GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Brevibacterium jeotgali SJ5-8

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_101589711.1 BJEO58_RS11990 acetyl-CoA C-acetyltransferase

Query= BRENDA::P45359
         (392 letters)



>NCBI__GCF_900169175.1:WP_101589711.1
          Length = 398

 Score =  358 bits (918), Expect = e-103
 Identities = 191/394 (48%), Positives = 261/394 (66%), Gaps = 6/394 (1%)

Query: 1   MKEVVIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIKPEDVNEVILGNVLQAG 60
           M E VI +  RT  G    +L  + AVDLGA AI  A+ +AG+ P+ V  VI+G VLQAG
Sbjct: 1   MTEAVIVAGSRTPFGKMSGALGSLSAVDLGAEAISGALSRAGVSPDQVQHVIMGQVLQAG 60

Query: 61  LGQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMSR 120
            GQ PARQA+ KAG+P+ + A+TINK+C SG+  ++ AA +++AG+ DV++AGG E+M+ 
Sbjct: 61  CGQGPARQAAVKAGIPMSVNAITINKLCLSGINAITQAAMLVRAGEYDVVVAGGQESMTN 120

Query: 121 APYLANNARWGYRMGNAKFVDEMITDGLWDAFNDYHMGITAENIAE----RWNISREEQD 176
           AP++   +R GY+ G  +  D M  DGLWDAF D  MG   E   +    + + +RE+QD
Sbjct: 121 APHMLEKSRAGYKFGTVQVRDHMDYDGLWDAFTDEAMGGLTEAANDDDDPKRSFTREQQD 180

Query: 177 EFALASQKKAEEAIKSGQFKDEIVPVVIKGRKGETVVDTDEHPRFGSTIEGLAKLKPAFK 236
           EFA  S ++A  A  SG+  +EI PV +K R+GE  V+ DE  R  ST E + KL+PAF+
Sbjct: 181 EFAATSHQRAAAAQDSGRLAEEITPVTLKSRRGEVTVELDEGVRADSTGESMGKLRPAFR 240

Query: 237 KDGTVTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYG-SAGVDPAIMGYGPFYA 295
           KDGT+TAGNAS ++D A  +V+MS  KA+ELG+  LA+I ++  +AG D ++  + P  +
Sbjct: 241 KDGTITAGNASQISDGAVAVVVMSKAKAEELGLPILAEIGAHAWTAGPDSSLQ-HQPSQS 299

Query: 296 TKAAIEKAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPIGASGA 355
            +AA E+AG   D  DL E NEAFAA  LA   DL  D  KVNVNGGAIALGHPIGASGA
Sbjct: 300 IRAAAERAGVAADSFDLYEINEAFAAVGLASTADLGVDAEKVNVNGGAIALGHPIGASGA 359

Query: 356 RILVTLVHAMQKRDAKKGLATLCIGGGQGTAILL 389
           RI + L   +++R    G+A LC GGGQG A+++
Sbjct: 360 RITLDLALELKRRGGGTGVAALCGGGGQGDALII 393


Lambda     K      H
   0.315    0.132    0.375 

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: 445
Number of extensions: 15
Number of successful extensions: 2
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: 392
Length of database: 398
Length adjustment: 31
Effective length of query: 361
Effective length of database: 367
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: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_101589711.1 BJEO58_RS11990 (acetyl-CoA C-acetyltransferase)
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.3409209.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-134  434.0   9.9   2.7e-134  433.9   9.9    1.0  1  NCBI__GCF_900169175.1:WP_101589711.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900169175.1:WP_101589711.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  433.9   9.9  2.7e-134  2.7e-134       1     384 [.       6     393 ..       6     394 .. 0.97

  Alignments for each domain:
  == domain 1  score: 433.9 bits;  conditional E-value: 2.7e-134
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 
                                           iv++ Rtp+gk+ g+l +lsa+dL+a++i+++l rag++p+++ +vi+G+vlqag+++ +aR+aa++ag+p s
  NCBI__GCF_900169175.1:WP_101589711.1   6 IVAGSRTPFGKMSGALGSLSAVDLGAEAISGALSRAGVSPDQVQHVIMGQVLQAGCGQGPARQAAVKAGIPMS 78 
                                           8************************************************************************ PP

                             TIGR01930  74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144
                                           v+a+t+n++C Sg++A+++aa+ ++aGe+dvvvaGG Esm+++p++l++s  r+++k+g+ +++d++ +d+  
  NCBI__GCF_900169175.1:WP_101589711.1  79 VNAITINKLCLSGINAITQAAMLVRAGEYDVVVAGGQESMTNAPHMLEKS--RAGYKFGTVQVRDHMDYDGlw 149
                                           ************************************************98..89****************9** PP

                             TIGR01930 145 .vktklsmgetAenlak....kygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDeg 210
                                            + t+ +mg  +e   +    k +++Re+qDe+a+ Shq+aa+A+++g++++ei+pv++k +  +++v+ Deg
  NCBI__GCF_900169175.1:WP_101589711.1 150 dAFTDEAMGGLTEAANDdddpKRSFTREQQDEFAATSHQRAAAAQDSGRLAEEITPVTLKSRrgEVTVELDEG 222
                                           *88999999888766652233679************************************99*********** PP

                             TIGR01930 211 irpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemg 283
                                           +r+++t e+++kL+paf++ +g t+tAgN+sq++DGA+a+++ms+++a+elgl +la+i ++a+++ + + ++
  NCBI__GCF_900169175.1:WP_101589711.1 223 VRADSTGESMGKLRPAFRK-DG-TITAGNASQISDGAVAVVVMSKAKAEELGLPILAEIGAHAWTAGPDSSLQ 293
                                           *****************95.9*.6************************************************* PP

                             TIGR01930 284 lgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltl 356
                                            +p ++i++a ++ag+ ++++dl+EinEAFAa+ la++ +lg  d ekvNvnGGAiAlGHP+GasGari+l l
  NCBI__GCF_900169175.1:WP_101589711.1 294 HQPSQSIRAAAERAGVAADSFDLYEINEAFAAVGLASTADLG-VDAEKVNVNGGAIALGHPIGASGARITLDL 365
                                           ******************************************.88**************************** PP

                             TIGR01930 357 lkeLkergkkyGlatlCvggGqGaAvil 384
                                           + eLk+rg+  G+a+lC ggGqG A+i+
  NCBI__GCF_900169175.1:WP_101589711.1 366 ALELKRRGGGTGVAALCGGGGQGDALII 393
                                           **************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (398 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: 25.94
//
[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