Alignments for a candidate for fadA in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Pseudomonas fluorescens FW300-N2C3

Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate AO356_02325 AO356_02325 3-ketoacyl-CoA thiolase

Query= BRENDA::P28790
         (391 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_02325
          Length = 391

 Score =  754 bits (1948), Expect = 0.0
 Identities = 375/391 (95%), Positives = 385/391 (98%)

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

Query: 61  CVNQTLEQGWNIARMASLMTQIPHTSAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG 120
           CVNQTLEQGWNIARMASLMTQIPHT+A QTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG
Sbjct: 61  CVNQTLEQGWNIARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG 120

Query: 121 GVEHMGHVSMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGISREQQDAFAVRSHQLA 180
           GVEHMGHVSMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGISREQQDAF VRSHQLA
Sbjct: 121 GVEHMGHVSMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGISREQQDAFGVRSHQLA 180

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

Query: 241 TSSQITDGASCMIVMSAQRAKDLGLEPLAVIRSMAVAGVDPAIMGYGPVPATQKALKRAG 300
           TSSQITDGASCMIVMSAQRA+DLG++P+AVIRSMAVAGVDPAIMGYGPVPATQKALKRAG
Sbjct: 241 TSSQITDGASCMIVMSAQRAQDLGIQPMAVIRSMAVAGVDPAIMGYGPVPATQKALKRAG 300

Query: 301 LNMADIDFIELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTL 360
           L +ADIDF ELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTL
Sbjct: 301 LGIADIDFFELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTL 360

Query: 361 LNVMKQNGGTFGLSTMCIGLGQGIATVFERV 391
           LNVMKQNGGTFG+STMCIGLGQGIATVFERV
Sbjct: 361 LNVMKQNGGTFGVSTMCIGLGQGIATVFERV 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: 688
Number of extensions: 14
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 AO356_02325 AO356_02325 (3-ketoacyl-CoA thiolase)
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.1822.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   1.6e-239  780.2   8.5   1.8e-239  780.1   8.5    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02325  AO356_02325 3-ketoacyl-CoA thiol


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02325  AO356_02325 3-ketoacyl-CoA thiolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  780.1   8.5  1.8e-239  1.8e-239       1     385 []       7     391 .]       7     391 .] 1.00

  Alignments for each domain:
  == domain 1  score: 780.1 bits;  conditional E-value: 1.8e-239
                                       TIGR02445   1 dvvivdalrtpmgrskggafrntraedlsahllkkllarnpkveaaevediywgcvqqtleqg 63 
                                                     dvvivd++rtpmgrskgg++rntraed+sahl++kll+rn kv++ eved++wgcv+qtleqg
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02325   7 DVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNVKVDPNEVEDVIWGCVNQTLEQG 69 
                                                     79************************************************************* PP

                                       TIGR02445  64 fniarnaallaevphevaavtvnrlcgssmqalhdaaraimtgdaevcliggvehmghvsmsh 126
                                                     +niar+a+l++++ph+ a +tv+rlcgssm+alh+aa+aimtg+++v+++ggvehmghvsm+h
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02325  70 WNIARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMGHVSMMH 132
                                                     *************************************************************** PP

                                       TIGR02445 127 gvdfhpglskhvakaagmmgltaemlgklhgisreqqdafaarsharahaatlegkfkneiip 189
                                                     gvd++p++s  +aka+gmmgltaemlgk+hgisreqqdaf++rsh++ah+at+egkfk+eiip
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02325 133 GVDPNPHMSLYAAKASGMMGLTAEMLGKMHGISREQQDAFGVRSHQLAHKATVEGKFKDEIIP 195
                                                     *************************************************************** PP

                                       TIGR02445 190 tegydadgvlkvldydevirpettvealaalrpafdpkngtvtagtssalsdgasamlvmsee 252
                                                     ++gyd++g+lk +dyde+irpett+e+laal+paf+pk+gtvtagtss+++dgas+m+vms++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02325 196 MQGYDENGFLKLFDYDETIRPETTLESLAALKPAFNPKGGTVTAGTSSQITDGASCMIVMSAQ 258
                                                     *************************************************************** PP

                                       TIGR02445 253 raqelgvkprarirsmavagvdpsimgygpvpatkkalkraglsisdidvlelneafaaqalp 315
                                                     raq+lg++p+a+irsmavagvdp+imgygpvpat+kalkragl i did++elneafaaqalp
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02325 259 RAQDLGIQPMAVIRSMAVAGVDPAIMGYGPVPATQKALKRAGLGIADIDFFELNEAFAAQALP 321
                                                     *************************************************************** PP

                                       TIGR02445 316 vlkdlglldkldekvnlnggaialghplgcsgaristtllnlmerkdakfglatmciglgqgi 378
                                                     vlkdl++ldk++ekvnl+ggaialghp+gcsgaris+tlln+m++++++fg++tmciglgqgi
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02325 322 VLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTLLNVMKQNGGTFGVSTMCIGLGQGI 384
                                                     *************************************************************** PP

                                       TIGR02445 379 atvferv 385
                                                     atvferv
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_02325 385 ATVFERV 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.96
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources