Alignments for a candidate for rbsK in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsK in Klebsiella michiganensis M5al

Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate BWI76_RS00290 BWI76_RS00290 ribokinase

Query= reanno::Koxy:BWI76_RS00290
         (309 letters)



>FitnessBrowser__Koxy:BWI76_RS00290
          Length = 309

 Score =  598 bits (1541), Expect = e-176
 Identities = 309/309 (100%), Positives = 309/309 (100%)

Query: 1   MKTAGKLVVLGSINADHILNLDAFPTPGETVTGHHYQVAFGGKGANQAVAAGRSGANISF 60
           MKTAGKLVVLGSINADHILNLDAFPTPGETVTGHHYQVAFGGKGANQAVAAGRSGANISF
Sbjct: 1   MKTAGKLVVLGSINADHILNLDAFPTPGETVTGHHYQVAFGGKGANQAVAAGRSGANISF 60

Query: 61  IACTGDDDIGERVRRQLESDNIDVAPVRAVAGESTGVALIFVNAEGENTIGIHAGANAAL 120
           IACTGDDDIGERVRRQLESDNIDVAPVRAVAGESTGVALIFVNAEGENTIGIHAGANAAL
Sbjct: 61  IACTGDDDIGERVRRQLESDNIDVAPVRAVAGESTGVALIFVNAEGENTIGIHAGANAAL 120

Query: 121 CVAQVDAEKERIASAQALLMQLESPLESVLAAAKIAHQNQTSVILNPAPARELPDELLTL 180
           CVAQVDAEKERIASAQALLMQLESPLESVLAAAKIAHQNQTSVILNPAPARELPDELLTL
Sbjct: 121 CVAQVDAEKERIASAQALLMQLESPLESVLAAAKIAHQNQTSVILNPAPARELPDELLTL 180

Query: 181 VDIITPNETEAEKLTGVRVENDEDAAKAAKVLHDKGIGTVIITLGSRGVWASSEGNGRRV 240
           VDIITPNETEAEKLTGVRVENDEDAAKAAKVLHDKGIGTVIITLGSRGVWASSEGNGRRV
Sbjct: 181 VDIITPNETEAEKLTGVRVENDEDAAKAAKVLHDKGIGTVIITLGSRGVWASSEGNGRRV 240

Query: 241 PGFKVQAVDTIAAGDTFNGALVTALLEGRELAEAIRFAHAAAAIAVTRKGAQPSVPWRKE 300
           PGFKVQAVDTIAAGDTFNGALVTALLEGRELAEAIRFAHAAAAIAVTRKGAQPSVPWRKE
Sbjct: 241 PGFKVQAVDTIAAGDTFNGALVTALLEGRELAEAIRFAHAAAAIAVTRKGAQPSVPWRKE 300

Query: 301 IDEFLRQQG 309
           IDEFLRQQG
Sbjct: 301 IDEFLRQQG 309


Lambda     K      H
   0.315    0.131    0.366 

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: 485
Number of extensions: 13
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: 309
Length of database: 309
Length adjustment: 27
Effective length of query: 282
Effective length of database: 282
Effective search space:    79524
Effective search space used:    79524
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 48 (23.1 bits)

Align candidate BWI76_RS00290 BWI76_RS00290 (ribokinase)
to HMM TIGR02152 (rbsK: ribokinase (EC 2.7.1.15))

# 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/TIGR02152.hmm
# target sequence database:        /tmp/gapView.24789.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02152  [M=298]
Accession:   TIGR02152
Description: D_ribokin_bact: ribokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   4.1e-115  370.1   5.7   4.7e-115  370.0   5.7    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS00290  BWI76_RS00290 ribokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS00290  BWI76_RS00290 ribokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  370.0   5.7  4.7e-115  4.7e-115       2     297 ..       8     302 ..       7     303 .. 0.99

  Alignments for each domain:
  == domain 1  score: 370.0 bits;  conditional E-value: 4.7e-115
                               TIGR02152   2 vvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefgeellenlk 72 
                                             vv+GSin+D++l+ +++p pGetv+++++++a GGKGANQAvaa r ga++s+i++ G+D++ge+++++l+
  lcl|FitnessBrowser__Koxy:BWI76_RS00290   8 VVLGSINADHILNLDAFPTPGETVTGHHYQVAFGGKGANQAVAAGRSGANISFIACTGDDDIGERVRRQLE 78 
                                             8********************************************************************** PP

                               TIGR02152  73 kegidteyvkkvkktstGvAlilvdeegeNsIvvvaGaneeltpedvkaaeekikesdlvllQlEipletv 143
                                             +++id+  v+ v+ +stGvAli+v+ egeN+I + aGan+ l  ++v+a++e+i++++ +l+QlE+ple+v
  lcl|FitnessBrowser__Koxy:BWI76_RS00290  79 SDNIDVAPVRAVAGESTGVALIFVNAEGENTIGIHAGANAALCVAQVDAEKERIASAQALLMQLESPLESV 149
                                             *********************************************************************** PP

                               TIGR02152 144 eealkiakkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgievedledaekaaekllekgvka 214
                                              +a+kia+++++ v+lnPAPa++ l++ell+lvdii+pNetEae Ltg++ve+ eda kaa+ l++kg+ +
  lcl|FitnessBrowser__Koxy:BWI76_RS00290 150 LAAAKIAHQNQTSVILNPAPARE-LPDELLTLVDIITPNETEAEKLTGVRVENDEDAAKAAKVLHDKGIGT 219
                                             *********************65.99********************************************* PP

                               TIGR02152 215 viitlGskGallvskdekklipalkvkavDttaAGDtFigalavaLaegksledavrfanaaaalsVtrkG 285
                                             viitlGs+G+  +s+++ + +p +kv+avDt aAGDtF+gal++aL eg++l++a+rfa+aaaa++VtrkG
  lcl|FitnessBrowser__Koxy:BWI76_RS00290 220 VIITLGSRGVWASSEGNGRRVPGFKVQAVDTIAAGDTFNGALVTALLEGRELAEAIRFAHAAAAIAVTRKG 290
                                             *********************************************************************** PP

                               TIGR02152 286 aqssiPtkeeve 297
                                             aq+s+P ++e++
  lcl|FitnessBrowser__Koxy:BWI76_RS00290 291 AQPSVPWRKEID 302
                                             **********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (309 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: 6.24
//
[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