Aligments for a candidate for uxuA in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Aligments for a candidate for uxuA in Bacteroides thetaiotaomicron VPI-5482

Align mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate 349657 BT0129 mannonate dehydratase (NCBI ptt file)

Query= BRENDA::P24215
         (394 letters)



>lcl|FitnessBrowser__Btheta:349657 BT0129 mannonate dehydratase
           (NCBI ptt file)
          Length = 395

 Score =  345 bits (884), Expect = 2e-99
 Identities = 183/390 (46%), Positives = 246/390 (63%), Gaps = 17/390 (4%)

Query: 1   MEQTWRWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWS 60
           ME+TWRW+G  D ++L  +RQ G  G+VTALH IPNGE+W++E I   K+ IE  GL WS
Sbjct: 2   MEKTWRWFGKKDKITLPMLRQIGVEGIVTALHDIPNGEIWTIEAINALKSYIESYGLRWS 61

Query: 61  VVESVPIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLP 120
           VVES+P+ E IK      EQ I NY+ +L NL +CGI+TVCYNFMPV+DW RTDL+Y+ P
Sbjct: 62  VVESLPVCEAIKYGGTEREQLIENYKVSLTNLGKCGIKTVCYNFMPVIDWIRTDLQYLCP 121

Query: 121 DGSKALRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAG 180
           DG+ +L +D+I FA F+M IL+R GAE DYTEEE+ + +E    +++++K  L   II  
Sbjct: 122 DGTSSLYYDRIRFAYFDMKILEREGAEKDYTEEELHKVSELDQVITEKEKDDLIDTIIVK 181

Query: 181 LPGAEEGYTLD-------QFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVH 233
             G   G   +        F++ L LYKDI++  LREN   FL AI+PV EE GV M VH
Sbjct: 182 TQGFVNGNIKEGDKEPVVLFKRLLTLYKDINRDILRENMCHFLSAIMPVCEEYGVNMCVH 241

Query: 234 PDDPPRPILGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPR 293
           PDDPP  +LGLPRIV+  ED+ W ++ V++  NG T C GS      ND  ++ K+F  R
Sbjct: 242 PDDPPFQVLGLPRIVTNEEDIAWFLNAVDNPHNGLTFCAGSLSAGEHNDTRELAKKFAKR 301

Query: 294 IYFTHLRSTMREDNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHG 353
            +F HLRST        F E++HL G   + ++++ I E+E+          +PMR DHG
Sbjct: 302 THFIHLRSTAAMPG-GNFIESSHLAGRGHIIDLIR-IFEKENPG--------LPMRIDHG 351

Query: 354 HQMLDDLKKKTNPGYSAIGRLKGLAEVRGV 383
             ML D  K  NPGYS  GR+  LA+V G+
Sbjct: 352 RMMLGDEDKGYNPGYSFYGRMLALAQVEGM 381


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: 462
Number of extensions: 17
Number of successful extensions: 3
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: 395
Length adjustment: 31
Effective length of query: 363
Effective length of database: 364
Effective search space:   132132
Effective search space used:   132132
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 349657 BT0129 (mannonate dehydratase (NCBI ptt file))
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.16015.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
     6e-134  433.0   0.0   7.1e-134  432.7   0.0    1.0  1  lcl|FitnessBrowser__Btheta:349657  BT0129 mannonate dehydratase (NC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:349657  BT0129 mannonate dehydratase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  432.7   0.0  7.1e-134  7.1e-134       1     389 [.       2     387 ..       2     392 .. 0.95

  Alignments for each domain:
  == domain 1  score: 432.7 bits;  conditional E-value: 7.1e-134
                          TIGR00695   1 meqtfrwyGrndpvsledvrqaGakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvheeiklqte 76 
                                        me+t+rw+G++d ++l  +rq+G++Givtalh+ipnGe+w +e i++ k++ie++Gl +svves+pv e+ik +  
  lcl|FitnessBrowser__Btheta:349657   2 MEKTWRWFGKKDKITLPMLRQIGVEGIVTALHDIPNGEIWTIEAINALKSYIESYGLRWSVVESLPVCEAIKYGGT 77 
                                        9*************************************************************************** PP

                          TIGR00695  77 eyekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaalelhilkrpdaekdyte 152
                                        e+e+ ienyk +l nl +cGik+vcynfmpv+dw rtdl+y  +dG+ +l++d+i++a ++++il+r +aekdyte
  lcl|FitnessBrowser__Btheta:349657  78 EREQLIENYKVSLTNLGKCGIKTVCYNFMPVIDWIRTDLQYLCPDGTSSLYYDRIRFAYFDMKILEREGAEKDYTE 153
                                        **************************************************************************** PP

                          TIGR00695 153 eelvraveeasdmseedkarltrniiaglpGaeeg.....ek..ldrikelleaykdideeklrenlafflkeilp 221
                                        eel +  e  + ++e++k  l   ii    G+ +g     +k  +  +k+ll +ykdi+++ lren++ fl +i+p
  lcl|FitnessBrowser__Btheta:349657 154 EELHKVSELDQVITEKEKDDLIDTIIVKTQGFVNGnikegDKepVVLFKRLLTLYKDINRDILRENMCHFLSAIMP 229
                                        **************************9998876652111132225679**************************** PP

                          TIGR00695 222 vaeevGvkmaihpddpprpilGlprivstiedmkklveisdspangitlctGsyGvradndlvelakqfadriyfa 297
                                        v ee+Gv+m +hpddpp  +lGlpriv+ +ed+ ++ + +d p ng+t+c+Gs+ +   nd  elak+fa+r +f 
  lcl|FitnessBrowser__Btheta:349657 230 VCEEYGVNMCVHPDDPPFQVLGLPRIVTNEEDIAWFLNAVDNPHNGLTFCAGSLSAGEHNDTRELAKKFAKRTHFI 305
                                        **************************************************************************** PP

                          TIGR00695 298 hlrsvkreenpktfheaahlekdvdlyevvkavleeehrrkaeGkedlipvrpdhGrqllddlkkktnpGysaigr 373
                                        hlrs+     + +f+e++hl + + + ++++      + +++ G    +p+r dhGr +l+d  k  npGys +gr
  lcl|FitnessBrowser__Btheta:349657 306 HLRSTAAMPGG-NFIESSHLAGRGHIIDLIR-----IFEKENPG----LPMRIDHGRMMLGDEDKGYNPGYSFYGR 371
                                        *******9999.***************9987.....46678899....9*************************** PP

                          TIGR00695 374 lkGlaelrGlelalkk 389
                                        ++ la+++G+ + ++ 
  lcl|FitnessBrowser__Btheta:349657 372 MLALAQVEGMMTVVDD 387
                                        *********9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (395 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 6.97
//
[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, or view the source code.

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