Alignments for a candidate for rbsK in Weissella oryzae SG25

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsK in Weissella oryzae SG25

Align Ribokinase; RK; EC 2.7.1.15 (characterized)
to candidate WP_027698937.1 TT13_RS04745 ribokinase

Query= SwissProt::A0A0H2WZY4
         (304 letters)



>NCBI__GCF_000691805.2:WP_027698937.1
          Length = 311

 Score =  273 bits (699), Expect = 3e-78
 Identities = 151/309 (48%), Positives = 203/309 (65%), Gaps = 8/309 (2%)

Query: 1   MTNKVVILGSTNVDQFLTVERYAQPGETLHVEEAQKAFGGGKGANQAIATARMQADTTFI 60
           M N + +LGSTN+D+ + V R+   GET+H         GGKG NQ +A AR    T  I
Sbjct: 1   MANVITVLGSTNIDKVVAVPRFGNSGETIHTPNHLVEAMGGKGLNQGVAVARSGVKTNMI 60

Query: 61  TKIGTDGVADFILEDFKVAHIDTSYIIKTAEAKTGQAFITVNAE-GQNTIYVYGGANMTM 119
           TK+G +     I ++  VA++ T +++++A  +TGQA+ITV+AE G N IY+YGGAN  M
Sbjct: 61  TKVGQEFD---IAKNMNVANLMTDHVMRSATEETGQAYITVSAETGDNLIYIYGGANADM 117

Query: 120 TPEDVINAKDAIINADFVVAQLEVPIPAIISAFEIAKAHGVTTVLNPAPAK---ALPNEL 176
           T  DV     AI  ++FV+AQLE  +  +I AF+IA  +GV T+LNPAP      LP EL
Sbjct: 118 TAADVREHTSAIAESEFVIAQLETSMETVIEAFKIAHENGVKTILNPAPMPEVGGLPAEL 177

Query: 177 LSLIDIIVPNETEAELLSGIKVTNEQSMKDNANYFLSIGIKTVLITLGKQGTYFATKNQS 236
           L+L DII PNE E  LL+ I++T+E SM +NA Y+   G+ TV+IT+G +G +F  KN  
Sbjct: 178 LALTDIIAPNEHETFLLTEIEITDEHSMIENAQYYFERGVDTVIITVGSEGAFFMRKNGD 237

Query: 237 QHI-EAYKVNAIDTTAAGDTFIGAFVSRLNKSQDNLADAIDFGNKASSLTVQKHGAQASI 295
           + I  A+K NA+DTTAAGDTFIGA  +RLN + DNLA+A+ +G  ASSLTV + GAQ SI
Sbjct: 238 EGIVPAFKTNAVDTTAAGDTFIGATSTRLNPALDNLAEAMRYGAAASSLTVSRAGAQPSI 297

Query: 296 PLLEEVNQV 304
           PL  EV  V
Sbjct: 298 PLEAEVLSV 306


Lambda     K      H
   0.314    0.130    0.352 

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: 298
Number of extensions: 20
Number of successful extensions: 5
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: 304
Length of database: 311
Length adjustment: 27
Effective length of query: 277
Effective length of database: 284
Effective search space:    78668
Effective search space used:    78668
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: 42 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate WP_027698937.1 TT13_RS04745 (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.1419201.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.8e-96  308.3   8.3    3.2e-96  308.1   8.3    1.0  1  NCBI__GCF_000691805.2:WP_027698937.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000691805.2:WP_027698937.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.1   8.3   3.2e-96   3.2e-96       1     296 [.       5     303 ..       5     305 .. 0.96

  Alignments for each domain:
  == domain 1  score: 308.1 bits;  conditional E-value: 3.2e-96
                             TIGR02152   1 ivvvGSinvDlvlrvkrlpkpGetvkaeefki.aaGGKGANQAvaaarlgaevsmigkvGkDefgeellenlk 72 
                                           i+v+GS+n+D v+ v+r+ + Get+++ ++ + a+GGKG NQ va+ar g +++mi+kvG+     ++ +n++
  NCBI__GCF_000691805.2:WP_027698937.1   5 ITVLGSTNIDKVVAVPRFGNSGETIHTPNHLVeAMGGKGLNQGVAVARSGVKTNMITKVGQEF---DIAKNMN 74 
                                           89*************************97655169*************************974...79999** PP

                             TIGR02152  73 kegidteyvkkvkktstGvAlilvd.eegeNsIvvvaGaneeltpedvkaaeekikesdlvllQlEipletve 144
                                             ++ t++v ++++++tG+A+i+v+ e+g+N I+++ Gan+++t++dv++++++i+es++v++QlE+++etv+
  NCBI__GCF_000691805.2:WP_027698937.1  75 VANLMTDHVMRSATEETGQAYITVSaETGDNLIYIYGGANADMTAADVREHTSAIAESEFVIAQLETSMETVI 147
                                           ************************73689******************************************** PP

                             TIGR02152 145 ealkiakkagvkvllnPAPaekk..ldeellslvdiivpNetEaeiLtgievedledaekaaekllekgvkav 215
                                           ea+kia+++gvk++lnPAP  +   l++ell+l+dii pNe+E+ +Lt+ie++d++++ ++a+++ e+gv++v
  NCBI__GCF_000691805.2:WP_027698937.1 148 EAFKIAHENGVKTILNPAPMPEVggLPAELLALTDIIAPNEHETFLLTEIEITDEHSMIENAQYYFERGVDTV 220
                                           ******************986533389********************************************** PP

                             TIGR02152 216 iitlGskGallvskd.ekklipalkvkavDttaAGDtFigalavaLaeg.ksledavrfanaaaalsVtrkGa 286
                                           iit+Gs+Ga++++k+ ++ ++pa+k +avDttaAGDtFiga ++ L+   ++l++a+r+++aa++l+V r+Ga
  NCBI__GCF_000691805.2:WP_027698937.1 221 IITVGSEGAFFMRKNgDEGIVPAFKTNAVDTTAAGDTFIGATSTRLNPAlDNLAEAMRYGAAASSLTVSRAGA 293
                                           **************99999*****************************999********************** PP

                             TIGR02152 287 qssiPtkeev 296
                                           q+siP ++ev
  NCBI__GCF_000691805.2:WP_027698937.1 294 QPSIPLEAEV 303
                                           *******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (311 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 17.22
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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