Alignments for a candidate for uxuA in Escherichia coli BW25113

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.28639.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.65
//
[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