GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuA in Escherichia coli BW25113

Align mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate 18346 b4322 mannonate dehydratase (NCBI)

Query= BRENDA::P24215
         (394 letters)



>FitnessBrowser__Keio:18346
          Length = 394

 Score =  804 bits (2076), Expect = 0.0
 Identities = 394/394 (100%), Positives = 394/394 (100%)

Query: 1   MEQTWRWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWS 60
           MEQTWRWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWS
Sbjct: 1   MEQTWRWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWS 60

Query: 61  VVESVPIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLP 120
           VVESVPIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLP
Sbjct: 61  VVESVPIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLP 120

Query: 121 DGSKALRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAG 180
           DGSKALRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAG
Sbjct: 121 DGSKALRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAG 180

Query: 181 LPGAEEGYTLDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVHPDDPPRP 240
           LPGAEEGYTLDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVHPDDPPRP
Sbjct: 181 LPGAEEGYTLDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVHPDDPPRP 240

Query: 241 ILGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLR 300
           ILGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLR
Sbjct: 241 ILGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLR 300

Query: 301 STMREDNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDL 360
           STMREDNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDL
Sbjct: 301 STMREDNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDL 360

Query: 361 KKKTNPGYSAIGRLKGLAEVRGVELAIQRAFFSR 394
           KKKTNPGYSAIGRLKGLAEVRGVELAIQRAFFSR
Sbjct: 361 KKKTNPGYSAIGRLKGLAEVRGVELAIQRAFFSR 394


Lambda     K      H
   0.320    0.136    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: 730
Number of extensions: 23
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: 394
Length of database: 394
Length adjustment: 31
Effective length of query: 363
Effective length of database: 363
Effective search space:   131769
Effective search space used:   131769
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: 50 (23.9 bits)

Align candidate 18346 b4322 (mannonate dehydratase (NCBI))
to HMM TIGR00695 (uxuA: mannonate dehydratase (EC 4.2.1.8))

# 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/TIGR00695.hmm
# target sequence database:        /tmp/gapView.11451.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00695  [M=394]
Accession:   TIGR00695
Description: uxuA: mannonate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   8.5e-244  794.6   0.1   9.5e-244  794.5   0.1    1.0  1  lcl|FitnessBrowser__Keio:18346  b4322 mannonate dehydratase (NCB


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:18346  b4322 mannonate dehydratase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  794.5   0.1  9.5e-244  9.5e-244       1     394 []       1     394 []       1     394 [] 1.00

  Alignments for each domain:
  == domain 1  score: 794.5 bits;  conditional E-value: 9.5e-244
                       TIGR00695   1 meqtfrwyGrndpvsledvrqaGakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvheeiklqteeye 79 
                                     meqt+rwyG+ndpvsl+dvrqaGa+G+vtalhhipnGevw+veei krk++iedaGl++svvesvp+he+ik++t++ye
  lcl|FitnessBrowser__Keio:18346   1 MEQTWRWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWSVVESVPIHEDIKTHTGNYE 79 
                                     9****************************************************************************** PP

                       TIGR00695  80 kyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaalelhilkrpdaekdyteeelvra 158
                                     ++i+ny+qtlrnlaqcGi++vcynfmpvldwtrtdl+y+l+dGskalrfd+i++aa+e+hilkrp+ae+dyteee+++a
  lcl|FitnessBrowser__Keio:18346  80 QWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLPDGSKALRFDQIEFAAFEMHILKRPGAEADYTEEEIAQA 158
                                     ******************************************************************************* PP

                       TIGR00695 159 veeasdmseedkarltrniiaglpGaeegekldrikelleaykdideeklrenlafflkeilpvaeevGvkmaihpddp 237
                                     +e++++ms+edkarltrniiaglpGaeeg++ld+++++le+ykdid++klren+a+flk+i+pvaeevGv+ma+hpddp
  lcl|FitnessBrowser__Keio:18346 159 AERFATMSDEDKARLTRNIIAGLPGAEEGYTLDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVHPDDP 237
                                     ******************************************************************************* PP

                       TIGR00695 238 prpilGlprivstiedmkklveisdspangitlctGsyGvradndlvelakqfadriyfahlrsvkreenpktfheaah 316
                                     prpilGlprivstiedm+++v++++s+ang+t+ctGsyGvradndlv+++kqf++riyf+hlrs++re+npktfheaah
  lcl|FitnessBrowser__Keio:18346 238 PRPILGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLRSTMREDNPKTFHEAAH 316
                                     ******************************************************************************* PP

                       TIGR00695 317 lekdvdlyevvkavleeehrrkaeGkedlipvrpdhGrqllddlkkktnpGysaigrlkGlaelrGlelalkkvafkk 394
                                     l++dvd+yevvka++eeehrrkaeGkedlip+rpdhG+q+lddlkkktnpGysaigrlkGlae+rG+ela+++++f++
  lcl|FitnessBrowser__Keio:18346 317 LNGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDLKKKTNPGYSAIGRLKGLAEVRGVELAIQRAFFSR 394
                                     ***************************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (394 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: 7.17
//
[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:

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:

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:

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:

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