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

GapMind for catabolism of small carbon sources

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

Align Fumarylacetoacetase; FAA; Beta-diketonase; Fumarylacetoacetate hydrolase; EC 3.7.1.2 (characterized)
to candidate 3610430 Dshi_3811 fumarylacetoacetase (RefSeq)

Query= SwissProt::P16930
         (419 letters)



>FitnessBrowser__Dino:3610430
          Length = 413

 Score =  404 bits (1037), Expect = e-117
 Identities = 210/416 (50%), Positives = 272/416 (65%), Gaps = 15/416 (3%)

Query: 2   SFIPVAED--SDFPIHNLPYGVFSTRGDPRPRIGVAIGDQILDLSIIKHLFTGPVLSKHQ 59
           S++P A D    FP++NL +GVFST GD  PR  VAIGD++LDL+ ++      +L  H 
Sbjct: 7   SWVPGANDPAGAFPLNNLAFGVFST-GDG-PRCAVAIGDKVLDLAALQ---AAGLLPDHG 61

Query: 60  DVFNQPTLNSFMGLGQAAWKEARVFLQNLLSVSQARLRDDTELRKCAFISQASATMHLPA 119
             F+ P L++FMG GQ AW+  R  L  LL     R   +T   + A   +A   +HLP 
Sbjct: 62  --FDAPALDTFMGRGQPAWQAVREALTELL-----RAGAETAPVRAALHDRAGVRLHLPF 114

Query: 120 TIGDYTDFYSSRQHATNVGIMFRDKENALMPNWLHLPVGYHGRASSVVVSGTPIRRPMGQ 179
           T+ ++TDFY+ RQHA NVG +FRD  NAL PNWLH+P+GY+GRAS+VVVSGTPI RP GQ
Sbjct: 115 TLAEFTDFYAGRQHAFNVGSLFRDPANALPPNWLHMPIGYNGRASTVVVSGTPIHRPAGQ 174

Query: 180 MKPDDSKPPVYGACKLLDMELEMAFFVGPGNRLGEPIPISKAHEHIFGMVLMNDWSARDI 239
           +K      P +G C+ LD ELE+   VG  +++G P+ + +A E IFG VL+NDWSARDI
Sbjct: 175 IKDPSDPMPRFGPCERLDFELELGAVVGTPSQMGVPVTVDEADEMIFGYVLLNDWSARDI 234

Query: 240 QKWEYVPLGPFLGKSFGTTVSPWVVPMDALMPFAVPNPKQDPRPLPYLCHDEPYTFDINL 299
           Q WEYVPLGPF GK+F TT+SPWVVP  AL PF    P ++   LP+L    P   DI+L
Sbjct: 235 QAWEYVPLGPFQGKAFATTISPWVVPRAALAPFRCGPPVREVPLLPHLRDTGPMFHDIDL 294

Query: 300 SVNLKGEGMSQAATICKSNFKYMYWTMLQQLTHHSVNGCNLRPGDLLASGTISGPEPENF 359
           +V L   G      +C++N   +Y++  Q L HHS +GC +R GDLL SGTISGPE   F
Sbjct: 295 AVTLAPPG-GAPTEVCRTNSNALYYSAAQLLAHHSTSGCAMRTGDLLGSGTISGPEKGMF 353

Query: 360 GSMLELSWKGTKPIDLGNGQTRKFLLDGDEVIITGYCQGDGYRIGFGQCAGKVLPA 415
           GS+LE++W G  P+ L  G TR+FL DGD V + G  +GDGYRIGFG C G +LPA
Sbjct: 354 GSLLEITWGGRDPVALAGGATRRFLADGDTVTLKGEARGDGYRIGFGTCTGTILPA 409


Lambda     K      H
   0.321    0.139    0.440 

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: 612
Number of extensions: 20
Number of successful extensions: 5
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: 419
Length of database: 413
Length adjustment: 31
Effective length of query: 388
Effective length of database: 382
Effective search space:   148216
Effective search space used:   148216
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate 3610430 Dshi_3811 (fumarylacetoacetase (RefSeq))
to HMM TIGR01266 (fahA: fumarylacetoacetase (EC 3.7.1.2))

# 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/TIGR01266.hmm
# target sequence database:        /tmp/gapView.25010.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01266  [M=420]
Accession:   TIGR01266
Description: fum_ac_acetase: fumarylacetoacetase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   5.6e-157  508.8   0.0   6.3e-157  508.6   0.0    1.0  1  lcl|FitnessBrowser__Dino:3610430  Dshi_3811 fumarylacetoacetase (R


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3610430  Dshi_3811 fumarylacetoacetase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  508.6   0.0  6.3e-157  6.3e-157       1     419 [.       7     409 ..       7     410 .. 0.97

  Alignments for each domain:
  == domain 1  score: 508.6 bits;  conditional E-value: 6.3e-157
                         TIGR01266   1 sfvavak..nsdfplqnlPyGvfstkadssrrigvaiGdqildlskiaaaglfeglalkehqevfkestlnaflalg 75 
                                       s+v+ a+     fpl+nl +Gvfs  ++  +r++vaiGd++ldl++++aagl+ +       + f+  +l++f++ g
  lcl|FitnessBrowser__Dino:3610430   7 SWVPGANdpAGAFPLNNLAFGVFS--TGDGPRCAVAIGDKVLDLAALQAAGLLPD-------HGFDAPALDTFMGRG 74 
                                       789888844468************..56789********************9988.......89************* PP

                         TIGR01266  76 rparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirhatnvGilfrgkdnallPn 152
                                       +pa+++vre l +ll + ae+     a  + al+ +a ++ hlP ++ ++tdfy++++ha nvG lfr + nal Pn
  lcl|FitnessBrowser__Dino:3610430  75 QPAWQAVREALTELLRAGAET-----APVRAALHDRAGVRLHLPFTLAEFTDFYAGRQHAFNVGSLFRDPANALPPN 146
                                       ***************966655.....5566799******************************************** PP

                         TIGR01266 153 ykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelelaffvgtenelGeavpiekaeehifGv 229
                                       + h+P+gy Gras+vvvsGt+++rP Gqik +   +P fgpc++ld+elel+  vgt+ ++G +v ++ a+e ifG 
  lcl|FitnessBrowser__Dino:3610430 147 WLHMPIGYNGRASTVVVSGTPIHRPAGQIKDPSDPMPRFGPCERLDFELELGAVVGTPSQMGVPVTVDEADEMIFGY 223
                                       ***************************************************************************** PP

                         TIGR01266 230 vllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePfrvaqlePeqdpkplpylredradtafdielevs 306
                                       vllndwsardiqaweyvPlGPf +k+fatt+sPwvv+  al Pfr     P+++  +lp+lr+   ++ +di+l+v+
  lcl|FitnessBrowser__Dino:3610430 224 VLLNDWSARDIQAWEYVPLGPFQGKAFATTISPWVVPRAALAPFRCG--PPVREVPLLPHLRDT-GPMFHDIDLAVT 297
                                       *********************************************99..888888899****99.9*********** PP

                         TIGR01266 307 lkteGlaeaavisrsnakslywtlkqqlahhsvnGcnlraGdllgsGtisGkeeeafGsllelsakGkkevkladge 383
                                       l + G + ++ ++r+n+  ly++ +q lahhs +Gc +r+GdllgsGtisG+e++ fGslle++++G+++v la g 
  lcl|FitnessBrowser__Dino:3610430 298 LAPPG-GAPTEVCRTNSNALYYSAAQLLAHHSTSGCAMRTGDLLGSGTISGPEKGMFGSLLEITWGGRDPVALAGGA 373
                                       *****.99********************************************************************* PP

                         TIGR01266 384 trkfledGdevilrgvckkeGvrvGfGecaGkvlpa 419
                                       tr+fl dGd+v l+g ++ +G+r+GfG c+G++lpa
  lcl|FitnessBrowser__Dino:3610430 374 TRRFLADGDTVTLKGEARGDGYRIGFGTCTGTILPA 409
                                       **********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (413 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: 9.99
//
[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