Alignments for a candidate for gudD in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for gudD in Escherichia coli BW25113

Align glucarate dehydratase; EC 4.2.1.40 (characterized)
to candidate 16871 b2787 (D)-glucarate dehydratase 1 (NCBI)

Query= CharProtDB::CH_024866
         (446 letters)



>FitnessBrowser__Keio:16871
          Length = 446

 Score =  910 bits (2353), Expect = 0.0
 Identities = 446/446 (100%), Positives = 446/446 (100%)

Query: 1   MSSQFTTPVVTEMQVIPVAGHDSMLMNLSGAHAPFFTRNIVIIKDNSGHTGVGEIPGGEK 60
           MSSQFTTPVVTEMQVIPVAGHDSMLMNLSGAHAPFFTRNIVIIKDNSGHTGVGEIPGGEK
Sbjct: 1   MSSQFTTPVVTEMQVIPVAGHDSMLMNLSGAHAPFFTRNIVIIKDNSGHTGVGEIPGGEK 60

Query: 61  IRKTLEDAIPLVVGKTLGEYKNVLTLVRNTFADRDAGGRGLQTFDLRTTIHVVTGIEAAM 120
           IRKTLEDAIPLVVGKTLGEYKNVLTLVRNTFADRDAGGRGLQTFDLRTTIHVVTGIEAAM
Sbjct: 61  IRKTLEDAIPLVVGKTLGEYKNVLTLVRNTFADRDAGGRGLQTFDLRTTIHVVTGIEAAM 120

Query: 121 LDLLGQHLGVNVASLLGDGQQRSEVEMLGYLFFVGNRKATPLPYQSQPDDSCDWYRLRHE 180
           LDLLGQHLGVNVASLLGDGQQRSEVEMLGYLFFVGNRKATPLPYQSQPDDSCDWYRLRHE
Sbjct: 121 LDLLGQHLGVNVASLLGDGQQRSEVEMLGYLFFVGNRKATPLPYQSQPDDSCDWYRLRHE 180

Query: 181 EAMTPDAVVRLAEAAYEKYGFNDFKLKGGVLAGEEEAESIVALAQRFPQARITLDPNGAW 240
           EAMTPDAVVRLAEAAYEKYGFNDFKLKGGVLAGEEEAESIVALAQRFPQARITLDPNGAW
Sbjct: 181 EAMTPDAVVRLAEAAYEKYGFNDFKLKGGVLAGEEEAESIVALAQRFPQARITLDPNGAW 240

Query: 241 SLNEAIKIGKYLKGSLAYAEDPCGAEQGFSGREVMAEFRRATGLPTATNMIATDWRQMGH 300
           SLNEAIKIGKYLKGSLAYAEDPCGAEQGFSGREVMAEFRRATGLPTATNMIATDWRQMGH
Sbjct: 241 SLNEAIKIGKYLKGSLAYAEDPCGAEQGFSGREVMAEFRRATGLPTATNMIATDWRQMGH 300

Query: 301 TLSLQSVDIPLADPHFWTMQGSVRVAQMCHEFGLTWGSHSNNHFDISLAMFTHVAAAAPG 360
           TLSLQSVDIPLADPHFWTMQGSVRVAQMCHEFGLTWGSHSNNHFDISLAMFTHVAAAAPG
Sbjct: 301 TLSLQSVDIPLADPHFWTMQGSVRVAQMCHEFGLTWGSHSNNHFDISLAMFTHVAAAAPG 360

Query: 361 KITAIDTHWIWQEGNQRLTKEPFEIKGGLVQVPEKPGLGVEIDMDQVMKAHELYQKHGLG 420
           KITAIDTHWIWQEGNQRLTKEPFEIKGGLVQVPEKPGLGVEIDMDQVMKAHELYQKHGLG
Sbjct: 361 KITAIDTHWIWQEGNQRLTKEPFEIKGGLVQVPEKPGLGVEIDMDQVMKAHELYQKHGLG 420

Query: 421 ARDDAMGMQYLIPGWTFDNKRPCMVR 446
           ARDDAMGMQYLIPGWTFDNKRPCMVR
Sbjct: 421 ARDDAMGMQYLIPGWTFDNKRPCMVR 446


Lambda     K      H
   0.319    0.136    0.413 

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: 794
Number of extensions: 15
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: 446
Length of database: 446
Length adjustment: 32
Effective length of query: 414
Effective length of database: 414
Effective search space:   171396
Effective search space used:   171396
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 16871 b2787 ((D)-glucarate dehydratase 1 (NCBI))
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.12587.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
     3e-275  898.7   0.0   3.4e-275  898.5   0.0    1.0  1  lcl|FitnessBrowser__Keio:16871  b2787 (D)-glucarate dehydratase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16871  b2787 (D)-glucarate dehydratase 1 (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  898.5   0.0  3.4e-275  3.4e-275       2     441 .]       6     446 .]       5     446 .] 1.00

  Alignments for each domain:
  == domain 1  score: 898.5 bits;  conditional E-value: 3.4e-275
                       TIGR03247   2 atpvvtelrvvpvagrdsmllnlsgahapfftrnivilkdssgrtgvgevpggekirktledakalvvgktlgeyknvl 80 
                                     +tpvvte++v+pvag+dsml+nlsgahapfftrnivi+kd+sg+tgvge+pggekirktleda +lvvgktlgeyknvl
  lcl|FitnessBrowser__Keio:16871   6 TTPVVTEMQVIPVAGHDSMLMNLSGAHAPFFTRNIVIIKDNSGHTGVGEIPGGEKIRKTLEDAIPLVVGKTLGEYKNVL 84 
                                     79***************************************************************************** PP

                       TIGR03247  81 kkvrktfadrdaggrgkqtfdlrvtvhavtalesalldllgqhlevpvaallgegqqrdevevlgylffvgdrkktsld 159
                                     + vr+tfadrdaggrg+qtfdlr+t+h+vt++e+a+ldllgqhl+v+va+llg+gqqr+eve+lgylffvg+rk t l+
  lcl|FitnessBrowser__Keio:16871  85 TLVRNTFADRDAGGRGLQTFDLRTTIHVVTGIEAAMLDLLGQHLGVNVASLLGDGQQRSEVEMLGYLFFVGNRKATPLP 163
                                     ******************************************************************************* PP

                       TIGR03247 160 yrseeeakddwlrlrheealtpeavvrlaeaakdrygfkdfklkggvlrgeeeieavtalakrfpdaritldpngawsl 238
                                     y+s++++++dw+rlrheea+tp+avvrlaeaa+++ygf+dfklkggvl+geee+e+++ala+rfp+aritldpngawsl
  lcl|FitnessBrowser__Keio:16871 164 YQSQPDDSCDWYRLRHEEAMTPDAVVRLAEAAYEKYGFNDFKLKGGVLAGEEEAESIVALAQRFPQARITLDPNGAWSL 242
                                     ******************************************************************************* PP

                       TIGR03247 239 eeaialckdlkdvlayaedpvgaeegysgrevmaefrratglptatnmiatdwrelghalrlqavdipladphfwtlqg 317
                                     +eai+++k+lk+ layaedp+gae+g+sgrevmaefrratglptatnmiatdwr++gh+l+lq+vdipladphfwt+qg
  lcl|FitnessBrowser__Keio:16871 243 NEAIKIGKYLKGSLAYAEDPCGAEQGFSGREVMAEFRRATGLPTATNMIATDWRQMGHTLSLQSVDIPLADPHFWTMQG 321
                                     ******************************************************************************* PP

                       TIGR03247 318 svrvaqlceeygltwgshsnnhfdislamfthvaaaapgkvtaidthwiwqdg.qrltkepleikegkikvpekpglgv 395
                                     svrvaq+c+e+gltwgshsnnhfdislamfthvaaaapgk+taidthwiwq+g qrltkep+eik+g ++vpekpglgv
  lcl|FitnessBrowser__Keio:16871 322 SVRVAQMCHEFGLTWGSHSNNHFDISLAMFTHVAAAAPGKITAIDTHWIWQEGnQRLTKEPFEIKGGLVQVPEKPGLGV 400
                                     *****************************************************9************************* PP

                       TIGR03247 396 eldedavekahelykkkglgarddavamqllipnwkfdekrpclvr 441
                                     e+d+d+v+kahely+k+glgardda++mq+lip+w+fd+krpc+vr
  lcl|FitnessBrowser__Keio:16871 401 EIDMDQVMKAHELYQKHGLGARDDAMGMQYLIPGWTFDNKRPCMVR 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: 7.57
//
[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