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

GapMind for catabolism of small carbon sources

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

Align Rhamnulokinase (EC 2.7.1.5) (characterized)
to candidate 353289 BT3763 rhamnulose kinase/L-fuculose kinase (NCBI ptt file)

Query= reanno::Koxy:BWI76_RS00680
         (488 letters)



>lcl|FitnessBrowser__Btheta:353289 BT3763 rhamnulose
           kinase/L-fuculose kinase (NCBI ptt file)
          Length = 485

 Score =  365 bits (937), Expect = e-105
 Identities = 210/464 (45%), Positives = 275/464 (59%), Gaps = 9/464 (1%)

Query: 8   AVDLGASSGRVMLASYQPGQQTLALREIHRFTNSLQKVDGFDCWDLDSLEGEIRRGLEKV 67
           AVDLGA+SGR +L S+  G   L L EI+RF N L +V G   WD+ +L   I  GL+ V
Sbjct: 7   AVDLGATSGRTILGSFIEGG--LNLEEINRFPNHLIEVGGHFYWDIYALYRHIIDGLKLV 64

Query: 68  CEQGILIDSIGIDTWGVDYVLLDKRGQRVGLPVSYRDSRTQGLMRHAEAQLGRAEIYRRS 127
             +G  I SIGIDTWGVD+VLL K G  +  P +YRD  T G      +++ R+E+Y ++
Sbjct: 65  AHRGESIASIGIDTWGVDFVLLGKDGNLLRQPYAYRDPHTVGAPEAFFSRISRSEVYGKT 124

Query: 128 GIQFLPFNTLYQLRALVEQQPELVSQAAHALLIPDYFSFRLTGNMNWEYTNATTTQLVNI 187
           GIQ + FN+L+QL  L       +  A   L +PD  S+ LTG M  EYT A+T QLVN 
Sbjct: 125 GIQVMNFNSLFQLDTLRRNHDSALEAADKVLFMPDALSYMLTGKMVTEYTIASTAQLVNA 184

Query: 188 NSDSWDEDLLNWSGAPREWFGTPTHPGNVIG------HWICPQGNHIPVVAVASHDTASA 241
           ++   + +LL   G   E FG    PG  IG        I   G  IPV+AVA HDT SA
Sbjct: 185 HTQRLEPELLKAVGLQEENFGRFVFPGEKIGTLTEEVQKITGLGA-IPVIAVAGHDTGSA 243

Query: 242 VIASPLASKNAAYLSSGTWSLMGFESKIPCTSDAALRANITNEGGAEGRYRVLKNIMGLW 301
           V A P   +N AYLSSGTWSLMG E+  P  +      N TNEGG EG  R+LKNI G+W
Sbjct: 244 VAAVPALDRNFAYLSSGTWSLMGVETDAPVITAETEALNFTNEGGVEGTIRLLKNICGMW 303

Query: 302 LLQRVLREQNVSDLPALIARTAALPACRFVIDCNDDRFINPDDMSAEIQAACRESGQPVP 361
           LL+R       +  P LI    +    R +I+ +DD F NP DM   I+  CR +GQPVP
Sbjct: 304 LLERCRLNWGDTSYPELITEADSCEPFRSLINPDDDCFANPADMEQAIREYCRTTGQPVP 363

Query: 362 DTDAELARCIFDSLALLYTRVLNELAALRGQPFSQLHIVGGGCQNELLNQLCADACGITV 421
           +   ++ RCIF+SLAL Y +VL  L AL  +P   LH++GGG +N+LLNQ  A+A GI V
Sbjct: 364 EQRGQIVRCIFESLALRYRQVLENLRALSPRPIETLHVIGGGSRNDLLNQFTANAIGIPV 423

Query: 422 VAGPVEASTLGNIGIQLMTLDELNNVDEFRQVVRQNYALTTFTP 465
           VAGP EA+ +GN+ IQ MT+ E  +V   RQ++ ++  L T+ P
Sbjct: 424 VAGPSEATAIGNVMIQAMTVGEATDVAGMRQLISRSIPLKTYHP 467


Lambda     K      H
   0.320    0.135    0.413 

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: 596
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: 488
Length of database: 485
Length adjustment: 34
Effective length of query: 454
Effective length of database: 451
Effective search space:   204754
Effective search space used:   204754
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: 52 (24.6 bits)

Align candidate 353289 BT3763 (rhamnulose kinase/L-fuculose kinase (NCBI ptt file))
to HMM TIGR02627 (rhaB: rhamnulokinase (EC 2.7.1.5))

# 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/TIGR02627.hmm
# target sequence database:        /tmp/gapView.2652.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02627  [M=454]
Accession:   TIGR02627
Description: rhamnulo_kin: rhamnulokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.2e-169  550.7   0.0   1.3e-169  550.5   0.0    1.0  1  lcl|FitnessBrowser__Btheta:353289  BT3763 rhamnulose kinase/L-fucul


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:353289  BT3763 rhamnulose kinase/L-fuculose kinase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  550.5   0.0  1.3e-169  1.3e-169       2     454 .]       7     462 ..       6     462 .. 0.99

  Alignments for each domain:
  == domain 1  score: 550.5 bits;  conditional E-value: 1.3e-169
                          TIGR02627   2 avdlGassGrvilaklenetkkltleeihrfknklvsqdgyevWdidaleqeillGlkkvkeeGialdslGidtWg 77 
                                        avdlGa+sGr il+++ ++   l+leei rf n+l++  g++ Wdi al+++i+ Glk v ++G ++ s+GidtWg
  lcl|FitnessBrowser__Btheta:353289   7 AVDLGATSGRTILGSFIEG--GLNLEEINRFPNHLIEVGGHFYWDIYALYRHIIDGLKLVAHRGESIASIGIDTWG 80 
                                        9*****************9..9****************************************************** PP

                          TIGR02627  78 vdyvlldkngervgdpvsyrdkrtdgvmakvqselgkeaiykktGiqflkfntlyqlkalkeenpdllekveklll 153
                                        vd+vll+k+g+ + +p++yrd  t g+ ++ +s++++ ++y ktGiq ++fn l+ql +l++++   le ++k+l+
  lcl|FitnessBrowser__Btheta:353289  81 VDFVLLGKDGNLLRQPYAYRDPHTVGAPEAFFSRISRSEVYGKTGIQVMNFNSLFQLDTLRRNHDSALEAADKVLF 156
                                        **************************************************************************** PP

                          TIGR02627 154 iPdylnyrltGklvaeytnasttqllnieekkwdkdlleylgvdaewfakitkpgsviG.....lleeldveevpv 224
                                        +Pd l+y+ltGk+v+eyt ast+ql+n+++++ + +ll+ +g+++e f++   pg++iG     +++ ++   +pv
  lcl|FitnessBrowser__Btheta:353289 157 MPDALSYMLTGKMVTEYTIASTAQLVNAHTQRLEPELLKAVGLQEENFGRFVFPGEKIGtlteeVQKITGLGAIPV 232
                                        ***********************************************************88777677778889*** PP

                          TIGR02627 225 vavathdtasavvaaPledenaaylssGtWsliGlesetPitnekalkanitnegGadgryrvlknimGlWllqrv 300
                                        +ava hdt+sav a+P+ d+n aylssGtWsl+G+e+++P+ + ++ + n+tnegG++g+ r+lkni G+Wll+r 
  lcl|FitnessBrowser__Btheta:353289 233 IAVAGHDTGSAVAAVPALDRNFAYLSSGTWSLMGVETDAPVITAETEALNFTNEGGVEGTIRLLKNICGMWLLERC 308
                                        **************************************************************************** PP

                          TIGR02627 301 arerdikdlaelieeakaepafkslinvnddrfinPenmveeikaycretnqavPesaaelarcifdslallyrqv 376
                                          +   ++ +eli+ea++   f+slin++dd+f nP +m ++i++ycr t+q+vPe  +++ rcif+slal yrqv
  lcl|FitnessBrowser__Btheta:353289 309 RLNWGDTSYPELITEADSCEPFRSLINPDDDCFANPADMEQAIREYCRTTGQPVPEQRGQIVRCIFESLALRYRQV 384
                                        **************************************************************************** PP

                          TIGR02627 377 leelaelrgkdisklyivGGGsqnallnqliadlcgieviaGpveasalGnlgvqlialdeiedvaefrkivkksf 452
                                        le+l  l  ++i++l+++GGGs+n+llnq++a++ gi v+aGp+ea+a+Gn+++q ++++e +dva +r+++++s+
  lcl|FitnessBrowser__Btheta:353289 385 LENLRALSPRPIETLHVIGGGSRNDLLNQFTANAIGIPVVAGPSEATAIGNVMIQAMTVGEATDVAGMRQLISRSI 460
                                        *************************************************************************998 PP

                          TIGR02627 453 el 454
                                        +l
  lcl|FitnessBrowser__Btheta:353289 461 PL 462
                                        86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (454 nodes)
Target sequences:                          1  (485 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: 00:00:00.02
# Mc/sec: 8.09
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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