Alignments for a candidate for gudD in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gudD in Herbaspirillum seropedicae SmR1

Align Glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (characterized)
to candidate HSERO_RS05800 HSERO_RS05800 glucarate dehydratase

Query= SwissProt::P42206
         (451 letters)



>FitnessBrowser__HerbieS:HSERO_RS05800
          Length = 455

 Score =  736 bits (1899), Expect = 0.0
 Identities = 350/444 (78%), Positives = 398/444 (89%)

Query: 8   QAATGAPVITDLKVVPVAGHDSMLLNLSGAHGPLFTRNILILTDSSGHVGVGEVPGGEGI 67
           Q   GAP +T+++V+PVAGHDSMLLNLSGAHGP FTRN++ILTDS+G+ GVGEVPGGEGI
Sbjct: 12  QPVQGAPRVTEMRVIPVAGHDSMLLNLSGAHGPYFTRNLVILTDSAGNTGVGEVPGGEGI 71

Query: 68  RKTLEDARHLLINQSIGNYQSLLNKVRNAFADRDVGGRGLQTFDLRIAVHAVTAVESALL 127
           R+TLEDAR L++ QSIGN Q +LN+ R AFADRD GGRGLQTFDLRIA+HAVTA+E+ALL
Sbjct: 72  RQTLEDARTLVVGQSIGNVQGILNRARTAFADRDTGGRGLQTFDLRIAIHAVTALEAALL 131

Query: 128 DLLGQHLQVPVAALLGEGQQRDAVEMLGYLFYVGDRNKTDLGYRSEHEADNEWFRLRNKE 187
           DLLG+ L VPVAALLGEGQQRD VEMLGYLFYV DRNKTDL Y +  +A ++W RLR++ 
Sbjct: 132 DLLGKFLDVPVAALLGEGQQRDEVEMLGYLFYVADRNKTDLPYLAAPDAQDDWTRLRHEA 191

Query: 188 ALTPESVVALAEAAYDRYGFKDFKLKGGVLRGEDEIAAVTALSERFPDARITLDPNGAWS 247
           ALTPE+VV LAEAAY RYGF DFKLKGGV+RGE+EIAAVTAL+ERFP ARITLDPNG W 
Sbjct: 192 ALTPEAVVRLAEAAYARYGFNDFKLKGGVMRGEEEIAAVTALAERFPKARITLDPNGGWL 251

Query: 248 LKEAVALCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRSTGLRTATNMIATDWRQMGHA 307
           LK+A+ LCRDQH VLAYAEDPCGAE+GYSGREVMAEFRR+TGL+TATNM+ATDWRQMGHA
Sbjct: 252 LKDAIRLCRDQHDVLAYAEDPCGAEDGYSGREVMAEFRRATGLQTATNMVATDWRQMGHA 311

Query: 308 IQLQSVDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGN 367
           I LQSVDIPLADPHFWTMQGSVRVAQMC+EWGLTWGSHSNNHFD+SLAMFTHVAAAAPG 
Sbjct: 312 ISLQSVDIPLADPHFWTMQGSVRVAQMCHEWGLTWGSHSNNHFDVSLAMFTHVAAAAPGK 371

Query: 368 ITAIDTHWIWQDGQRLTKEPLQIKGGLVEVPKKPGLGVELDWDALMKAHEVYKSMGLGAR 427
           ITAIDTHWIWQDGQRLT+EPLQI GG V+VP KPGLGVELD   +  AH+ Y++MGLGAR
Sbjct: 372 ITAIDTHWIWQDGQRLTREPLQIVGGKVQVPTKPGLGVELDMAQVEAAHQTYRNMGLGAR 431

Query: 428 DDATAMRYLVSGWEFNNKRPCMVR 451
           DDA AM+YL+ GW+F+ K+PC+VR
Sbjct: 432 DDAVAMQYLIPGWKFDPKKPCLVR 455


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: 710
Number of extensions: 16
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: 455
Length adjustment: 33
Effective length of query: 418
Effective length of database: 422
Effective search space:   176396
Effective search space used:   176396
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 HSERO_RS05800 HSERO_RS05800 (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.20364.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   2.6e-266  869.2   0.8   2.9e-266  869.0   0.8    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS05800  HSERO_RS05800 glucarate dehydrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS05800  HSERO_RS05800 glucarate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  869.0   0.8  2.9e-266  2.9e-266       3     441 .]      17     455 .]      15     455 .] 1.00

  Alignments for each domain:
  == domain 1  score: 869.0 bits;  conditional E-value: 2.9e-266
                                  TIGR03247   3 tpvvtelrvvpvagrdsmllnlsgahapfftrnivilkdssgrtgvgevpggekirktledakalvvg 70 
                                                +p+vte+rv+pvag+dsmllnlsgah+p+ftrn+vil+ds+g+tgvgevpgge ir+tleda++lvvg
  lcl|FitnessBrowser__HerbieS:HSERO_RS05800  17 APRVTEMRVIPVAGHDSMLLNLSGAHGPYFTRNLVILTDSAGNTGVGEVPGGEGIRQTLEDARTLVVG 84 
                                                79****************************************************************** PP

                                  TIGR03247  71 ktlgeyknvlkkvrktfadrdaggrgkqtfdlrvtvhavtalesalldllgqhlevpvaallgegqqr 138
                                                +++g+ + +l++ r++fadrd+ggrg+qtfdlr+++havtale+alldllg++l+vpvaallgegqqr
  lcl|FitnessBrowser__HerbieS:HSERO_RS05800  85 QSIGNVQGILNRARTAFADRDTGGRGLQTFDLRIAIHAVTALEAALLDLLGKFLDVPVAALLGEGQQR 152
                                                ******************************************************************** PP

                                  TIGR03247 139 devevlgylffvgdrkktsldyrseeeakddwlrlrheealtpeavvrlaeaakdrygfkdfklkggv 206
                                                deve+lgylf+v dr+kt+l+y + ++a+ddw rlrhe altpeavvrlaeaa++rygf+dfklkggv
  lcl|FitnessBrowser__HerbieS:HSERO_RS05800 153 DEVEMLGYLFYVADRNKTDLPYLAAPDAQDDWTRLRHEAALTPEAVVRLAEAAYARYGFNDFKLKGGV 220
                                                ******************************************************************** PP

                                  TIGR03247 207 lrgeeeieavtalakrfpdaritldpngawsleeaialckdlkdvlayaedpvgaeegysgrevmaef 274
                                                +rgeeei+avtala+rfp+aritldpng+w l++ai+lc+d++dvlayaedp+gae+gysgrevmaef
  lcl|FitnessBrowser__HerbieS:HSERO_RS05800 221 MRGEEEIAAVTALAERFPKARITLDPNGGWLLKDAIRLCRDQHDVLAYAEDPCGAEDGYSGREVMAEF 288
                                                ******************************************************************** PP

                                  TIGR03247 275 rratglptatnmiatdwrelghalrlqavdipladphfwtlqgsvrvaqlceeygltwgshsnnhfdi 342
                                                rratgl tatnm+atdwr++gha++lq+vdipladphfwt+qgsvrvaq+c+e+gltwgshsnnhfd+
  lcl|FitnessBrowser__HerbieS:HSERO_RS05800 289 RRATGLQTATNMVATDWRQMGHAISLQSVDIPLADPHFWTMQGSVRVAQMCHEWGLTWGSHSNNHFDV 356
                                                ******************************************************************** PP

                                  TIGR03247 343 slamfthvaaaapgkvtaidthwiwqdgqrltkepleikegkikvpekpglgveldedavekahelyk 410
                                                slamfthvaaaapgk+taidthwiwqdgqrlt+epl+i +gk++vp+kpglgveld+++ve+ah++y+
  lcl|FitnessBrowser__HerbieS:HSERO_RS05800 357 SLAMFTHVAAAAPGKITAIDTHWIWQDGQRLTREPLQIVGGKVQVPTKPGLGVELDMAQVEAAHQTYR 424
                                                ******************************************************************** PP

                                  TIGR03247 411 kkglgarddavamqllipnwkfdekrpclvr 441
                                                ++glgarddavamq+lip+wkfd k+pclvr
  lcl|FitnessBrowser__HerbieS:HSERO_RS05800 425 NMGLGARDDAVAMQYLIPGWKFDPKKPCLVR 455
                                                ******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (441 nodes)
Target sequences:                          1  (455 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: 9.51
//
[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