GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadA in Pseudomonas fluorescens GW456-L13

Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate PfGW456L13_4040 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= BRENDA::P28790
         (391 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4040
           3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA
           acetyltransferase (EC 2.3.1.9)
          Length = 391

 Score =  751 bits (1938), Expect = 0.0
 Identities = 373/391 (95%), Positives = 384/391 (98%)

Query: 1   MSLNPRDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKVLERNSKVDPGEVEDVIWG 60
           MSLNPRDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISK+LERN KVDP EVEDVIWG
Sbjct: 1   MSLNPRDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNVKVDPNEVEDVIWG 60

Query: 61  CVNQTLEQGWNIARMASLMTQIPHTSAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG 120
           CVNQTLEQGWNIARMASLMTQIPHTSA QTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG
Sbjct: 61  CVNQTLEQGWNIARMASLMTQIPHTSAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG 120

Query: 121 GVEHMGHVSMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGISREQQDAFAVRSHQLA 180
           GVEHMGHVSMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGI+REQQDAF VRSHQLA
Sbjct: 121 GVEHMGHVSMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGITREQQDAFGVRSHQLA 180

Query: 181 HKATVEGKFKDEIIPMQGYDENGFLKIFDYDETIRPDTTLESLAALKPAFNPKGGTVTAG 240
           HKATVEGKFKDEIIPMQGYDENGFLK FDYDETIRP+TTLESLAALKPAFNPKGGTVTAG
Sbjct: 181 HKATVEGKFKDEIIPMQGYDENGFLKTFDYDETIRPETTLESLAALKPAFNPKGGTVTAG 240

Query: 241 TSSQITDGASCMIVMSAQRAKDLGLEPLAVIRSMAVAGVDPAIMGYGPVPATQKALKRAG 300
           TSSQITDGASCMIVMSAQRA+DLG++PLAVIRSMAVAGVDPAIMGYGPVPATQKALKRAG
Sbjct: 241 TSSQITDGASCMIVMSAQRAQDLGIQPLAVIRSMAVAGVDPAIMGYGPVPATQKALKRAG 300

Query: 301 LNMADIDFIELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTL 360
           L ++DIDF ELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTL
Sbjct: 301 LGISDIDFFELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTL 360

Query: 361 LNVMKQNGGTFGLSTMCIGLGQGIATVFERV 391
           LNVMKQNGGTFG++TMCIGLGQGI+TVFERV
Sbjct: 361 LNVMKQNGGTFGVATMCIGLGQGISTVFERV 391


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: 681
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: 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 PfGW456L13_4040 (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.21900.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   2.8e-240  782.7   7.7   3.2e-240  782.6   7.7    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4040  3-ketoacyl-CoA thiolase (EC 2.3.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4040  3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltran
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  782.6   7.7  3.2e-240  3.2e-240       1     385 []       7     391 .]       7     391 .] 1.00

  Alignments for each domain:
  == domain 1  score: 782.6 bits;  conditional E-value: 3.2e-240
                                               TIGR02445   1 dvvivdalrtpmgrskggafrntraedlsahllkkllarnpkveaaevediywgc 55 
                                                             dvvivd++rtpmgrskgg++rntraed+sahl++kll+rn kv++ eved++wgc
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4040   7 DVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNVKVDPNEVEDVIWGC 61 
                                                             79***************************************************** PP

                                               TIGR02445  56 vqqtleqgfniarnaallaevphevaavtvnrlcgssmqalhdaaraimtgdaev 110
                                                             v+qtleqg+niar+a+l++++ph++a +tv+rlcgssm+alh+aa+aimtg+++v
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4040  62 VNQTLEQGWNIARMASLMTQIPHTSAGQTVSRLCGSSMSALHTAAQAIMTGNGDV 116
                                                             ******************************************************* PP

                                               TIGR02445 111 cliggvehmghvsmshgvdfhpglskhvakaagmmgltaemlgklhgisreqqda 165
                                                             +++ggvehmghvsm+hgvd++p++s  +aka+gmmgltaemlgk+hgi+reqqda
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4040 117 FVVGGVEHMGHVSMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGITREQQDA 171
                                                             ******************************************************* PP

                                               TIGR02445 166 faarsharahaatlegkfkneiiptegydadgvlkvldydevirpettvealaal 220
                                                             f++rsh++ah+at+egkfk+eiip++gyd++g+lk++dyde+irpett+e+laal
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4040 172 FGVRSHQLAHKATVEGKFKDEIIPMQGYDENGFLKTFDYDETIRPETTLESLAAL 226
                                                             ******************************************************* PP

                                               TIGR02445 221 rpafdpkngtvtagtssalsdgasamlvmseeraqelgvkprarirsmavagvdp 275
                                                             +paf+pk+gtvtagtss+++dgas+m+vms++raq+lg++p+a+irsmavagvdp
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4040 227 KPAFNPKGGTVTAGTSSQITDGASCMIVMSAQRAQDLGIQPLAVIRSMAVAGVDP 281
                                                             ******************************************************* PP

                                               TIGR02445 276 simgygpvpatkkalkraglsisdidvlelneafaaqalpvlkdlglldkldekv 330
                                                             +imgygpvpat+kalkragl isdid++elneafaaqalpvlkdl++ldk++ekv
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4040 282 AIMGYGPVPATQKALKRAGLGISDIDFFELNEAFAAQALPVLKDLKVLDKMNEKV 336
                                                             ******************************************************* PP

                                               TIGR02445 331 nlnggaialghplgcsgaristtllnlmerkdakfglatmciglgqgiatvferv 385
                                                             nl+ggaialghp+gcsgaris+tlln+m++++++fg+atmciglgqgi+tvferv
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4040 337 NLHGGAIALGHPFGCSGARISGTLLNVMKQNGGTFGVATMCIGLGQGISTVFERV 391
                                                             ******************************************************7 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.69
//
[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