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 350960 BT1432 mannonate dehydratase (NCBI ptt file)

Query= BRENDA::P24215
         (394 letters)



>FitnessBrowser__Btheta:350960
          Length = 389

 Score =  520 bits (1340), Expect = e-152
 Identities = 245/389 (62%), Positives = 309/389 (79%), Gaps = 6/389 (1%)

Query: 2   EQTWRWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWSV 61
           EQTWRWYGPNDPVSL D++QAGATG+V ALHHIPNGEVW+VEEI+KRK +IE+ GL WSV
Sbjct: 5   EQTWRWYGPNDPVSLWDIKQAGATGIVNALHHIPNGEVWTVEEIMKRKQMIEEVGLTWSV 64

Query: 62  VESVPIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLPD 121
           VESVP+HE IKT TG Y ++I NY++++RNLA+CG+  V YNFMPVLDWTRTDL Y +PD
Sbjct: 65  VESVPVHEHIKTQTGEYLKYIENYKESIRNLAKCGVMVVTYNFMPVLDWTRTDLAYTMPD 124

Query: 122 GSKALRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAGL 181
           GSKALRF++  F AF++ ILKRP AE DYT EEIA+A  RF  MS++DK  L RN+IAGL
Sbjct: 125 GSKALRFEKAAFLAFDLFILKRPNAEKDYTPEEIAKAKARFEQMSEDDKKLLVRNMIAGL 184

Query: 182 PGAEEGYTLDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVHPDDPPRPI 241
           PG+EE +T++QF++ L+ Y DID  KLR N   FLK I PVA+EVGV++ +HPDDPP  I
Sbjct: 185 PGSEESFTVEQFQEALDRYNDIDAEKLRSNLIFFLKEIAPVADEVGVKLVIHPDDPPYTI 244

Query: 242 LGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLRS 301
           LGLPRI+ST ED + +++ V + +NG  +CTGS+GVRADNDL  M+++FG R+ F HLRS
Sbjct: 245 LGLPRILSTEEDFKKLIEAVPNESNGLCLCTGSFGVRADNDLAGMMERFGDRVNFVHLRS 304

Query: 302 TMREDNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDLK 361
           T R D    F+EA HL G+VDMY V+K+++  + RRK       I MRPDHGHQM+DDLK
Sbjct: 305 TQR-DEEGNFYEANHLEGNVDMYNVMKSLILLQQRRKCS-----IAMRPDHGHQMIDDLK 358

Query: 362 KKTNPGYSAIGRLKGLAEVRGVELAIQRA 390
           KKTNPGYS +GRL+GLAE+RG+E+ I ++
Sbjct: 359 KKTNPGYSCLGRLRGLAELRGLEMGIAKS 387


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: 539
Number of extensions: 22
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: 389
Length adjustment: 31
Effective length of query: 363
Effective length of database: 358
Effective search space:   129954
Effective search space used:   129954
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 350960 BT1432 (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.13263.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   6.2e-187  607.4   0.0   7.1e-187  607.2   0.0    1.0  1  lcl|FitnessBrowser__Btheta:350960  BT1432 mannonate dehydratase (NC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:350960  BT1432 mannonate dehydratase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  607.2   0.0  7.1e-187  7.1e-187       2     389 ..       5     386 ..       4     389 .] 0.99

  Alignments for each domain:
  == domain 1  score: 607.2 bits;  conditional E-value: 7.1e-187
                          TIGR00695   2 eqtfrwyGrndpvsledvrqaGakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvheeiklqtee 77 
                                        eqt+rwyG+ndpvsl d++qaGa+Giv alhhipnGevw veei krk++ie++Gl++svvesvpvhe+ik+qt+e
  lcl|FitnessBrowser__Btheta:350960   5 EQTWRWYGPNDPVSLWDIKQAGATGIVNALHHIPNGEVWTVEEIMKRKQMIEEVGLTWSVVESVPVHEHIKTQTGE 80 
                                        89************************************************************************** PP

                          TIGR00695  78 yekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaalelhilkrpdaekdytee 153
                                        y kyienyk+++rnla+cG+ vv ynfmpvldwtrtdlay+++dGskalrf+k+++ a++l+ilkrp+aekdyt e
  lcl|FitnessBrowser__Btheta:350960  81 YLKYIENYKESIRNLAKCGVMVVTYNFMPVLDWTRTDLAYTMPDGSKALRFEKAAFLAFDLFILKRPNAEKDYTPE 156
                                        **************************************************************************** PP

                          TIGR00695 154 elvraveeasdmseedkarltrniiaglpGaeegekldrikelleaykdideeklrenlafflkeilpvaeevGvk 229
                                        e+++a+ ++++mse+dk  l+rn+iaglpG ee  ++++++e l++y+did eklr nl fflkei pva+evGvk
  lcl|FitnessBrowser__Btheta:350960 157 EIAKAKARFEQMSEDDKKLLVRNMIAGLPGSEESFTVEQFQEALDRYNDIDAEKLRSNLIFFLKEIAPVADEVGVK 232
                                        **************************************************************************** PP

                          TIGR00695 230 maihpddpprpilGlprivstiedmkklveisdspangitlctGsyGvradndlvelakqfadriyfahlrsvkre 305
                                        + ihpddpp+ ilGlpri+st+ed+kkl+e ++  +ng+ lctGs+Gvradndl  ++++f+dr+ f hlrs++r+
  lcl|FitnessBrowser__Btheta:350960 233 LVIHPDDPPYTILGLPRILSTEEDFKKLIEAVPNESNGLCLCTGSFGVRADNDLAGMMERFGDRVNFVHLRSTQRD 308
                                        **************************************************************************** PP

                          TIGR00695 306 enpktfheaahlekdvdlyevvkavleeehrrkaeGkedlipvrpdhGrqllddlkkktnpGysaigrlkGlaelr 381
                                        e++ +f+ea hle++vd+y+v+k+++  + rrk       i +rpdhG+q++ddlkkktnpGys +grl+Glaelr
  lcl|FitnessBrowser__Btheta:350960 309 EEG-NFYEANHLEGNVDMYNVMKSLILLQQRRKCS-----IAMRPDHGHQMIDDLKKKTNPGYSCLGRLRGLAELR 378
                                        ***.**********************988888765.....68********************************** PP

                          TIGR00695 382 Glelalkk 389
                                        Gle+ + k
  lcl|FitnessBrowser__Btheta:350960 379 GLEMGIAK 386
                                        ****9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (389 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: 9.46
//
[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