Alignments for a candidate for fadA in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Acidovorax sp. GW101-3H11

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate Ac3H11_3920 Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)

Query= metacyc::MONOMER-3207
         (400 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3920
          Length = 403

 Score =  507 bits (1305), Expect = e-148
 Identities = 261/400 (65%), Positives = 307/400 (76%), Gaps = 2/400 (0%)

Query: 2   RDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAG 61
           R  FICDAIRTP GR+GGAL+ VR DDL A+P+KAL++ NP V W  V +VF+GCANQAG
Sbjct: 5   RQAFICDAIRTPFGRYGGALSSVRTDDLGAIPIKALMDRNPGVDWAAVTDVFYGCANQAG 64

Query: 62  EDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMS 121
           EDNRNVA M+ LLAGLP  + G T+NRLC SG+DA+GTA RAI +GE  L IAGGVESMS
Sbjct: 65  EDNRNVAHMSSLLAGLPIEVAGATINRLCGSGLDAVGTAARAIKAGEAGLMIAGGVESMS 124

Query: 122 RAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRADQ 181
           RAPFVM KAES +SRN  + DTTIGWRF+N LMK +YGVDSMPETA+NVA D+++ R  Q
Sbjct: 125 RAPFVMPKAESAFSRNSAVYDTTIGWRFVNKLMKEKYGVDSMPETAENVATDFKIEREAQ 184

Query: 182 DAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGET-IVERDEHLRPETTLEALTKLKPV 240
           D  ALRSQ  A AA  AG  A EIVPV I  KKG+  IV +DEH R ET+LEAL KLK V
Sbjct: 185 DQMALRSQLNAVAAIKAGHLAREIVPVHIPQKKGDAIIVSQDEHPR-ETSLEALAKLKGV 243

Query: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300
             PD TVTAGNASGVNDGA AL+LA      K+GL PRARV+GMA  GVAPR+MG GP P
Sbjct: 244 VRPDGTVTAGNASGVNDGACALLLADEANAAKYGLKPRARVVGMAVAGVAPRIMGFGPTP 303

Query: 301 AVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360
           A +K+  + G+ +   DVIELNEAFA+QGLAVLR LG+ DD  +VN  GGAIALGHPLG 
Sbjct: 304 ATQKVLAQTGLTIDHMDVIELNEAFAAQGLAVLRALGLKDDDGRVNAWGGAIALGHPLGA 363

Query: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           SGARLV TA+++L +  G+  L TMC+GVGQG+A+ +ERV
Sbjct: 364 SGARLVTTAVNRLHEHAGQYALCTMCIGVGQGIAVILERV 403


Lambda     K      H
   0.318    0.134    0.383 

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: 502
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: 400
Length of database: 403
Length adjustment: 31
Effective length of query: 369
Effective length of database: 372
Effective search space:   137268
Effective search space used:   137268
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 Ac3H11_3920 (Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl CoA thiolase (EC 2.3.1.-))
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.1108.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   4.6e-134  433.1   4.9   5.2e-134  432.9   4.9    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920  Acetyl-CoA acetyltransferase (EC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920  Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl CoA thio
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  432.9   4.9  5.2e-134  5.2e-134       1     385 []       9     401 ..       9     401 .. 0.95

  Alignments for each domain:
  == domain 1  score: 432.9 bits;  conditional E-value: 5.2e-134
                                        TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.ani 60 
                                                      i da+Rtp+g++gg+l++++ +dL+a  ik+l++r+ g+d +++ +v +G++ qage+  n+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920   9 ICDAIRTPFGRYGGALSSVRTDDLGAIPIKALMDRNpGVDWAAVTDVFYGCANQAGEDnRNV 70 
                                                      789*******99**********************************************9*** PP

                                        TIGR01930  61 aReaalaaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillka 122
                                                      a +  l aglp +v++ t+nr+C+Sgl+Av +aa++ikaGea +++aGGvEsmSr+p+++++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920  71 AHMSSLLAGLPIEVAGATINRLCGSGLDAVGTAARAIKAGEAGLMIAGGVESMSRAPFVMPK 132
                                                      **********************************************************9999 PP

                                        TIGR01930 123 slrreslklgkakledqllkdl........vktklsmgetAenlakkygisReeqDeyalrS 176
                                                      +   es+  +++ ++d+++           ++   sm etAen+a++++i+Re qD+ alrS
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920 133 A---ESAFSRNSAVYDTTIGWRfvnklmkeKYGVDSMPETAENVATDFKIEREAQDQMALRS 191
                                                      7...44444555555533332267777887677789************************** PP

                                        TIGR01930 177 hqkaakAieegkfkdeivpvevkgk...kkvvskDegirpnttlekLakLkpafkekkgstv 235
                                                      + +a +Ai++g++++eivpv++++k   + +vs+De++r +t+le+LakLk + + ++g tv
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920 192 QLNAVAAIKAGHLAREIVPVHIPQKkgdAIIVSQDEHPR-ETSLEALAKLKGVVR-PDG-TV 250
                                                      ***********************9999999999****99.89************9.69*.6* PP

                                        TIGR01930 236 tAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkka 297
                                                      tAgN+s++nDGA+alll+ e+ a+++gl+p ar+v++avagv p++mg+gp+pA++k+L+++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920 251 TAGNASGVNDGACALLLADEANAAKYGLKPRARVVGMAVAGVAPRIMGFGPTPATQKVLAQT 312
                                                      ************************************************************** PP

                                        TIGR01930 298 glsisdidlvEinEAFAaqvlavekelgsld.lekvNvnGGAiAlGHPlGasGarivltllk 358
                                                      gl+i+ +d++E+nEAFAaq lav ++lg++d + +vN +GGAiAlGHPlGasGar+v+t ++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920 313 GLTIDHMDVIELNEAFAAQGLAVLRALGLKDdDGRVNAWGGAIALGHPLGASGARLVTTAVN 374
                                                      ****************************866799**************************** PP

                                        TIGR01930 359 eLkergkkyGlatlCvggGqGaAvile 385
                                                      +L+e+ ++y+l t+C+g GqG+Avile
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920 375 RLHEHAGQYALCTMCIGVGQGIAVILE 401
                                                      *************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (403 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.43
//
[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:

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