arnaallaevphevaavtvnrlcgssmqalhdaaraimtgdaevcliggvehmghvsmshgvdf 130
                                                    ar+a+l++++ph+ a +tv+rlcgssm+alh+aa+aimtg+++v+++ggvehmghvsm+hgvd+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2289  65 ARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMGHVSMMHGVDP 128
                                                    **************************************************************** PP

                                      TIGR02445 131 hpglskhvakaagmmgltaemlgklhgisreqqdafaarsharahaatlegkfkneiiptegyd 194
                                                    +p++s  +aka+gmmgltaemlgk+hgi+reqqdaf++rsh++ah+at+egkfk+eiip++gyd
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2289 129 NPHMSLYAAKASGMMGLTAEMLGKMHGITREQQDAFGVRSHQLAHKATVEGKFKDEIIPMQGYD 192
                                                    **************************************************************** PP

                                      TIGR02445 195 adgvlkvldydevirpettvealaalrpafdpkngtvtagtssalsdgasamlvmseeraqelg 258
                                                    ++g+lk +dyde+irpett+e+laal+paf+pk+gtvtagtss+++dgas+m+vms++raq+lg
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2289 193 ENGFLKLFDYDETIRPETTLESLAALKPAFNPKGGTVTAGTSSQITDGASCMIVMSAQRAQDLG 256
                                                    **************************************************************** PP

                                      TIGR02445 259 vkprarirsmavagvdpsimgygpvpatkkalkraglsisdidvlelneafaaqalpvlkdlgl 322
                                                    ++p+a+irsmavagvdp+imgygpvpat+kalkragl i did++elneafaaqalpvlkdl++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2289 257 IQPMAVIRSMAVAGVDPAIMGYGPVPATQKALKRAGLGIADIDFFELNEAFAAQALPVLKDLKV 320
                                                    **************************************************************** PP

                                      TIGR02445 323 ldkldekvnlnggaialghplgcsgaristtllnlmerkdakfglatmciglgqgiatvferv 385
                                                    ldk++ekvnl+ggaialghp+gcsgaris+tlln+m++++++fg++tmciglgqgiatvferv
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2289 321 LDKMNEKVNLHGGAIALGHPFGCSGARISGTLLNVMKQNGGTFGVSTMCIGLGQGIATVFERV 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: 10.22
//
[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