Alignments for a candidate for fadA in Mucilaginibacter mallensis MP1X4

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Mucilaginibacter mallensis MP1X4

Align Acetyl-CoA acetyltransferase, mitochondrial; Acetoacetyl-CoA thiolase; T2; EC 2.3.1.9 (characterized)
to candidate WP_091371536.1 BLU33_RS09250 acetyl-CoA C-acyltransferase

Query= SwissProt::P24752
         (427 letters)



>NCBI__GCF_900105165.1:WP_091371536.1
          Length = 392

 Score =  409 bits (1052), Expect = e-119
 Identities = 218/393 (55%), Positives = 284/393 (72%), Gaps = 6/393 (1%)

Query: 39  LKEVVIVSATRTPIGSFLGSLSLLPATKLGSIAIQGAIEKAGIPKEEVKEAYMGNVLQGG 98
           +KEVVIV+ATRTPIGSF GSLS L AT+LGSI I+ AIEK+G+  E ++E YMGNV+   
Sbjct: 1   MKEVVIVAATRTPIGSFGGSLSALSATQLGSIVIKSAIEKSGLKPEHIQEVYMGNVMSAN 60

Query: 99  EGQAPTRQAVLGAGLPISTPCTTINKVCASGMKAIMMASQSLMCGHQDVMVAGGMESMSN 158
            GQAP  QA + AGLP   P TT+NKVCASGMKAIM+A+QS+  G  D+++AGGMESMSN
Sbjct: 61  VGQAPATQAAIFAGLPY-LPATTVNKVCASGMKAIMLAAQSIALGENDIVLAGGMESMSN 119

Query: 159 VPYVMNRGSTPY--GGVKLEDLIVKDGLTDVYNKIHMGSCAENTAKKLNIARNEQDAYAI 216
           VPY +++    Y  G  ++ D +VKDGL DVYN  HMGS AE  A+K +I+R +QDA+AI
Sbjct: 120 VPYYLDKARNGYRLGNGQIIDGLVKDGLWDVYNDYHMGSAAELCAEKCHISREDQDAFAI 179

Query: 217 NSYTRSKAAWEAGKFGNEVIPVTVTVKGQPDVVVKEDEEYKRVDFSKVPKLKTVFQKENG 276
            SY RS+     GKF +E+ PV +  K     +  +DEE + V F K+P LK VF+K NG
Sbjct: 180 ESYHRSQKTQSVGKFKDEITPVELKDKKGDITLFTDDEEPQAVKFDKIPSLKPVFKK-NG 238

Query: 277 TVTAANASTLNDGAAALVLMTADAAKRLNVTPLARIVAFADAAVEPIDFPIAPVYAASMV 336
           TVTAANASTLNDGAAA++LM+ D A  L + PLA+++A+ADA   P  F  AP  A  + 
Sbjct: 239 TVTAANASTLNDGAAAVILMSKDKADELGIKPLAKVIAYADAQQAPEWFTTAPSKAIPLA 298

Query: 337 LKDVGLKKEDIAMWEVNEAFSLVVLANIKMLEIDPQKVNINGGAVSLGHPIGMSGARIVG 396
           L   GL  + +  +E+NEAFS+V +AN + L+++P KVN+NGGAVSLGHP+G SGARI+ 
Sbjct: 299 LHRAGLAIDQVDYFEINEAFSVVAIANNQNLKLNPAKVNVNGGAVSLGHPLGASGARIIV 358

Query: 397 HLTHALKQ--GEYGLASICNGGGGASAMLIQKL 427
            L + L+Q  G+YG+A ICNGGGGASA++I+ L
Sbjct: 359 TLLNVLQQNKGKYGVAGICNGGGGASAIVIENL 391


Lambda     K      H
   0.316    0.132    0.368 

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: 492
Number of extensions: 19
Number of successful extensions: 5
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: 427
Length of database: 392
Length adjustment: 31
Effective length of query: 396
Effective length of database: 361
Effective search space:   142956
Effective search space used:   142956
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_091371536.1 BLU33_RS09250 (acetyl-CoA C-acyltransferase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (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/TIGR01930.hmm
# target sequence database:        /tmp/gapView.3640145.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01930  [M=385]
Accession:   TIGR01930
Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.4e-141  457.1   2.7   2.7e-141  456.9   2.7    1.0  1  NCBI__GCF_900105165.1:WP_091371536.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900105165.1:WP_091371536.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.9   2.7  2.7e-141  2.7e-141       1     385 []       6     389 ..       6     389 .. 0.99

  Alignments for each domain:
  == domain 1  score: 456.9 bits;  conditional E-value: 2.7e-141
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 
                                           iv+a+Rtpig++ggsl+ lsa +L++ vik+++e++gl+pe+i ev++Gnv++a+ ++++a +aa+ aglp+ 
  NCBI__GCF_900105165.1:WP_091371536.1   6 IVAATRTPIGSFGGSLSALSATQLGSIVIKSAIEKSGLKPEHIQEVYMGNVMSANVGQAPATQAAIFAGLPY- 77 
                                           8**********************************************************************9. PP

                             TIGR01930  74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144
                                           +pa+tvn+vCaSg++A++laaq+i+ Ge+d+v+aGG+EsmS+vp++l+++  r++++lg+ +  d l+kd+  
  NCBI__GCF_900105165.1:WP_091371536.1  78 LPATTVNKVCASGMKAIMLAAQSIALGENDIVLAGGMESMSNVPYYLDKA--RNGYRLGNGQIIDGLVKDGlw 148
                                           ************************************************98..89******************* PP

                             TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214
                                            v+++++mg  Ae +a+k +isRe+qD++a++S+++++k ++ gkfkdei+pve+k+k  + ++ +D++  + 
  NCBI__GCF_900105165.1:WP_091371536.1 149 dVYNDYHMGSAAELCAEKCHISREDQDAFAIESYHRSQKTQSVGKFKDEITPVELKDKkgDITLFTDDEEPQA 221
                                           *99******************************************************999899999999999* PP

                             TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287
                                           ++ +k+ +Lkp+fk+ +g tvtA+N+s lnDGAaa++lms+++a+elg++pla+++++a a   pe ++++p 
  NCBI__GCF_900105165.1:WP_091371536.1 222 VKFDKIPSLKPVFKK-NG-TVTAANASTLNDGAAAVILMSKDKADELGIKPLAKVIAYADAQQAPEWFTTAPS 292
                                           *************95.9*.6***************************************************** PP

                             TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360
                                           +Ai+ aL++agl i+++d++EinEAF+++++a++++l+ l+++kvNvnGGA++lGHPlGasGari++tll+ L
  NCBI__GCF_900105165.1:WP_091371536.1 293 KAIPLALHRAGLAIDQVDYFEINEAFSVVAIANNQNLK-LNPAKVNVNGGAVSLGHPLGASGARIIVTLLNVL 364
                                           **************************************.88******************************** PP

                             TIGR01930 361 kergkkyGlatlCvggGqGaAvile 385
                                           +++++kyG+a +C+ggG ++A+++e
  NCBI__GCF_900105165.1:WP_091371536.1 365 QQNKGKYGVAGICNGGGGASAIVIE 389
                                           ***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (392 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 26.71
//
[ok]

This GapMind analysis is from Sep 24 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