GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Btheta:349657
          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.17094.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 7.49
//
[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