Alignments for a candidate for rhaB in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for rhaB in Escherichia coli BW25113

Align L-Rhamnulokinase; RhaB; RhuK; ATP:L-rhamnulose phosphotransferase; L-rhamnulose 1-kinase; Rhamnulose kinase; EC 2.7.1.5 (characterized)
to candidate 17944 b3904 rhamnulokinase (NCBI)

Query= SwissProt::P32171
         (489 letters)



>FitnessBrowser__Keio:17944
          Length = 489

 Score =  992 bits (2564), Expect = 0.0
 Identities = 489/489 (100%), Positives = 489/489 (100%)

Query: 1   MTFRNCVAVDLGASSGRVMLARYERECRSLTLREIHRFNNGLHSQNGYVTWDVDSLESAI 60
           MTFRNCVAVDLGASSGRVMLARYERECRSLTLREIHRFNNGLHSQNGYVTWDVDSLESAI
Sbjct: 1   MTFRNCVAVDLGASSGRVMLARYERECRSLTLREIHRFNNGLHSQNGYVTWDVDSLESAI 60

Query: 61  RLGLNKVCEEGIRIDSIGIDTWGVDFVLLDQQGQRVGLPVAYRDSRTNGLMAQAQQQLGK 120
           RLGLNKVCEEGIRIDSIGIDTWGVDFVLLDQQGQRVGLPVAYRDSRTNGLMAQAQQQLGK
Sbjct: 61  RLGLNKVCEEGIRIDSIGIDTWGVDFVLLDQQGQRVGLPVAYRDSRTNGLMAQAQQQLGK 120

Query: 121 RDIYQRSGIQFLPFNTLYQLRALTEQQPELIPHIAHALLMPDYFSYRLTGKMNWEYTNAT 180
           RDIYQRSGIQFLPFNTLYQLRALTEQQPELIPHIAHALLMPDYFSYRLTGKMNWEYTNAT
Sbjct: 121 RDIYQRSGIQFLPFNTLYQLRALTEQQPELIPHIAHALLMPDYFSYRLTGKMNWEYTNAT 180

Query: 181 TTQLVNINSDDWDESLLAWSGANKAWFGRPTHPGNVIGHWICPQGNEIPVVAVASHDTAS 240
           TTQLVNINSDDWDESLLAWSGANKAWFGRPTHPGNVIGHWICPQGNEIPVVAVASHDTAS
Sbjct: 181 TTQLVNINSDDWDESLLAWSGANKAWFGRPTHPGNVIGHWICPQGNEIPVVAVASHDTAS 240

Query: 241 AVIASPLNGSRAAYLSSGTWSLMGFESQTPFTNDTALAANITNEGGAEGRYRVLKNIMGL 300
           AVIASPLNGSRAAYLSSGTWSLMGFESQTPFTNDTALAANITNEGGAEGRYRVLKNIMGL
Sbjct: 241 AVIASPLNGSRAAYLSSGTWSLMGFESQTPFTNDTALAANITNEGGAEGRYRVLKNIMGL 300

Query: 301 WLLQRVLQEQQINDLPALISATQALPACRFIINPNDDRFINPETMCSEIQAACRETAQPI 360
           WLLQRVLQEQQINDLPALISATQALPACRFIINPNDDRFINPETMCSEIQAACRETAQPI
Sbjct: 301 WLLQRVLQEQQINDLPALISATQALPACRFIINPNDDRFINPETMCSEIQAACRETAQPI 360

Query: 361 PESDAELARCIFDSLALLYADVLHELAQLRGEDFSQLHIVGGGCQNTLLNQLCADACGIR 420
           PESDAELARCIFDSLALLYADVLHELAQLRGEDFSQLHIVGGGCQNTLLNQLCADACGIR
Sbjct: 361 PESDAELARCIFDSLALLYADVLHELAQLRGEDFSQLHIVGGGCQNTLLNQLCADACGIR 420

Query: 421 VIAGPVEASTLGNIGIQLMTLDELNNVDDFRQVVSTTANLTTFTPNPDSEIAHYVAQIHS 480
           VIAGPVEASTLGNIGIQLMTLDELNNVDDFRQVVSTTANLTTFTPNPDSEIAHYVAQIHS
Sbjct: 421 VIAGPVEASTLGNIGIQLMTLDELNNVDDFRQVVSTTANLTTFTPNPDSEIAHYVAQIHS 480

Query: 481 TRQTKELCA 489
           TRQTKELCA
Sbjct: 481 TRQTKELCA 489


Lambda     K      H
   0.320    0.134    0.408 

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: 979
Number of extensions: 19
Number of successful extensions: 1
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: 489
Length of database: 489
Length adjustment: 34
Effective length of query: 455
Effective length of database: 455
Effective search space:   207025
Effective search space used:   207025
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 17944 b3904 (rhamnulokinase (NCBI))
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.18735.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.2e-248  809.6   0.0   3.6e-248  809.4   0.0    1.0  1  lcl|FitnessBrowser__Keio:17944  b3904 rhamnulokinase (NCBI)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17944  b3904 rhamnulokinase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  809.4   0.0  3.6e-248  3.6e-248       1     454 []       7     460 ..       7     460 .. 1.00

  Alignments for each domain:
  == domain 1  score: 809.4 bits;  conditional E-value: 3.6e-248
                       TIGR02627   1 vavdlGassGrvilaklenetkkltleeihrfknklvsqdgyevWdidaleqeillGlkkvkeeGialdslGidtWgvd 79 
                                     vavdlGassGrv+la++e+e+++ltl+eihrf+n+l+sq+gy +Wd+d+le++i+lGl+kv+eeGi++ds+GidtWgvd
  lcl|FitnessBrowser__Keio:17944   7 VAVDLGASSGRVMLARYERECRSLTLREIHRFNNGLHSQNGYVTWDVDSLESAIRLGLNKVCEEGIRIDSIGIDTWGVD 85 
                                     8****************************************************************************** PP

                       TIGR02627  80 yvlldkngervgdpvsyrdkrtdgvmakvqselgkeaiykktGiqflkfntlyqlkalkeenpdllekvekllliPdyl 158
                                     +vlld++g+rvg pv+yrd+rt+g+ma++q++lgk++iy+++Giqfl+fntlyql+al+e++p+l+ +++++ll+Pdy+
  lcl|FitnessBrowser__Keio:17944  86 FVLLDQQGQRVGLPVAYRDSRTNGLMAQAQQQLGKRDIYQRSGIQFLPFNTLYQLRALTEQQPELIPHIAHALLMPDYF 164
                                     ******************************************************************************* PP

                       TIGR02627 159 nyrltGklvaeytnasttqllnieekkwdkdlleylgvdaewfakitkpgsviGlleeldveevpvvavathdtasavv 237
                                     +yrltGk+++eytna+ttql+ni++++wd++ll+++g++++wf+++t+pg+viG++ +++++e+pvvava+hdtasav+
  lcl|FitnessBrowser__Keio:17944 165 SYRLTGKMNWEYTNATTTQLVNINSDDWDESLLAWSGANKAWFGRPTHPGNVIGHWICPQGNEIPVVAVASHDTASAVI 243
                                     ******************************************************************************* PP

                       TIGR02627 238 aaPledenaaylssGtWsliGlesetPitnekalkanitnegGadgryrvlknimGlWllqrvarerdikdlaelieea 316
                                     a+Pl++++aaylssGtWsl+G+es+tP+tn++al+anitnegGa+gryrvlknimGlWllqrv++e++i+dl++li+++
  lcl|FitnessBrowser__Keio:17944 244 ASPLNGSRAAYLSSGTWSLMGFESQTPFTNDTALAANITNEGGAEGRYRVLKNIMGLWLLQRVLQEQQINDLPALISAT 322
                                     ******************************************************************************* PP

                       TIGR02627 317 kaepafkslinvnddrfinPenmveeikaycretnqavPesaaelarcifdslallyrqvleelaelrgkdisklyivG 395
                                     +a pa++++in+nddrfinPe+m++ei+a+cret+q++Pes+aelarcifdslally++vl+ela+lrg+d+s+l+ivG
  lcl|FitnessBrowser__Keio:17944 323 QALPACRFIINPNDDRFINPETMCSEIQAACRETAQPIPESDAELARCIFDSLALLYADVLHELAQLRGEDFSQLHIVG 401
                                     ******************************************************************************* PP

                       TIGR02627 396 GGsqnallnqliadlcgieviaGpveasalGnlgvqlialdeiedvaefrkivkksfel 454
                                     GG+qn+llnql+ad+cgi+viaGpveas+lGn+g+ql++lde+++v++fr++v+++++l
  lcl|FitnessBrowser__Keio:17944 402 GGCQNTLLNQLCADACGIRVIAGPVEASTLGNIGIQLMTLDELNNVDDFRQVVSTTANL 460
                                     ******************************************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (454 nodes)
Target sequences:                          1  (489 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.50
//
[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
the source code
instructions for running GapMind on your computer

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