Alignments for a candidate for gudD in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for gudD in Pseudomonas fluorescens FW300-N2E3

Align Glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (characterized)
to candidate AO353_29040 AO353_29040 glucarate dehydratase

Query= SwissProt::P42206
         (451 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_29040
          Length = 449

 Score =  741 bits (1914), Expect = 0.0
 Identities = 352/439 (80%), Positives = 406/439 (92%), Gaps = 1/439 (0%)

Query: 13  APVITDLKVVPVAGHDSMLLNLSGAHGPLFTRNILILTDSSGHVGVGEVPGGEGIRKTLE 72
           AP+IT L+V+PVAGHDSML+NLSGAHGP FTRNI+IL DS+G+VGVGEVPGGE IR+TLE
Sbjct: 12  APLITSLQVIPVAGHDSMLMNLSGAHGPFFTRNIVILKDSAGNVGVGEVPGGERIRETLE 71

Query: 73  DARHLLINQSIGNYQSLLNKVRNAFADRDVGGRGLQTFDLRIAVHAVTAVESALLDLLGQ 132
           DAR L++ Q IGNYQS+LN +R+AFA RD  GRG QTFDLRI +HAVTA+E+ALLDLLGQ
Sbjct: 72  DARSLVVGQPIGNYQSILNAMRSAFAARDSAGRGQQTFDLRITIHAVTAMEAALLDLLGQ 131

Query: 133 HLQVPVAALLGEGQQRDAVEMLGYLFYVGDRNKTDLGYRSEHEADNEWFRLRNKEALTPE 192
            L+VPVAALLGEGQQRDAV+MLGYLFY+GDR++TDL YRSE +AD +WFRLR+++A+TPE
Sbjct: 132 FLEVPVAALLGEGQQRDAVKMLGYLFYIGDRHQTDLAYRSEPDAD-DWFRLRHEQAMTPE 190

Query: 193 SVVALAEAAYDRYGFKDFKLKGGVLRGEDEIAAVTALSERFPDARITLDPNGAWSLKEAV 252
           +VV LAEAA  +YGF DFKLKGGVLRGE+EI AVTAL+ERFPDARITLDPNGAWSLKEA+
Sbjct: 191 AVVRLAEAAKAKYGFNDFKLKGGVLRGEEEIEAVTALAERFPDARITLDPNGAWSLKEAI 250

Query: 253 ALCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRSTGLRTATNMIATDWRQMGHAIQLQS 312
            LCRDQHHVLAYAEDPCGAENGYSGREVMAEFRR+TGL+TATNMIATDWR+MGHAIQLQS
Sbjct: 251 RLCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRATGLKTATNMIATDWREMGHAIQLQS 310

Query: 313 VDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGNITAID 372
           VDIPLADPHFWTMQGSVRVAQMC+EWGLTWGSHSNNHFDISLAMFT VAAAAPG+ITAID
Sbjct: 311 VDIPLADPHFWTMQGSVRVAQMCHEWGLTWGSHSNNHFDISLAMFTQVAAAAPGDITAID 370

Query: 373 THWIWQDGQRLTKEPLQIKGGLVEVPKKPGLGVELDWDALMKAHEVYKSMGLGARDDATA 432
           THWIWQDGQRLT+EPLQI  G ++VP +PGLGV++D DA+ KAHE+YK MGLGARDD+ A
Sbjct: 371 THWIWQDGQRLTQEPLQIVDGYIKVPARPGLGVDIDMDAVAKAHELYKGMGLGARDDSVA 430

Query: 433 MRYLVSGWEFNNKRPCMVR 451
           M++++ GW+F+NK+PC+VR
Sbjct: 431 MQFMIPGWKFDNKKPCLVR 449


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: 678
Number of extensions: 14
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: 451
Length of database: 449
Length adjustment: 33
Effective length of query: 418
Effective length of database: 416
Effective search space:   173888
Effective search space used:   173888
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 AO353_29040 AO353_29040 (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.15382.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   2.2e-268  876.0   0.5   2.5e-268  875.8   0.5    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_29040  AO353_29040 glucarate dehydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_29040  AO353_29040 glucarate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  875.8   0.5  2.5e-268  2.5e-268       3     441 .]      12     449 .]      10     449 .] 0.99

  Alignments for each domain:
  == domain 1  score: 875.8 bits;  conditional E-value: 2.5e-268
                                     TIGR03247   3 tpvvtelrvvpvagrdsmllnlsgahapfftrnivilkdssgrtgvgevpggekirktledakal 67 
                                                   +p +t+l+v+pvag+dsml+nlsgah+pfftrnivilkds+g++gvgevpgge+ir+tleda++l
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_29040  12 APLITSLQVIPVAGHDSMLMNLSGAHGPFFTRNIVILKDSAGNVGVGEVPGGERIRETLEDARSL 76 
                                                   799************************************************************** PP

                                     TIGR03247  68 vvgktlgeyknvlkkvrktfadrdaggrgkqtfdlrvtvhavtalesalldllgqhlevpvaall 132
                                                   vvg+++g+y+++l+++r++fa+rd++grg+qtfdlr+t+havta+e+alldllgq+levpvaall
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_29040  77 VVGQPIGNYQSILNAMRSAFAARDSAGRGQQTFDLRITIHAVTAMEAALLDLLGQFLEVPVAALL 141
                                                   ***************************************************************** PP

                                     TIGR03247 133 gegqqrdevevlgylffvgdrkktsldyrseeeakddwlrlrheealtpeavvrlaeaakdrygf 197
                                                   gegqqrd+v++lgylf++gdr++t+l+yrse++a ddw+rlrhe+a+tpeavvrlaeaak++ygf
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_29040 142 GEGQQRDAVKMLGYLFYIGDRHQTDLAYRSEPDA-DDWFRLRHEQAMTPEAVVRLAEAAKAKYGF 205
                                                   ******************************9875.79**************************** PP

                                     TIGR03247 198 kdfklkggvlrgeeeieavtalakrfpdaritldpngawsleeaialckdlkdvlayaedpvgae 262
                                                   +dfklkggvlrgeeeieavtala+rfpdaritldpngawsl+eai+lc+d++ vlayaedp+gae
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_29040 206 NDFKLKGGVLRGEEEIEAVTALAERFPDARITLDPNGAWSLKEAIRLCRDQHHVLAYAEDPCGAE 270
                                                   ***************************************************************** PP

                                     TIGR03247 263 egysgrevmaefrratglptatnmiatdwrelghalrlqavdipladphfwtlqgsvrvaqlcee 327
                                                   +gysgrevmaefrratgl tatnmiatdwre+gha++lq+vdipladphfwt+qgsvrvaq+c+e
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_29040 271 NGYSGREVMAEFRRATGLKTATNMIATDWREMGHAIQLQSVDIPLADPHFWTMQGSVRVAQMCHE 335
                                                   ***************************************************************** PP

                                     TIGR03247 328 ygltwgshsnnhfdislamfthvaaaapgkvtaidthwiwqdgqrltkepleikegkikvpekpg 392
                                                   +gltwgshsnnhfdislamft vaaaapg++taidthwiwqdgqrlt+epl+i +g ikvp++pg
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_29040 336 WGLTWGSHSNNHFDISLAMFTQVAAAAPGDITAIDTHWIWQDGQRLTQEPLQIVDGYIKVPARPG 400
                                                   ***************************************************************** PP

                                     TIGR03247 393 lgveldedavekahelykkkglgarddavamqllipnwkfdekrpclvr 441
                                                   lgv++d+dav+kahelyk +glgardd+vamq++ip+wkfd+k+pclvr
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_29040 401 LGVDIDMDAVAKAHELYKGMGLGARDDSVAMQFMIPGWKFDNKKPCLVR 449
                                                   ************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (441 nodes)
Target sequences:                          1  (449 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 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 10.56
//
[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