GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gudD in Pseudomonas fluorescens FW300-N2C3

Align Glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (characterized)
to candidate AO356_01240 AO356_01240 glucarate dehydratase

Query= SwissProt::P42206
         (451 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_01240
          Length = 447

 Score =  752 bits (1942), Expect = 0.0
 Identities = 358/439 (81%), Positives = 398/439 (90%)

Query: 13  APVITDLKVVPVAGHDSMLLNLSGAHGPLFTRNILILTDSSGHVGVGEVPGGEGIRKTLE 72
           AP+IT ++VVPVAGHD MLLNLSGAHGP FTRNI+IL D++GH GVGEVPGGE IR+TLE
Sbjct: 9   APIITSMQVVPVAGHDGMLLNLSGAHGPFFTRNIVILKDNAGHTGVGEVPGGERIRQTLE 68

Query: 73  DARHLLINQSIGNYQSLLNKVRNAFADRDVGGRGLQTFDLRIAVHAVTAVESALLDLLGQ 132
           DAR L++   IG YQ +LN VRNAFADRD GGRGLQTFDLRI +HAVT +E+ALLDLLGQ
Sbjct: 69  DARSLVVGSPIGTYQKILNTVRNAFADRDAGGRGLQTFDLRITIHAVTGLEAALLDLLGQ 128

Query: 133 HLQVPVAALLGEGQQRDAVEMLGYLFYVGDRNKTDLGYRSEHEADNEWFRLRNKEALTPE 192
           HL VPVAALLGEGQQRD V+MLGYLFYVGDR +TDL YRSE +ADN+WFR+R+++AL  +
Sbjct: 129 HLDVPVAALLGEGQQRDEVKMLGYLFYVGDRQQTDLAYRSEPDADNDWFRVRHEKALDAD 188

Query: 193 SVVALAEAAYDRYGFKDFKLKGGVLRGEDEIAAVTALSERFPDARITLDPNGAWSLKEAV 252
           +VV LAEAA  RYGF+DFKLKGGVL+G+ EI AVTAL+ERFP ARITLDPNGAWSLKEA+
Sbjct: 189 AVVRLAEAAQARYGFQDFKLKGGVLQGDAEIEAVTALAERFPQARITLDPNGAWSLKEAI 248

Query: 253 ALCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRSTGLRTATNMIATDWRQMGHAIQLQS 312
            LCRDQH VLAYAEDPCGAENGYSGREVMAEFRR+TGL+TATNMIATDWR+MGHAI LQS
Sbjct: 249 RLCRDQHKVLAYAEDPCGAENGYSGREVMAEFRRATGLKTATNMIATDWREMGHAITLQS 308

Query: 313 VDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGNITAID 372
           VDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPG+ITAID
Sbjct: 309 VDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGDITAID 368

Query: 373 THWIWQDGQRLTKEPLQIKGGLVEVPKKPGLGVELDWDALMKAHEVYKSMGLGARDDATA 432
           THWIWQDGQRLTK PLQI+GG V+VPKKPGLG+ELD D L KAHE+YK MGLGARDDA A
Sbjct: 369 THWIWQDGQRLTKAPLQIQGGCVQVPKKPGLGIELDTDQLAKAHELYKGMGLGARDDAVA 428

Query: 433 MRYLVSGWEFNNKRPCMVR 451
           M++L+ GW FNNKRPC+VR
Sbjct: 429 MQFLIPGWTFNNKRPCLVR 447


Lambda     K      H
   0.319    0.135    0.410 

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: 700
Number of extensions: 19
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: 451
Length of database: 447
Length adjustment: 33
Effective length of query: 418
Effective length of database: 414
Effective search space:   173052
Effective search space used:   173052
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: 51 (24.3 bits)

Align candidate AO356_01240 AO356_01240 (glucarate dehydratase)
to HMM TIGR03247 (gudD: glucarate dehydratase (EC 4.2.1.40))

# 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/TIGR03247.hmm
# target sequence database:        /tmp/gapView.4824.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03247  [M=441]
Accession:   TIGR03247
Description: glucar-dehydr: glucarate dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   1.7e-269  879.7   0.8   1.9e-269  879.5   0.8    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01240  AO356_01240 glucarate dehydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01240  AO356_01240 glucarate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  879.5   0.8  1.9e-269  1.9e-269       2     441 .]       8     447 .]       7     447 .] 1.00

  Alignments for each domain:
  == domain 1  score: 879.5 bits;  conditional E-value: 1.9e-269
                                       TIGR03247   2 atpvvtelrvvpvagrdsmllnlsgahapfftrnivilkdssgrtgvgevpggekirktleda 64 
                                                     ++p++t+++vvpvag+d mllnlsgah+pfftrnivilkd++g+tgvgevpgge+ir+tleda
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01240   8 KAPIITSMQVVPVAGHDGMLLNLSGAHGPFFTRNIVILKDNAGHTGVGEVPGGERIRQTLEDA 70 
                                                     689************************************************************ PP

                                       TIGR03247  65 kalvvgktlgeyknvlkkvrktfadrdaggrgkqtfdlrvtvhavtalesalldllgqhlevp 127
                                                     ++lvvg ++g+y+++l++vr++fadrdaggrg+qtfdlr+t+havt+le+alldllgqhl+vp
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01240  71 RSLVVGSPIGTYQKILNTVRNAFADRDAGGRGLQTFDLRITIHAVTGLEAALLDLLGQHLDVP 133
                                                     *************************************************************** PP

                                       TIGR03247 128 vaallgegqqrdevevlgylffvgdrkktsldyrseeeakddwlrlrheealtpeavvrlaea 190
                                                     vaallgegqqrdev++lgylf+vgdr++t+l+yrse++a++dw+r+rhe+al  +avvrlaea
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01240 134 VAALLGEGQQRDEVKMLGYLFYVGDRQQTDLAYRSEPDADNDWFRVRHEKALDADAVVRLAEA 196
                                                     *************************************************************** PP

                                       TIGR03247 191 akdrygfkdfklkggvlrgeeeieavtalakrfpdaritldpngawsleeaialckdlkdvla 253
                                                     a++rygf+dfklkggvl+g+ eieavtala+rfp+aritldpngawsl+eai+lc+d+++vla
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01240 197 AQARYGFQDFKLKGGVLQGDAEIEAVTALAERFPQARITLDPNGAWSLKEAIRLCRDQHKVLA 259
                                                     *************************************************************** PP

                                       TIGR03247 254 yaedpvgaeegysgrevmaefrratglptatnmiatdwrelghalrlqavdipladphfwtlq 316
                                                     yaedp+gae+gysgrevmaefrratgl tatnmiatdwre+gha+ lq+vdipladphfwt+q
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01240 260 YAEDPCGAENGYSGREVMAEFRRATGLKTATNMIATDWREMGHAITLQSVDIPLADPHFWTMQ 322
                                                     *************************************************************** PP

                                       TIGR03247 317 gsvrvaqlceeygltwgshsnnhfdislamfthvaaaapgkvtaidthwiwqdgqrltkeple 379
                                                     gsvrvaq+c+e+gltwgshsnnhfdislamfthvaaaapg++taidthwiwqdgqrltk+pl+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01240 323 GSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGDITAIDTHWIWQDGQRLTKAPLQ 385
                                                     *************************************************************** PP

                                       TIGR03247 380 ikegkikvpekpglgveldedavekahelykkkglgarddavamqllipnwkfdekrpclvr 441
                                                     i++g+++vp+kpglg+eld+d+++kahelyk +glgarddavamq+lip+w+f++krpclvr
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01240 386 IQGGCVQVPKKPGLGIELDTDQLAKAHELYKGMGLGARDDAVAMQFLIPGWTFNNKRPCLVR 447
                                                     *************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (441 nodes)
Target sequences:                          1  (447 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.59
//
[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