GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__psRCH2:GFF1043 Psest_1076 acetyl-CoA
           acetyltransferases
          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.4990.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  lcl|FitnessBrowser__psRCH2:GFF1043  Psest_1076 acetyl-CoA acetyltran


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF1043  Psest_1076 acetyl-CoA acetyltransferases
   #    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 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesvp 75 
                                         iv+a+Rt+ig+++gsl++++a++L+a+vi++lle++g++p+++devilG+vl+ag+++n+aR+a ++aglp+ vp
  lcl|FitnessBrowser__psRCH2:GFF1043   6 IVAATRTAIGSFQGSLANVPAVELGATVIRALLEKTGIEPAQVDEVILGHVLTAGAGQNTARQASIKAGLPHAVP 80 
                                         8************************************************************************** PP

                           TIGR01930  76 altvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl...vkt 147
                                         ++t+n+vC+Sgl+Av+la+q+i++G+adv++aGG+E+mS +p++l+ +  r +l++g+a+  d+++ d+   + +
  lcl|FitnessBrowser__psRCH2:GFF1043  81 SMTLNKVCGSGLKAVHLAVQAIRCGDADVIIAGGMENMSLAPYVLPGA--RTGLRMGHAQIVDTMITDGlwdAFN 153
                                         **********************************************98..89********************99* PP

                           TIGR01930 148 klsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kkvvskDegirpnttlek 219
                                         +++mg+tAenla+kygi R +qD++a++S+q+aa+Aie+g+f++ei+pv ++++   +  +++De++r++tt+e+
  lcl|FitnessBrowser__psRCH2:GFF1043 154 DYHMGITAENLAEKYGIDRAQQDAFAAQSQQRAAAAIESGRFDAEITPVMIPQRkgdPLAFARDEQPRAGTTAES 228
                                         ****************************************************9999999**************** PP

                           TIGR01930 220 LakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaL 294
                                         L++L++afk+ +g  vtAgN+s lnDGAaa++lms ++a++lgl +la+i ++a+agvdp++mg+gpv A++++L
  lcl|FitnessBrowser__psRCH2:GFF1043 229 LGGLRAAFKK-DG-CVTAGNASTLNDGAAAVVLMSASKAEALGLPVLAKIAGYANAGVDPAIMGIGPVTATRRCL 301
                                         ********95.9*.6************************************************************ PP

                           TIGR01930 295 kkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGl 369
                                         +kag+++ ++dl+E nEAFA+q+l v kelg  d +kvNvnGGAiAlGHP+GasG+ri++tll+e+++r+++ Gl
  lcl|FitnessBrowser__psRCH2:GFF1043 302 DKAGWTLAELDLIEANEAFAVQALSVGKELG-WDADKVNVNGGAIALGHPIGASGCRILVTLLHEMQRRDVRKGL 375
                                         *******************************.88***************************************** PP

                           TIGR01930 370 atlCvggGqGaAvile 385
                                         atlC+ggGqG+A+ +e
  lcl|FitnessBrowser__psRCH2:GFF1043 376 ATLCIGGGQGVALAVE 391
                                         ************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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.30
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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