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.9093.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: 00:00:00.01
# Mc/sec: 8.30
//
[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