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 350960 BT1432 mannonate dehydratase (NCBI ptt file)

Query= BRENDA::P24215
         (394 letters)



>lcl|FitnessBrowser__Btheta:350960 BT1432 mannonate dehydratase
           (NCBI ptt file)
          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.15464.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: 8.48
//
[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