Alignments for a candidate for fadA in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Shewanella oneidensis MR-1

Align Acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate 199217 SO0020 fatty oxidation complex, beta subunit (NCBI ptt file)

Query= reanno::ANA3:7022768
         (387 letters)



>FitnessBrowser__MR1:199217
          Length = 387

 Score =  743 bits (1919), Expect = 0.0
 Identities = 377/387 (97%), Positives = 383/387 (98%)

Query: 1   MKQAVIVDCIRTPMGRSKAGVFRNVRAETLSAELMKGLLLRNPQLDPNTIEDVIWGCVQQ 60
           MKQAVIVDCIRTPMGRSKAGVFRNVRAETLSAELMKGLLLRNPQLDPNTIEDVIWGCVQQ
Sbjct: 1   MKQAVIVDCIRTPMGRSKAGVFRNVRAETLSAELMKGLLLRNPQLDPNTIEDVIWGCVQQ 60

Query: 61  TLEQGFNIARNASLLAGIPKTAGAVTVNRLCGSSMEAIHQAARAIMTGMGDTFIIGGVEH 120
           TLEQGFNIARNASLLAGIPKTAGAVTVNRLCGSSMEAIHQAARAIMTGMGDTFIIGGVEH
Sbjct: 61  TLEQGFNIARNASLLAGIPKTAGAVTVNRLCGSSMEAIHQAARAIMTGMGDTFIIGGVEH 120

Query: 121 MGHVPMNHGVDFHPGLANNVAKASGMMGLTAEMLGKLHGITREQQDAFAVRSHQRAHAAT 180
           MGHVPMNHGVDFHPGLANNVAKASGMMGLTAEMLGKLHGITREQQDAFAVRSHQRA+AAT
Sbjct: 121 MGHVPMNHGVDFHPGLANNVAKASGMMGLTAEMLGKLHGITREQQDAFAVRSHQRAYAAT 180

Query: 181 VEGRFAKEIYGIEGHDANGALIKVLHDEVIRPETSMESLAALRPVFDPANGTVTAGTSSA 240
           +EGRFAKEIYGIEGHDA GALIKVL DEVIRPET+MESLA LRPVFDP NGTVTAGTSSA
Sbjct: 181 IEGRFAKEIYGIEGHDATGALIKVLQDEVIRPETTMESLAVLRPVFDPVNGTVTAGTSSA 240

Query: 241 LSDGASAMLVMEESKARALGLPIRARIRSMAVAGCDAAIMGYGPVPATQKALARAGITVN 300
           LSDGASAML+MEESKARALGLPIRARIRSMAVAGCDAAIMGYGPVPATQKALARAGITVN
Sbjct: 241 LSDGASAMLIMEESKARALGLPIRARIRSMAVAGCDAAIMGYGPVPATQKALARAGITVN 300

Query: 301 DLDVIELNEAFAAQSLPCVKDLGLLDVVEDKINLNGGAIALGHPLGCSGARISTTLINLM 360
           DLDVIELNEAFAAQSLPCVKDLGLLDVV++KINLNGGAIALGHPLGCSGARISTTLINLM
Sbjct: 301 DLDVIELNEAFAAQSLPCVKDLGLLDVVDEKINLNGGAIALGHPLGCSGARISTTLINLM 360

Query: 361 EHKDATLGLATMCIGLGQGIATVFERV 387
           EHKDATLGLATMCIGLGQGIATVFERV
Sbjct: 361 EHKDATLGLATMCIGLGQGIATVFERV 387


Lambda     K      H
   0.320    0.134    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: 689
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: 387
Length of database: 387
Length adjustment: 30
Effective length of query: 357
Effective length of database: 357
Effective search space:   127449
Effective search space used:   127449
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate 199217 SO0020 (fatty oxidation complex, beta subunit (NCBI ptt file))
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.15485.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   6.6e-221  719.0   9.9   7.4e-221  718.8   9.9    1.0  1  lcl|FitnessBrowser__MR1:199217  SO0020 fatty oxidation complex, 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199217  SO0020 fatty oxidation complex, beta subunit (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  718.8   9.9  7.4e-221  7.4e-221       2     385 .]       4     387 .]       3     387 .] 1.00

  Alignments for each domain:
  == domain 1  score: 718.8 bits;  conditional E-value: 7.4e-221
                       TIGR02445   2 vvivdalrtpmgrskggafrntraedlsahllkkllarnpkveaaevediywgcvqqtleqgfniarnaallaevphev 80 
                                      vivd++rtpmgrsk g+frn+rae lsa l+k+ll rnp++++  +ed++wgcvqqtleqgfniarna+lla++p++ 
  lcl|FitnessBrowser__MR1:199217   4 AVIVDCIRTPMGRSKAGVFRNVRAETLSAELMKGLLLRNPQLDPNTIEDVIWGCVQQTLEQGFNIARNASLLAGIPKTA 82 
                                     79***************************************************************************** PP

                       TIGR02445  81 aavtvnrlcgssmqalhdaaraimtgdaevcliggvehmghvsmshgvdfhpglskhvakaagmmgltaemlgklhgis 159
                                     +avtvnrlcgssm+a+h+aaraimtg ++ ++iggvehmghv+m+hgvdfhpgl+++vaka+gmmgltaemlgklhgi+
  lcl|FitnessBrowser__MR1:199217  83 GAVTVNRLCGSSMEAIHQAARAIMTGMGDTFIIGGVEHMGHVPMNHGVDFHPGLANNVAKASGMMGLTAEMLGKLHGIT 161
                                     ******************************************************************************* PP

                       TIGR02445 160 reqqdafaarsharahaatlegkfkneiiptegydadgvlkvldydevirpettvealaalrpafdpkngtvtagtssa 238
                                     reqqdafa+rsh+ra+aat+eg+f +ei  +eg+da g l ++  devirpett+e+la lrp+fdp+ngtvtagtssa
  lcl|FitnessBrowser__MR1:199217 162 REQQDAFAVRSHQRAYAATIEGRFAKEIYGIEGHDATGALIKVLQDEVIRPETTMESLAVLRPVFDPVNGTVTAGTSSA 240
                                     ******************************************************************************* PP

                       TIGR02445 239 lsdgasamlvmseeraqelgvkprarirsmavagvdpsimgygpvpatkkalkraglsisdidvlelneafaaqalpvl 317
                                     lsdgasaml+m e++a+ lg+ +rarirsmavag+d +imgygpvpat+kal rag++++d+dv+elneafaaq+lp++
  lcl|FitnessBrowser__MR1:199217 241 LSDGASAMLIMEESKARALGLPIRARIRSMAVAGCDAAIMGYGPVPATQKALARAGITVNDLDVIELNEAFAAQSLPCV 319
                                     ******************************************************************************* PP

                       TIGR02445 318 kdlglldkldekvnlnggaialghplgcsgaristtllnlmerkdakfglatmciglgqgiatvferv 385
                                     kdlglld++dek+nlnggaialghplgcsgaristtl+nlme+kda+ glatmciglgqgiatvferv
  lcl|FitnessBrowser__MR1:199217 320 KDLGLLDVVDEKINLNGGAIALGHPLGCSGARISTTLINLMEHKDATLGLATMCIGLGQGIATVFERV 387
                                     *******************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (387 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: 00:00:00.02
# Mc/sec: 7.04
//
[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