GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Shewanella amazonensis SB2B

Align 3-ketoacyl-CoA thiolase FadI; ACSs; Acetyl-CoA acyltransferase; Acyl-CoA ligase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 (characterized)
to candidate 6938035 Sama_2168 3-ketoacyl-CoA thiolase (RefSeq)

Query= SwissProt::P76503
         (436 letters)



>FitnessBrowser__SB2B:6938035
          Length = 436

 Score =  625 bits (1613), Expect = 0.0
 Identities = 305/426 (71%), Positives = 366/426 (85%)

Query: 11  QGDRIAIVSGLRTPFARQATAFHGIPAVDLGKMVVGELLARSEIPAEVIEQLVFGQVVQM 70
           +G+RIAIVSGLRTPFA+QATAFHG+ A+D+GKMVV ELL+RSE+  +++EQLV+GQVVQM
Sbjct: 11  RGERIAIVSGLRTPFAKQATAFHGVSALDMGKMVVNELLSRSELDPKLVEQLVYGQVVQM 70

Query: 71  PEAPNIAREIVLGTGMNVHTDAYSVSRACATSFQAVANVAESLMAGTIRAGIAGGADSSS 130
           P APNIAREIVLGTGMNV TDAYSV+RACATSFQ+  N+AES+M G I  GIAGGADSSS
Sbjct: 71  PAAPNIAREIVLGTGMNVATDAYSVTRACATSFQSTVNIAESIMTGNIEIGIAGGADSSS 130

Query: 131 VLPIGVSKKLARVLVDVNKARTMSQRLKLFSRLRLRDLMPVPPAVAEYSTGLRMGDTAEQ 190
           VLPIGVSKKLA  LVD+ KART  Q+L +F RL ++DL+PVPPAVAEYSTGL MG TAEQ
Sbjct: 131 VLPIGVSKKLAHALVDLTKARTFGQKLAIFRRLGIKDLLPVPPAVAEYSTGLSMGQTAEQ 190

Query: 191 MAKTYGITREQQDALAHRSHQRAAQAWSDGKLKEEVMTAFIPPYKQPLVEDNNIRGNSSL 250
           MAKT+GI+R  QDA+AHRSH  AAQ W+ G +K EVM A +PPY Q + +DNNIR +S L
Sbjct: 191 MAKTHGISRADQDAMAHRSHTLAAQTWASGVMKNEVMVAHVPPYNQFIEKDNNIRESSDL 250

Query: 251 ADYAKLRPAFDRKHGTVTAANSTPLTDGAAAVILMTESRAKELGLVPLGYLRSYAFTAID 310
           A YAKLRP FDRKHG+VTAANSTPLTDGA+A++LM+E RAK LG  P+GY++SYAF AID
Sbjct: 251 ASYAKLRPVFDRKHGSVTAANSTPLTDGASALLLMSEGRAKALGYTPIGYIKSYAFAAID 310

Query: 311 VWQDMLLGPAWSTPLALERAGLTMSDLTLIDMHEAFAAQTLANIQLLGSERFAREALGRA 370
           VW+DML+GP+++TP+AL+RAG+ + DLTLI+MHEAFAAQ LAN+++  S++FA E LG+ 
Sbjct: 311 VWEDMLMGPSYATPMALKRAGMQLEDLTLIEMHEAFAAQALANMKMFASKKFAEEKLGQN 370

Query: 371 HATGEVDDSKFNVLGGSIAYGHPFAATGARMITQTLHELRRRGGGFGLVTACAAGGLGAA 430
            A GE+D SKFNVLGGS+AYGHPFAATGAR+ITQ  +EL+RRGGG GL TACAAGGLGAA
Sbjct: 371 RAIGEIDMSKFNVLGGSLAYGHPFAATGARLITQMCNELKRRGGGVGLTTACAAGGLGAA 430

Query: 431 MVLEAE 436
           M+LE E
Sbjct: 431 MILEVE 436


Lambda     K      H
   0.319    0.133    0.377 

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: 573
Number of extensions: 9
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: 436
Length of database: 436
Length adjustment: 32
Effective length of query: 404
Effective length of database: 404
Effective search space:   163216
Effective search space used:   163216
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: 51 (24.3 bits)

Align candidate 6938035 Sama_2168 (3-ketoacyl-CoA thiolase (RefSeq))
to HMM TIGR02446 (fadI: acetyl-CoA C-acyltransferase FadI (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/TIGR02446.hmm
# target sequence database:        /tmp/gapView.16493.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02446  [M=430]
Accession:   TIGR02446
Description: FadI: acetyl-CoA C-acyltransferase FadI
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   7.7e-269  877.7   8.1   8.7e-269  877.5   8.1    1.0  1  lcl|FitnessBrowser__SB2B:6938035  Sama_2168 3-ketoacyl-CoA thiolas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6938035  Sama_2168 3-ketoacyl-CoA thiolase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  877.5   8.1  8.7e-269  8.7e-269       1     430 []       7     436 .]       7     436 .] 1.00

  Alignments for each domain:
  == domain 1  score: 877.5 bits;  conditional E-value: 8.7e-269
                         TIGR02446   1 vktrqgeriaivaglrtpfarqatafhgipavdlgkmvvsellarseidaklieqlvfgqvvqmpeapniareivlg 77 
                                       v++++geriaiv+glrtpfa+qatafhg++a+d+gkmvv+ell+rse+d+kl+eqlv+gqvvqmp+apniareivlg
  lcl|FitnessBrowser__SB2B:6938035   7 VTNARGERIAIVSGLRTPFAKQATAFHGVSALDMGKMVVNELLSRSELDPKLVEQLVYGQVVQMPAAPNIAREIVLG 83 
                                       689************************************************************************** PP

                         TIGR02446  78 tgmnvhtdaysvtracatsfqsavnvaesimagaieigiaggadsssvlpigvskklaralvdlnkartlgqklkvl 154
                                       tgmnv tdaysvtracatsfqs+vn+aesim+g+ieigiaggadsssvlpigvskkla+alvdl+kart+gqkl ++
  lcl|FitnessBrowser__SB2B:6938035  84 TGMNVATDAYSVTRACATSFQSTVNIAESIMTGNIEIGIAGGADSSSVLPIGVSKKLAHALVDLTKARTFGQKLAIF 160
                                       ***************************************************************************** PP

                         TIGR02446 155 srlglkdllpvppavaeystglsmgqtaeqmaktygitraeqdalahrshtlaaqawadgklkeevmtafvepykkf 231
                                       +rlg+kdllpvppavaeystglsmgqtaeqmakt+gi+ra+qda+ahrshtlaaq+wa+g +k+evm+a+v+py++f
  lcl|FitnessBrowser__SB2B:6938035 161 RRLGIKDLLPVPPAVAEYSTGLSMGQTAEQMAKTHGISRADQDAMAHRSHTLAAQTWASGVMKNEVMVAHVPPYNQF 237
                                       ***************************************************************************** PP

                         TIGR02446 232 iaednnirenssladyaklrpafdrkygsvtaanstpltdgaaavilmsegrakelgleilgyirsyaftaidveqd 308
                                       i++dnnire s+la+yaklrp fdrk+gsvtaanstpltdga+a++lmsegrak+lg++++gyi+syaf+aidv++d
  lcl|FitnessBrowser__SB2B:6938035 238 IEKDNNIRESSDLASYAKLRPVFDRKHGSVTAANSTPLTDGASALLLMSEGRAKALGYTPIGYIKSYAFAAIDVWED 314
                                       ***************************************************************************** PP

                         TIGR02446 309 mllgpsyatplalkraglelsdltlidmheafaaqtlanvkllasekfaeeklgrakaigeidmskfnvlggsiayg 385
                                       ml+gpsyatp+alkrag++l+dltli+mheafaaq+lan+k++as+kfaeeklg+++aigeidmskfnvlggs+ayg
  lcl|FitnessBrowser__SB2B:6938035 315 MLMGPSYATPMALKRAGMQLEDLTLIEMHEAFAAQALANMKMFASKKFAEEKLGQNRAIGEIDMSKFNVLGGSLAYG 391
                                       ***************************************************************************** PP

                         TIGR02446 386 hpfaatgarlitqtlrelkrrggglglatacaagglgaamileve 430
                                       hpfaatgarlitq+++elkrrggg+gl+tacaagglgaamileve
  lcl|FitnessBrowser__SB2B:6938035 392 HPFAATGARLITQMCNELKRRGGGVGLTTACAAGGLGAAMILEVE 436
                                       *******************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (430 nodes)
Target sequences:                          1  (436 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: 8.12
//
[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