GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Pseudomonas stutzeri RCH2

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate GFF1043 Psest_1076 acetyl-CoA acetyltransferases

Query= metacyc::MONOMER-20831
         (393 letters)



>FitnessBrowser__psRCH2:GFF1043
          Length = 393

 Score =  656 bits (1693), Expect = 0.0
 Identities = 327/392 (83%), Positives = 363/392 (92%)

Query: 1   MQDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAG 60
           MQDVVIVAATRTA+GSFQGSLA++PA ELGA VIR LLE+TG++PAQVDEVILG VLTAG
Sbjct: 1   MQDVVIVAATRTAIGSFQGSLANVPAVELGATVIRALLEKTGIEPAQVDEVILGHVLTAG 60

Query: 61  SGQNPARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120
           +GQN ARQASI AGLPHAVPS+TLNKVCGSGLKA+HL  QAIRCGDA+VIIAGGMENMSL
Sbjct: 61  AGQNTARQASIKAGLPHAVPSMTLNKVCGSGLKAVHLAVQAIRCGDADVIIAGGMENMSL 120

Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180
           APYVLP ARTGLRMGHA+++D+MITDGLWDAFNDYHMGITAENL +KYGI R  QDAFAA
Sbjct: 121 APYVLPGARTGLRMGHAQIVDTMITDGLWDAFNDYHMGITAENLAEKYGIDRAQQDAFAA 180

Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDG 240
            SQQ+A AAIE+GRF  EITP++IPQRKGDP+AFA DEQPRAGTTAESL  L+ AFKKDG
Sbjct: 181 QSQQRAAAAIESGRFDAEITPVMIPQRKGDPLAFARDEQPRAGTTAESLGGLRAAFKKDG 240

Query: 241 SVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRC 300
            VTAGNAS+LNDGAAAV+LMSA KA+ALGLPVLA+IA YANAGVDPAIMGIGPV+ATRRC
Sbjct: 241 CVTAGNASTLNDGAAAVVLMSASKAEALGLPVLAKIAGYANAGVDPAIMGIGPVTATRRC 300

Query: 301 LDKAGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVLV 360
           LDKAGW+L +LDLIEANEAFA Q+L+VGKEL WDA+KVNVNGGAIA+GHPIGASGCR+LV
Sbjct: 301 LDKAGWTLAELDLIEANEAFAVQALSVGKELGWDADKVNVNGGAIALGHPIGASGCRILV 360

Query: 361 TLLHEMIKRDAKKGLATLCIGGGQGVALALER 392
           TLLHEM +RD +KGLATLCIGGGQGVALA+ER
Sbjct: 361 TLLHEMQRRDVRKGLATLCIGGGQGVALAVER 392


Lambda     K      H
   0.317    0.133    0.378 

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: 537
Number of extensions: 13
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: 393
Length of database: 393
Length adjustment: 31
Effective length of query: 362
Effective length of database: 362
Effective search space:   131044
Effective search space used:   131044
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate GFF1043 Psest_1076 (acetyl-CoA acetyltransferases)
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.2368049.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   8.6e-153  494.7   8.8   9.7e-153  494.6   8.8    1.0  1  FitnessBrowser__psRCH2:GFF1043  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__psRCH2:GFF1043  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  494.6   8.8  9.7e-153  9.7e-153       1     385 []       6     391 ..       6     391 .. 0.99

  Alignments for each domain:
  == domain 1  score: 494.6 bits;  conditional E-value: 9.7e-153
                       TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesvpaltv 79 
                                     iv+a+Rt+ig+++gsl++++a++L+a+vi++lle++g++p+++devilG+vl+ag+++n+aR+a ++aglp+ vp++t+
  FitnessBrowser__psRCH2:GFF1043   6 IVAATRTAIGSFQGSLANVPAVELGATVIRALLEKTGIEPAQVDEVILGHVLTAGAGQNTARQASIKAGLPHAVPSMTL 84 
                                     8****************************************************************************** PP

                       TIGR01930  80 nrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl...vktklsmgetA 155
                                     n+vC+Sgl+Av+la+q+i++G+adv++aGG+E+mS +p++l+ +  r +l++g+a+  d+++ d+   + ++++mg+tA
  FitnessBrowser__psRCH2:GFF1043  85 NKVCGSGLKAVHLAVQAIRCGDADVIIAGGMENMSLAPYVLPGA--RTGLRMGHAQIVDTMITDGlwdAFNDYHMGITA 161
                                     ******************************************98..89********************99********* PP

                       TIGR01930 156 enlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kkvvskDegirpnttlekLakLkpafkekk 231
                                     enla+kygi R +qD++a++S+q+aa+Aie+g+f++ei+pv ++++   +  +++De++r++tt+e+L++L++afk+ +
  FitnessBrowser__psRCH2:GFF1043 162 ENLAEKYGIDRAQQDAFAAQSQQRAAAAIESGRFDAEITPVMIPQRkgdPLAFARDEQPRAGTTAESLGGLRAAFKK-D 239
                                     ********************************************9999999************************95.9 PP

                       TIGR01930 232 gstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEin 310
                                     g  vtAgN+s lnDGAaa++lms ++a++lgl +la+i ++a+agvdp++mg+gpv A++++L+kag+++ ++dl+E n
  FitnessBrowser__psRCH2:GFF1043 240 G-CVTAGNASTLNDGAAAVVLMSASKAEALGLPVLAKIAGYANAGVDPAIMGIGPVTATRRCLDKAGWTLAELDLIEAN 317
                                     *.6**************************************************************************** PP

                       TIGR01930 311 EAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                     EAFA+q+l v kelg  d +kvNvnGGAiAlGHP+GasG+ri++tll+e+++r+++ GlatlC+ggGqG+A+ +e
  FitnessBrowser__psRCH2:GFF1043 318 EAFAVQALSVGKELG-WDADKVNVNGGAIALGHPIGASGCRILVTLLHEMQRRDVRKGLATLCIGGGQGVALAVE 391
                                     ***************.88*****************************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (393 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: 28.05
//
[ok]

This GapMind analysis is from Apr 09 2024. 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