Alignments for a candidate for gudD in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for gudD in Pseudomonas stutzeri RCH2

Align Glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (characterized)
to candidate GFF375 Psest_0376 glucarate dehydratase

Query= SwissProt::P42206
         (451 letters)



>FitnessBrowser__psRCH2:GFF375
          Length = 446

 Score =  741 bits (1914), Expect = 0.0
 Identities = 355/443 (80%), Positives = 392/443 (88%)

Query: 9   AATGAPVITDLKVVPVAGHDSMLLNLSGAHGPLFTRNILILTDSSGHVGVGEVPGGEGIR 68
           AATG P IT+L VVPVAG DSML+NLSGAHGP FTRNILIL DS+GHVGVGEVPGGE IR
Sbjct: 4   AATGTPRITELTVVPVAGQDSMLMNLSGAHGPWFTRNILILKDSAGHVGVGEVPGGEAIR 63

Query: 69  KTLEDARHLLINQSIGNYQSLLNKVRNAFADRDVGGRGLQTFDLRIAVHAVTAVESALLD 128
           +TLEDAR LL+ + IG Y +LLN+ R AFADRD GGRGLQTFDLRIA+HAVTA+ESALLD
Sbjct: 64  QTLEDARVLLVGEPIGQYNALLNRARRAFADRDSGGRGLQTFDLRIAIHAVTALESALLD 123

Query: 129 LLGQHLQVPVAALLGEGQQRDAVEMLGYLFYVGDRNKTDLGYRSEHEADNEWFRLRNKEA 188
           LLGQHL+VPVAALLG+GQQRD VEMLGYLF++GDRNKTD GYR E  AD+ WFRLRN+EA
Sbjct: 124 LLGQHLEVPVAALLGDGQQRDEVEMLGYLFFIGDRNKTDFGYRDESGADDAWFRLRNEEA 183

Query: 189 LTPESVVALAEAAYDRYGFKDFKLKGGVLRGEDEIAAVTALSERFPDARITLDPNGAWSL 248
           +TPES+V  AEAAY+RYGFKDFKLKGGVLRGE+E+ A+ AL+ RFPDAR+TLDPNGAWSL
Sbjct: 184 MTPESIVRQAEAAYERYGFKDFKLKGGVLRGEEEVEAIRALAARFPDARVTLDPNGAWSL 243

Query: 249 KEAVALCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRSTGLRTATNMIATDWRQMGHAI 308
            EA+ LCRD H VLAYAEDPCGAENGYSGREVMAEFRR+TGL TATNMIATDWRQM H +
Sbjct: 244 DEAIGLCRDLHGVLAYAEDPCGAENGYSGREVMAEFRRATGLPTATNMIATDWRQMSHTV 303

Query: 309 QLQSVDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGNI 368
           QL SVDIPLADPHFWTM GSVRVAQMC ++GLTWGSHSNNHFDISLAMFTHVAAAAPG +
Sbjct: 304 QLNSVDIPLADPHFWTMAGSVRVAQMCADFGLTWGSHSNNHFDISLAMFTHVAAAAPGRV 363

Query: 369 TAIDTHWIWQDGQRLTKEPLQIKGGLVEVPKKPGLGVELDWDALMKAHEVYKSMGLGARD 428
           TAIDTHWIWQDGQ LT EPL+I GG V VP+KPGLGVELDWDAL +AH  Y+  GLGARD
Sbjct: 364 TAIDTHWIWQDGQHLTLEPLKIVGGKVAVPQKPGLGVELDWDALQQAHAHYQEKGLGARD 423

Query: 429 DATAMRYLVSGWEFNNKRPCMVR 451
           DA AM+YL+  W FNNK+PCMVR
Sbjct: 424 DAIAMQYLIPDWTFNNKKPCMVR 446


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: 706
Number of extensions: 18
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: 446
Length adjustment: 33
Effective length of query: 418
Effective length of database: 413
Effective search space:   172634
Effective search space used:   172634
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 GFF375 Psest_0376 (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.26450.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
     1e-265  867.2   0.3   1.2e-265  867.0   0.3    1.0  1  lcl|FitnessBrowser__psRCH2:GFF375  Psest_0376 glucarate dehydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF375  Psest_0376 glucarate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  867.0   0.3  1.2e-265  1.2e-265       2     441 .]       7     446 .]       6     446 .] 1.00

  Alignments for each domain:
  == domain 1  score: 867.0 bits;  conditional E-value: 1.2e-265
                          TIGR03247   2 atpvvtelrvvpvagrdsmllnlsgahapfftrnivilkdssgrtgvgevpggekirktledakalvvgktlgeyk 77 
                                         tp++tel vvpvag+dsml+nlsgah+p+ftrni+ilkds+g++gvgevpgge+ir+tleda+ l+vg+++g+y+
  lcl|FitnessBrowser__psRCH2:GFF375   7 GTPRITELTVVPVAGQDSMLMNLSGAHGPWFTRNILILKDSAGHVGVGEVPGGEAIRQTLEDARVLLVGEPIGQYN 82 
                                        69************************************************************************** PP

                          TIGR03247  78 nvlkkvrktfadrdaggrgkqtfdlrvtvhavtalesalldllgqhlevpvaallgegqqrdevevlgylffvgdr 153
                                        ++l++ r++fadrd+ggrg+qtfdlr+++havtalesalldllgqhlevpvaallg+gqqrdeve+lgylff+gdr
  lcl|FitnessBrowser__psRCH2:GFF375  83 ALLNRARRAFADRDSGGRGLQTFDLRIAIHAVTALESALLDLLGQHLEVPVAALLGDGQQRDEVEMLGYLFFIGDR 158
                                        **************************************************************************** PP

                          TIGR03247 154 kktsldyrseeeakddwlrlrheealtpeavvrlaeaakdrygfkdfklkggvlrgeeeieavtalakrfpdarit 229
                                        +kt++ yr+e+ a+d+w+rlr+eea+tpe++vr aeaa++rygfkdfklkggvlrgeee+ea++ala+rfpdar+t
  lcl|FitnessBrowser__psRCH2:GFF375 159 NKTDFGYRDESGADDAWFRLRNEEAMTPESIVRQAEAAYERYGFKDFKLKGGVLRGEEEVEAIRALAARFPDARVT 234
                                        **************************************************************************** PP

                          TIGR03247 230 ldpngawsleeaialckdlkdvlayaedpvgaeegysgrevmaefrratglptatnmiatdwrelghalrlqavdi 305
                                        ldpngawsl+eai lc+dl++vlayaedp+gae+gysgrevmaefrratglptatnmiatdwr+++h+++l++vdi
  lcl|FitnessBrowser__psRCH2:GFF375 235 LDPNGAWSLDEAIGLCRDLHGVLAYAEDPCGAENGYSGREVMAEFRRATGLPTATNMIATDWRQMSHTVQLNSVDI 310
                                        **************************************************************************** PP

                          TIGR03247 306 pladphfwtlqgsvrvaqlceeygltwgshsnnhfdislamfthvaaaapgkvtaidthwiwqdgqrltkepleik 381
                                        pladphfwt++gsvrvaq+c ++gltwgshsnnhfdislamfthvaaaapg+vtaidthwiwqdgq+lt epl+i 
  lcl|FitnessBrowser__psRCH2:GFF375 311 PLADPHFWTMAGSVRVAQMCADFGLTWGSHSNNHFDISLAMFTHVAAAAPGRVTAIDTHWIWQDGQHLTLEPLKIV 386
                                        **************************************************************************** PP

                          TIGR03247 382 egkikvpekpglgveldedavekahelykkkglgarddavamqllipnwkfdekrpclvr 441
                                        +gk++vp+kpglgveld+da+++ah  y++kglgardda+amq+lip+w+f++k+pc+vr
  lcl|FitnessBrowser__psRCH2:GFF375 387 GGKVAVPQKPGLGVELDWDALQQAHAHYQEKGLGARDDAIAMQYLIPDWTFNNKKPCMVR 446
                                        ***********************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (441 nodes)
Target sequences:                          1  (446 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: 00:00:00.02
# Mc/sec: 7.50
//
[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