Alignments for a candidate for fadA in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Dinoroseobacter shibae DFL-12

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate 3609950 Dshi_3331 acetyl-CoA acetyltransferase (RefSeq)

Query= SwissProt::Q0KBP1
         (394 letters)



>FitnessBrowser__Dino:3609950
          Length = 394

 Score =  460 bits (1184), Expect = e-134
 Identities = 238/394 (60%), Positives = 288/394 (73%), Gaps = 2/394 (0%)

Query: 1   MTREVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQT 60
           + +++V++ G RTAIGTFGGSL   AP  LGA V + AL R+ V G  +GHVVFG+VI T
Sbjct: 3   LDQDIVILDGARTAIGTFGGSLAGTAPITLGATVAKAALERSGVEGAQIGHVVFGHVINT 62

Query: 61  EPRDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESM 120
           EPRDMYL RVAA+  G+    PA+ VNRLCGSG QA+VS  Q+++LGD    + GGAESM
Sbjct: 63  EPRDMYLSRVAAMEAGIPDTTPAMNVNRLCGSGAQALVSVIQSLMLGDAQFGLAGGAESM 122

Query: 121 SRAPYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAA 180
           SR+PY  P ARWG +MGDA  +DMMLGAL+ PF   HMGVTAENVA E+ I RA QD  A
Sbjct: 123 SRSPYAMPVARWGQKMGDATAMDMMLGALNCPFGTGHMGVTAENVAAEHGIGRADQDAFA 182

Query: 181 LESHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKEN 240
           LES  RA+ A +AG+F  QIVPV  K ++  V F  DEH +   T + +  LR VF K+ 
Sbjct: 183 LESQARAARAQEAGHFNSQIVPVPVKVKRDMVDFVRDEHPK-PTTAEALAGLRTVFQKD- 240

Query: 241 GTVTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKI 300
           GTVTAGNASG+ND AAA+V+   + AE  GLKP AR++ Y HAGV P+ MGIGPVPA + 
Sbjct: 241 GTVTAGNASGINDGAAALVLARASAAESAGLKPRARILGYAHAGVRPEVMGIGPVPAVQA 300

Query: 301 ALERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALIT 360
            L +  L VSD DVIE+NEAFAAQA AV K LGLDPAKVNPNG  I+LGHP+GATGA+I 
Sbjct: 301 LLAKTDLSVSDFDVIESNEAFAAQALAVNKGLGLDPAKVNPNGGAIALGHPVGATGAIIA 360

Query: 361 VKALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           +KAL+EL R+ G+ ALVTMCIGGGQGIA  FE +
Sbjct: 361 LKALYELERIGGKRALVTMCIGGGQGIALAFEAL 394


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: 515
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: 394
Length of database: 394
Length adjustment: 31
Effective length of query: 363
Effective length of database: 363
Effective search space:   131769
Effective search space used:   131769
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 3609950 Dshi_3331 (acetyl-CoA acetyltransferase (RefSeq))
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.24453.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     5e-135  436.3   9.1   5.7e-135  436.1   9.1    1.0  1  lcl|FitnessBrowser__Dino:3609950  Dshi_3331 acetyl-CoA acetyltrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3609950  Dshi_3331 acetyl-CoA acetyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  436.1   9.1  5.7e-135  5.7e-135       1     385 []       9     392 ..       9     392 .. 0.98

  Alignments for each domain:
  == domain 1  score: 436.1 bits;  conditional E-value: 5.7e-135
                         TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaaglpesvpa 76 
                                       i+d++Rt+ig++ggsl+ + + +L+a+v k++ler+g++ ++i +v++G+v+++    + + R aa++ag+p+++pa
  lcl|FitnessBrowser__Dino:3609950   9 ILDGARTAIGTFGGSLAGTAPITLGATVAKAALERSGVEGAQIGHVVFGHVINTEPRdMYLSRVAAMEAGIPDTTPA 85 
                                       89***************************************************99988******************* PP

                         TIGR01930  77 ltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl..vktklsm 151
                                       ++vnr+C+Sg qA+ ++ q+++ G+a+  +aGG+EsmSr+p+ ++ +  r++ k+g+a+ +d++l  l  +    +m
  lcl|FitnessBrowser__Dino:3609950  86 MNVNRLCGSGAQALVSVIQSLMLGDAQFGLAGGAESMSRSPYAMPVA--RWGQKMGDATAMDMMLGALncPFGTGHM 160
                                       *********************************************97..9************99998899999**** PP

                         TIGR01930 152 getAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpnttlekLakLkpa 226
                                       g+tAen+a+++gi R +qD++al+S+ +aa+A+e+g+f+++ivpv vk k   + + +De+++p tt+e+La+L+++
  lcl|FitnessBrowser__Dino:3609950 161 GVTAENVAAEHGIGRADQDAFALESQARAARAQEAGHFNSQIVPVPVKVKrdMVDFVRDEHPKP-TTAEALAGLRTV 236
                                       ********************************************9999998778889*****95.789********* PP

                         TIGR01930 227 fkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisd 303
                                       f++ +g tvtAgN+s++nDGAaal+l+  ++a++ gl+p ari ++a+agv pe+mg+gpvpA++++L+k++ls+sd
  lcl|FitnessBrowser__Dino:3609950 237 FQK-DG-TVTAGNASGINDGAAALVLARASAAESAGLKPRARILGYAHAGVRPEVMGIGPVPAVQALLAKTDLSVSD 311
                                       *95.9*.6********************************************************************* PP

                         TIGR01930 304 idlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGa 380
                                       +d++E nEAFAaq+lav+k lg ld++kvN nGGAiAlGHP+Ga+Ga+i l+ l+eL++ g+k++l+t+C+ggGqG+
  lcl|FitnessBrowser__Dino:3609950 312 FDVIESNEAFAAQALAVNKGLG-LDPAKVNPNGGAIALGHPVGATGAIIALKALYELERIGGKRALVTMCIGGGQGI 387
                                       **********************.99**************************************************** PP

                         TIGR01930 381 Avile 385
                                       A+ +e
  lcl|FitnessBrowser__Dino:3609950 388 ALAFE 392
                                       *9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (394 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: 00:00:00.01
# Mc/sec: 9.05
//
[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