GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Lacinutrix algicola AKS293

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 (characterized)
to candidate WP_055437058.1 ASC41_RS12920 acetyl-CoA C-acyltransferase

Query= SwissProt::P41338
         (398 letters)



>NCBI__GCF_001418085.1:WP_055437058.1
          Length = 392

 Score =  417 bits (1071), Expect = e-121
 Identities = 221/400 (55%), Positives = 292/400 (73%), Gaps = 12/400 (3%)

Query: 1   MSQNVYIVSTARTPIGSFQGSLSSKTAVELGAVALKGALAKV---PELDASKDFDEIIFG 57
           M++ V IVS ARTPIGSF G+LS+  A +LGA+A+KGAL K+   PEL       E++ G
Sbjct: 1   MNKEVVIVSAARTPIGSFLGALSTIPAPKLGAIAIKGALEKINLNPEL-----VQEVLMG 55

Query: 58  NVLSANLGQAPARQVALAAGLSNHIVASTVNKVCASAMKAIILGAQSIKCGNADVVVAGG 117
           NV+ A  GQAPARQ A+ AG+ N +  +T+NKVCAS MK ++  AQSI  G+A++VVAGG
Sbjct: 56  NVVQAGTGQAPARQAAIFAGIPNTVPCTTINKVCASGMKTVMQAAQSIALGDAEIVVAGG 115

Query: 118 CESMTNAPYYMPAARAGAKFGQTVLVDGVERDGLNDAYDGLAMGVHAEKCARDWDITREQ 177
            E+M+  P+Y  A R+  KFG   +VDG+++DGL D YD  AMGV A+ CA  ++ +RE 
Sbjct: 116 MENMSLIPHYFHA-RSATKFGPATMVDGMQKDGLVDVYDQQAMGVSADACATKYEFSRED 174

Query: 178 QDNFAIESYQKSQKSQKEGKFDNEIVPVTIKGFRGKPDTQVTKDEEPARLHVEKLRSART 237
           QD +AI+SY++S  + + GKF+NEIVPV +   RG  D  VT+DEE   + ++K+ + R 
Sbjct: 175 QDAYAIQSYKRSAAAWEAGKFNNEIVPVAVPQRRGD-DVIVTEDEEYKNVRMDKIPTLRA 233

Query: 238 VFQKENGTVTAANASPINDGAAAVILVSEKVLKEKNLKPLAIIKGWGEAAHQPADFTWAP 297
            F KE GTVTAANAS INDGA A++L+S +   E  LK LA IKG+ +AAH+P  FT AP
Sbjct: 234 AFTKE-GTVTAANASTINDGAGAMVLMSREKANELGLKVLATIKGYADAAHEPEWFTTAP 292

Query: 298 SLAVPKALKHAGIEDINSVDYFEFNEAFSVVGLVNTKILKLDPSKVNVYGGAVALGHPLG 357
           S+A+PKAL  AG+ DI  VD+FEFNEAFS+VGL N KIL L+ S VNV GGAV+LGHPLG
Sbjct: 293 SIALPKALNKAGL-DIKDVDFFEFNEAFSIVGLANMKILGLNDSNVNVNGGAVSLGHPLG 351

Query: 358 CSGARVVVTLLSILQQEGGKIGVAAICNGGGGASSIVIEK 397
           CSG R+++TLL++L+Q   KIG AAICNGGGGAS++V+E+
Sbjct: 352 CSGVRILITLLNVLEQNDAKIGAAAICNGGGGASALVLER 391


Lambda     K      H
   0.315    0.131    0.372 

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: 420
Number of extensions: 14
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: 398
Length of database: 392
Length adjustment: 31
Effective length of query: 367
Effective length of database: 361
Effective search space:   132487
Effective search space used:   132487
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: 42 (22.0 bits)
S2: 50 (23.9 bits)

Align candidate WP_055437058.1 ASC41_RS12920 (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.1430483.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-138  447.6   6.3     2e-138  447.5   6.3    1.0  1  NCBI__GCF_001418085.1:WP_055437058.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001418085.1:WP_055437058.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  447.5   6.3    2e-138    2e-138       1     385 []       7     390 ..       7     390 .. 0.98

  Alignments for each domain:
  == domain 1  score: 447.5 bits;  conditional E-value: 2e-138
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 
                                           iv+a+Rtpig++ g+l++++a +L+a +ik++le+ +l+pe + ev +Gnv+qag+++++aR+aa+ ag+p++
  NCBI__GCF_001418085.1:WP_055437058.1   7 IVSAARTPIGSFLGALSTIPAPKLGAIAIKGALEKINLNPELVQEVLMGNVVQAGTGQAPARQAAIFAGIPNT 79 
                                           8************************************************************************ PP

                             TIGR01930  74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144
                                           vp +t+n+vCaSg+++v++aaq+i+ G+a++vvaGG+E+mS +p++ +a+   +  k+g a++ d ++kd+  
  NCBI__GCF_001418085.1:WP_055437058.1  80 VPCTTINKVCASGMKTVMQAAQSIALGDAEIVVAGGMENMSLIPHYFHAR---SATKFGPATMVDGMQKDGlv 149
                                           **********************************************9995...7888899************* PP

                             TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214
                                            v+++ +mg++A+ +a+ky++sRe+qD+ya++S++++a+A+e+gkf++eivpv v+++  ++v+ ++++ ++n
  NCBI__GCF_001418085.1:WP_055437058.1 150 dVYDQQAMGVSADACATKYEFSREDQDAYAIQSYKRSAAAWEAGKFNNEIVPVAVPQRrgDDVIVTEDEEYKN 222
                                           *99*****************************************************99**777777777888* PP

                             TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287
                                           + ++k+ +L++af++ +g tvtA+N+s +nDGA+a++lms+e+a+elgl++la+i ++a a+++pe ++++p 
  NCBI__GCF_001418085.1:WP_055437058.1 223 VRMDKIPTLRAAFTK-EG-TVTAANASTINDGAGAMVLMSREKANELGLKVLATIKGYADAAHEPEWFTTAPS 293
                                           *************96.8*.6***************************************************** PP

                             TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360
                                            A +kaL+kagl+i+d+d++E+nEAF+ + la++k lg l++++vNvnGGA++lGHPlG+sG ri++tll+ L
  NCBI__GCF_001418085.1:WP_055437058.1 294 IALPKALNKAGLDIKDVDFFEFNEAFSIVGLANMKILG-LNDSNVNVNGGAVSLGHPLGCSGVRILITLLNVL 365
                                           **************************************.88******************************** PP

                             TIGR01930 361 kergkkyGlatlCvggGqGaAvile 385
                                           +++++k+G a++C+ggG ++A++le
  NCBI__GCF_001418085.1:WP_055437058.1 366 EQNDAKIGAAAICNGGGGASALVLE 390
                                           ***********************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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 22.18
//
[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:

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