GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fahA in Cupriavidus basilensis 4G11

Align Fumarylacetoacetase; FAA; Beta-diketonase; Fumarylacetoacetate hydrolase; EC 3.7.1.2 (characterized)
to candidate RR42_RS31270 RR42_RS31270 fumarylacetoacetase

Query= SwissProt::P16930
         (419 letters)



>FitnessBrowser__Cup4G11:RR42_RS31270
          Length = 420

 Score =  489 bits (1259), Expect = e-143
 Identities = 239/417 (57%), Positives = 303/417 (72%), Gaps = 5/417 (1%)

Query: 2   SFIPVAED--SDFPIHNLPYGVFSTRGDPRPRIGVAIGDQILDLSIIKHLFTGPVLSKHQ 59
           S+I  A D  + FP+ NLPYG+FS  G   PR+GVAIGD ILDLS++      P   K  
Sbjct: 7   SWIESANDGVTHFPLQNLPYGIFSPNGQG-PRVGVAIGDFILDLSVLDEAGLLPACVK-- 63

Query: 60  DVFNQPTLNSFMGLGQAAWKEARVFLQNLLSVSQARLRDDTELRKCAFISQASATMHLPA 119
            VF   TLN+F+ LG+ AW E R  L ++L+     L   + L + A +  A AT+HLP 
Sbjct: 64  GVFGGATLNAFIALGKPAWTETRQRLTSMLAADDTTLHPKSALHEQALVPMAWATLHLPV 123

Query: 120 TIGDYTDFYSSRQHATNVGIMFRDKENALMPNWLHLPVGYHGRASSVVVSGTPIRRPMGQ 179
            I  YTDFYSSR+HATNVG MFRD +NAL+PNWL +P+GY+GRASSVVVSGT +RRP GQ
Sbjct: 124 DIPGYTDFYSSREHATNVGRMFRDPDNALLPNWLEIPIGYNGRASSVVVSGTELRRPKGQ 183

Query: 180 MKPDDSKPPVYGACKLLDMELEMAFFVGPGNRLGEPIPISKAHEHIFGMVLMNDWSARDI 239
           +KP ++  PV+ AC+ LD ELEMAF VG  + LGEP+  + A  H+FGMV++NDWSARDI
Sbjct: 184 IKPPNAPRPVFTACQKLDYELEMAFIVGKPSTLGEPVSTAAAAGHMFGMVILNDWSARDI 243

Query: 240 QKWEYVPLGPFLGKSFGTTVSPWVVPMDALMPFAVPNPKQDPRPLPYLCHDEPYTFDINL 299
           Q+WEYVPLGPF  K FGT++SPWVV MDAL PF   NP Q P PL YL   E   +DI L
Sbjct: 244 QQWEYVPLGPFNSKGFGTSISPWVVTMDALEPFRRDNPVQSPEPLAYLQQPERNAYDIAL 303

Query: 300 SVNLKGEGMSQAATICKSNFKYMYWTMLQQLTHHSVNGCNLRPGDLLASGTISGPEPENF 359
            V+L+ EG +QA T+C++NFK MYWTM+QQL HH+V+GCN+R GDL+ SGTISG  P+++
Sbjct: 304 EVSLRPEGAAQATTVCRTNFKAMYWTMVQQLAHHTVSGCNVRVGDLMGSGTISGTTPDSY 363

Query: 360 GSMLELSWKGTKPIDLGNGQTRKFLLDGDEVIITGYCQGDGYRIGFGQCAGKVLPAL 416
           GS+LEL+  G +P+ L +G  R FL DGDEV++ G+CQGDGYR+GFG+ AGK+LPAL
Sbjct: 364 GSLLELTRNGAEPLTLADGSKRGFLEDGDEVVMAGWCQGDGYRVGFGEVAGKILPAL 420


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: 647
Number of extensions: 24
Number of successful extensions: 3
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: 420
Length adjustment: 32
Effective length of query: 387
Effective length of database: 388
Effective search space:   150156
Effective search space used:   150156
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 RR42_RS31270 RR42_RS31270 (fumarylacetoacetase)
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.18372.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.3e-186  604.4   0.0     6e-186  604.3   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS31270  RR42_RS31270 fumarylacetoacetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS31270  RR42_RS31270 fumarylacetoacetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  604.3   0.0    6e-186    6e-186       1     420 []       7     420 .]       7     420 .] 0.98

  Alignments for each domain:
  == domain 1  score: 604.3 bits;  conditional E-value: 6e-186
                                 TIGR01266   1 sfvavakn..sdfplqnlPyGvfstkadssrrigvaiGdqildlskiaaaglfeglalkehqevfkest 67 
                                               s++++a++  + fplqnlPyG+fs  +++ +r+gvaiGd ildls++ +agl+        + vf ++t
  lcl|FitnessBrowser__Cup4G11:RR42_RS31270   7 SWIESANDgvTHFPLQNLPYGIFS-PNGQGPRVGVAIGDFILDLSVLDEAGLLPA----CVKGVFGGAT 70 
                                               899999963379************.78899*********************9988....4578****** PP

                                 TIGR01266  68 lnaflalgrparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirhat 136
                                               lnaf+alg+pa++e r+rl  +l+++  +l  ++al+++al+++a at hlP+ i  ytdfyss++hat
  lcl|FitnessBrowser__Cup4G11:RR42_RS31270  71 LNAFIALGKPAWTETRQRLTSMLAADDTTLHPKSALHEQALVPMAWATLHLPVDIPGYTDFYSSREHAT 139
                                               ********************************************************************* PP

                                 TIGR01266 137 nvGilfrgkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelelaf 205
                                               nvG +fr +dnallPn+  +P+gy GrassvvvsGtelrrP+Gqik++na  Pvf++c+kld+ele+af
  lcl|FitnessBrowser__Cup4G11:RR42_RS31270 140 NVGRMFRDPDNALLPNWLEIPIGYNGRASSVVVSGTELRRPKGQIKPPNAPRPVFTACQKLDYELEMAF 208
                                               ********************************************************************* PP

                                 TIGR01266 206 fvgtenelGeavpiekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePfr 274
                                                vg++ +lGe+v    a+ h+fG+v+lndwsardiq+weyvPlGPf++k f+t++sPwvv+++alePfr
  lcl|FitnessBrowser__Cup4G11:RR42_RS31270 209 IVGKPSTLGEPVSTAAAAGHMFGMVILNDWSARDIQQWEYVPLGPFNSKGFGTSISPWVVTMDALEPFR 277
                                               ********************************************************************* PP

                                 TIGR01266 275 vaqlePeqdpkplpylredradtafdielevslkteGlaeaavisrsnakslywtlkqqlahhsvnGcn 343
                                               +   +P+q p+pl+yl++  +  a+di levsl++eG a+a++++r+n+k +ywt+ qqlahh+v+Gcn
  lcl|FitnessBrowser__Cup4G11:RR42_RS31270 278 RD--NPVQSPEPLAYLQQP-ERNAYDIALEVSLRPEGAAQATTVCRTNFKAMYWTMVQQLAHHTVSGCN 343
                                               **..*************99.999********************************************** PP

                                 TIGR01266 344 lraGdllgsGtisGkeeeafGsllelsakGkkevkladgetrkfledGdevilrgvckkeGvrvGfGec 412
                                               +r Gdl+gsGtisG+ ++++Gsllel+ +G++++ ladg++r fledGdev++ g c+ +G+rvGfGe 
  lcl|FitnessBrowser__Cup4G11:RR42_RS31270 344 VRVGDLMGSGTISGTTPDSYGSLLELTRNGAEPLTLADGSKRGFLEDGDEVVMAGWCQGDGYRVGFGEV 412
                                               ********************************************************************* PP

                                 TIGR01266 413 aGkvlpal 420
                                               aGk+lpal
  lcl|FitnessBrowser__Cup4G11:RR42_RS31270 413 AGKILPAL 420
                                               ******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (420 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: 7.97
//
[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:

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