Alignments for a candidate for fadA in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Phaeobacter inhibens BS107

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate GFF3382 PGA1_c34350 acetyl-CoA acetyltransferase PhbA

Query= SwissProt::Q0KBP1
         (394 letters)



>FitnessBrowser__Phaeo:GFF3382
          Length = 391

 Score =  457 bits (1176), Expect = e-133
 Identities = 230/391 (58%), Positives = 293/391 (74%), Gaps = 2/391 (0%)

Query: 4   EVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTEPR 63
           ++V++ G RTAIGTFGGSL    P +L  +  + A+ R+ V+ + +G+VVFG+VI TEPR
Sbjct: 3   DIVILDGARTAIGTFGGSLAGTTPIDLATVASKAAMERSGVAPEQIGNVVFGHVINTEPR 62

Query: 64  DMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMSRA 123
           DMYL RVAA+  G+    PA+ VNRLCGSG QAIVS  Q+++LGD + A+ GGAE+MSR+
Sbjct: 63  DMYLSRVAAMQAGIPNGTPAMNVNRLCGSGAQAIVSGIQSLMLGDAEFALTGGAENMSRS 122

Query: 124 PYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAALES 183
           P++ P+ARWG +MGDA  +DMMLGAL+ PF   HMGVTAENVA E+DI+RAQ DE AL S
Sbjct: 123 PFIVPSARWGQKMGDARALDMMLGALNCPFGTGHMGVTAENVADEHDITRAQMDEFALAS 182

Query: 184 HRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKENGTV 243
             RA+AAI+AGYF  QI PV  K ++  V FD DEH +  +T++ +  L+ VF K++G V
Sbjct: 183 QTRAAAAIEAGYFASQITPVEVKVKRDMVPFDVDEHPK-ASTLETLGGLKAVF-KKDGRV 240

Query: 244 TAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKIALE 303
           TAGNASG+ND AAA+VM     A + GLKP AR++ Y HAGV P+ MGIGPVPA +  L+
Sbjct: 241 TAGNASGINDGAAAIVMATADAARQAGLKPKARILGYAHAGVRPEVMGIGPVPAVQNLLK 300

Query: 304 RAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALITVKA 363
           + GL  SD DV+E+NEAFAAQA AV K LGLDPAKVNPNG  I+LGHP+GATGA+IT+K 
Sbjct: 301 KTGLSASDFDVVESNEAFAAQALAVNKELGLDPAKVNPNGGAIALGHPVGATGAIITLKT 360

Query: 364 LHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           L+EL R+ G   L+TMCIGGGQGIA   ER+
Sbjct: 361 LYELERIGGSKGLITMCIGGGQGIALAIERL 391


Lambda     K      H
   0.318    0.134    0.381 

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: 501
Number of extensions: 20
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: 394
Length of database: 391
Length adjustment: 31
Effective length of query: 363
Effective length of database: 360
Effective search space:   130680
Effective search space used:   130680
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 GFF3382 PGA1_c34350 (acetyl-CoA acetyltransferase PhbA)
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.31733.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   4.8e-136  439.6   7.5   5.4e-136  439.4   7.5    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3382  PGA1_c34350 acetyl-CoA acetyltra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3382  PGA1_c34350 acetyl-CoA acetyltransferase PhbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.4   7.5  5.4e-136  5.4e-136       1     385 []       6     389 ..       6     389 .. 0.98

  Alignments for each domain:
  == domain 1  score: 439.4 bits;  conditional E-value: 5.4e-136
                          TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaaglpesvp 75 
                                        i+d++Rt+ig++ggsl+ +++ dL++ + k+++er+g+ pe+i +v++G+v+++    + + R aa++ag+p+ +p
  lcl|FitnessBrowser__Phaeo:GFF3382   6 ILDGARTAIGTFGGSLAGTTPIDLATVASKAAMERSGVAPEQIGNVVFGHVINTEPRdMYLSRVAAMQAGIPNGTP 81 
                                        89***************************************************99988****************** PP

                          TIGR01930  76 altvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl..vktkl 149
                                        a++vnr+C+Sg qA+ ++ q+++ G+a+ +++GG+E+mSr+p++++++  r++ k+g+a+  d++l  l  +    
  lcl|FitnessBrowser__Phaeo:GFF3382  82 AMNVNRLCGSGAQAIVSGIQSLMLGDAEFALTGGAENMSRSPFIVPSA--RWGQKMGDARALDMMLGALncPFGTG 155
                                        **********************************************98..9************99998899999** PP

                          TIGR01930 150 smgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpnttlekLakL 223
                                        +mg+tAen+a++++i+R ++De+al+S+++aa+Aie+g+f+++i+pvevk k   + ++ De+++  +tle+L++L
  lcl|FitnessBrowser__Phaeo:GFF3382 156 HMGVTAENVADEHDITRAQMDEFALASQTRAAAAIEAGYFASQITPVEVKVKrdMVPFDVDEHPK-ASTLETLGGL 230
                                        **************************************************999889999****99.899******* PP

                          TIGR01930 224 kpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkagl 299
                                        k++fk+ +g+ vtAgN+s++nDGAaa+++++ ++a++ gl+p+ari ++a+agv pe+mg+gpvpA++++Lkk+gl
  lcl|FitnessBrowser__Phaeo:GFF3382 231 KAVFKK-DGR-VTAGNASGINDGAAAIVMATADAARQAGLKPKARILGYAHAGVRPEVMGIGPVPAVQNLLKKTGL 304
                                        ****95.9*6.***************************************************************** PP

                          TIGR01930 300 sisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvg 375
                                        s+sd+d+vE nEAFAaq+lav+kelg ld++kvN nGGAiAlGHP+Ga+Ga+i+l++l+eL++ g+  Gl+t+C+g
  lcl|FitnessBrowser__Phaeo:GFF3382 305 SASDFDVVESNEAFAAQALAVNKELG-LDPAKVNPNGGAIALGHPVGATGAIITLKTLYELERIGGSKGLITMCIG 379
                                        **************************.99*********************************************** PP

                          TIGR01930 376 gGqGaAvile 385
                                        gGqG+A+ +e
  lcl|FitnessBrowser__Phaeo:GFF3382 380 GGQGIALAIE 389
                                        ******9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (391 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: 00:00:00.02
# Mc/sec: 7.28
//
[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