Alignments for a candidate for gudD in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for gudD in Klebsiella michiganensis M5al

Align glucarate dehydratase; EC 4.2.1.40 (characterized)
to candidate BWI76_RS22825 BWI76_RS22825 glucarate dehydratase

Query= CharProtDB::CH_024866
         (446 letters)



>FitnessBrowser__Koxy:BWI76_RS22825
          Length = 446

 Score =  891 bits (2303), Expect = 0.0
 Identities = 432/446 (96%), Positives = 441/446 (98%)

Query: 1   MSSQFTTPVVTEMQVIPVAGHDSMLMNLSGAHAPFFTRNIVIIKDNSGHTGVGEIPGGEK 60
           MS+QF+TPVV+ MQVIPVAGHDSMLMNLSGAHAPFFTRNIV+IKDNSGHTGVGEIPGGEK
Sbjct: 1   MSAQFSTPVVSSMQVIPVAGHDSMLMNLSGAHAPFFTRNIVVIKDNSGHTGVGEIPGGEK 60

Query: 61  IRKTLEDAIPLVVGKTLGEYKNVLTLVRNTFADRDAGGRGLQTFDLRTTIHVVTGIEAAM 120
           IRKTLEDAIPLVVGKTLGEYKNVLT VRNTFADRDAGGRGLQTFDLRTTIHVVTGIEAAM
Sbjct: 61  IRKTLEDAIPLVVGKTLGEYKNVLTAVRNTFADRDAGGRGLQTFDLRTTIHVVTGIEAAM 120

Query: 121 LDLLGQHLGVNVASLLGDGQQRSEVEMLGYLFFVGNRKATPLPYQSQPDDSCDWYRLRHE 180
           LDLLGQHLGVNVASLLGDGQQRSEVEMLGYLFFVGNRKATPLPYQSQPDD CDWYRLRH+
Sbjct: 121 LDLLGQHLGVNVASLLGDGQQRSEVEMLGYLFFVGNRKATPLPYQSQPDDKCDWYRLRHD 180

Query: 181 EAMTPDAVVRLAEAAYEKYGFNDFKLKGGVLAGEEEAESIVALAQRFPQARITLDPNGAW 240
           EAMTPDAVVRLAEAAYEKYGFNDFKLKGGVLAGEEEAESIVALA+RFPQAR+TLDPNGAW
Sbjct: 181 EAMTPDAVVRLAEAAYEKYGFNDFKLKGGVLAGEEEAESIVALAKRFPQARVTLDPNGAW 240

Query: 241 SLNEAIKIGKYLKGSLAYAEDPCGAEQGFSGREVMAEFRRATGLPTATNMIATDWRQMGH 300
           SLNEAIKIGKYLKGSLAYAEDPCGAEQGFSGREVMAEFRRATGLPTATNMIATDWRQMGH
Sbjct: 241 SLNEAIKIGKYLKGSLAYAEDPCGAEQGFSGREVMAEFRRATGLPTATNMIATDWRQMGH 300

Query: 301 TLSLQSVDIPLADPHFWTMQGSVRVAQMCHEFGLTWGSHSNNHFDISLAMFTHVAAAAPG 360
           TLSLQSVDIPLADPHFWTMQGSVRVAQMCHEFGLTWGSHSNNHFDISLAMFTHVAAAAPG
Sbjct: 301 TLSLQSVDIPLADPHFWTMQGSVRVAQMCHEFGLTWGSHSNNHFDISLAMFTHVAAAAPG 360

Query: 361 KITAIDTHWIWQEGNQRLTKEPFEIKGGLVQVPEKPGLGVEIDMDQVMKAHELYQKHGLG 420
           KITAIDTHWIWQEGNQRLTKEPFEIKGG+VQVP KPGLGVE+DMDQVMKAHELYQKHGLG
Sbjct: 361 KITAIDTHWIWQEGNQRLTKEPFEIKGGMVQVPAKPGLGVELDMDQVMKAHELYQKHGLG 420

Query: 421 ARDDAMGMQYLIPGWTFDNKRPCMVR 446
           ARDDAMGMQYLIP WTFDNKRPCMVR
Sbjct: 421 ARDDAMGMQYLIPNWTFDNKRPCMVR 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: 787
Number of extensions: 14
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 BWI76_RS22825 BWI76_RS22825 (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.12668.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   8.9e-275  897.1   0.1     1e-274  896.9   0.1    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS22825  BWI76_RS22825 glucarate dehydrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS22825  BWI76_RS22825 glucarate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  896.9   0.1    1e-274    1e-274       2     441 .]       6     446 .]       5     446 .] 1.00

  Alignments for each domain:
  == domain 1  score: 896.9 bits;  conditional E-value: 1e-274
                               TIGR03247   2 atpvvtelrvvpvagrdsmllnlsgahapfftrnivilkdssgrtgvgevpggekirktledakalvvgkt 72 
                                             +tpvv++++v+pvag+dsml+nlsgahapfftrniv++kd+sg+tgvge+pggekirktleda +lvvgkt
  lcl|FitnessBrowser__Koxy:BWI76_RS22825   6 STPVVSSMQVIPVAGHDSMLMNLSGAHAPFFTRNIVVIKDNSGHTGVGEIPGGEKIRKTLEDAIPLVVGKT 76 
                                             79********************************************************************* PP

                               TIGR03247  73 lgeyknvlkkvrktfadrdaggrgkqtfdlrvtvhavtalesalldllgqhlevpvaallgegqqrdevev 143
                                             lgeyknvl++vr+tfadrdaggrg+qtfdlr+t+h+vt++e+a+ldllgqhl+v+va+llg+gqqr+eve+
  lcl|FitnessBrowser__Koxy:BWI76_RS22825  77 LGEYKNVLTAVRNTFADRDAGGRGLQTFDLRTTIHVVTGIEAAMLDLLGQHLGVNVASLLGDGQQRSEVEM 147
                                             *********************************************************************** PP

                               TIGR03247 144 lgylffvgdrkktsldyrseeeakddwlrlrheealtpeavvrlaeaakdrygfkdfklkggvlrgeeeie 214
                                             lgylffvg+rk t l+y+s++++k+dw+rlrh+ea+tp+avvrlaeaa+++ygf+dfklkggvl+geee+e
  lcl|FitnessBrowser__Koxy:BWI76_RS22825 148 LGYLFFVGNRKATPLPYQSQPDDKCDWYRLRHDEAMTPDAVVRLAEAAYEKYGFNDFKLKGGVLAGEEEAE 218
                                             *********************************************************************** PP

                               TIGR03247 215 avtalakrfpdaritldpngawsleeaialckdlkdvlayaedpvgaeegysgrevmaefrratglptatn 285
                                             +++alakrfp+ar+tldpngawsl+eai+++k+lk+ layaedp+gae+g+sgrevmaefrratglptatn
  lcl|FitnessBrowser__Koxy:BWI76_RS22825 219 SIVALAKRFPQARVTLDPNGAWSLNEAIKIGKYLKGSLAYAEDPCGAEQGFSGREVMAEFRRATGLPTATN 289
                                             *********************************************************************** PP

                               TIGR03247 286 miatdwrelghalrlqavdipladphfwtlqgsvrvaqlceeygltwgshsnnhfdislamfthvaaaapg 356
                                             miatdwr++gh+l+lq+vdipladphfwt+qgsvrvaq+c+e+gltwgshsnnhfdislamfthvaaaapg
  lcl|FitnessBrowser__Koxy:BWI76_RS22825 290 MIATDWRQMGHTLSLQSVDIPLADPHFWTMQGSVRVAQMCHEFGLTWGSHSNNHFDISLAMFTHVAAAAPG 360
                                             *********************************************************************** PP

                               TIGR03247 357 kvtaidthwiwqdg.qrltkepleikegkikvpekpglgveldedavekahelykkkglgarddavamqll 426
                                             k+taidthwiwq+g qrltkep+eik+g ++vp+kpglgveld+d+v+kahely+k+glgardda++mq+l
  lcl|FitnessBrowser__Koxy:BWI76_RS22825 361 KITAIDTHWIWQEGnQRLTKEPFEIKGGMVQVPAKPGLGVELDMDQVMKAHELYQKHGLGARDDAMGMQYL 431
                                             **************9******************************************************** PP

                               TIGR03247 427 ipnwkfdekrpclvr 441
                                             ipnw+fd+krpc+vr
  lcl|FitnessBrowser__Koxy:BWI76_RS22825 432 IPNWTFDNKRPCMVR 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.08
//
[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