Alignments for a candidate for rbsK in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsK in Shewanella oneidensis MR-1

Align ribokinase (EC 2.7.1.15) (characterized)
to candidate 199996 SO0810 ribokinase (NCBI ptt file)

Query= BRENDA::A0A0H2UL04
         (309 letters)



>FitnessBrowser__MR1:199996
          Length = 303

 Score =  277 bits (708), Expect = 3e-79
 Identities = 155/301 (51%), Positives = 200/301 (66%), Gaps = 3/301 (0%)

Query: 4   MNKLVVLGSVNADHVLQVPSFPRPGETLHGRNYQVIPGGKGANQAVAAARM---QADVGF 60
           M+ ++V+GS NADHV+     P PG+TL  R+Y++  GGKGANQAVA AR+    + V F
Sbjct: 1   MSHILVIGSANADHVMNFEYLPVPGQTLKSRSYRLEHGGKGANQAVACARLCLPDSRVDF 60

Query: 61  IACVGDDSFGINIRESFKLDGINTAGVKLQPNCPTGIAMIQVSDSGENSICISAEANAKL 120
           I  +G DS G  +R+S+  DGI   G+ L  N  TG AMI V+D+GEN+I I+A ANA L
Sbjct: 61  ICHLGQDSIGNEMRDSWLKDGIQAEGITLVDNVSTGTAMIFVADNGENAIGIAAGANAHL 120

Query: 121 TAAAIEPDLAAIRDARYLLMQLETPLDGILKAAQEAKTAKTNVILNPAPARELPDELLKC 180
           T   +E   A   +A+YLL+QLETP + +  A Q AK      +LNPAPA     + LK 
Sbjct: 121 TPLELEKHYALFANAQYLLIQLETPTETVSNALQMAKRLGITTVLNPAPAATQELDYLKW 180

Query: 181 VDLITPNETEAEVLTGITVYDDSSAQQAADALHCKGIEIVIITLGSKGVWLSQNGRGQRI 240
           VD+ITPNETEAE LTGI V  +  A+ AA  LH +GI  V+ITLGSKG ++S  G    I
Sbjct: 181 VDIITPNETEAEALTGIEVKHEEDAKLAAQWLHQQGITTVVITLGSKGAFISSPGFTGLI 240

Query: 241 PGFVVKATDTTAAGDTFNGALVTGLLQEMPLESAIKFAHAAAAISVTRFGAQTSIPTRAE 300
           P   V+A DT AAGDTFNGALV GL + M + +A+ FA+AA+AI+VTR GAQ +IP R+E
Sbjct: 241 PALTVQAIDTVAAGDTFNGALVVGLSEGMSIAAAVSFANAASAITVTREGAQRAIPYRSE 300

Query: 301 V 301
           V
Sbjct: 301 V 301


Lambda     K      H
   0.316    0.132    0.373 

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: 227
Number of extensions: 9
Number of successful extensions: 2
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: 303
Length adjustment: 27
Effective length of query: 282
Effective length of database: 276
Effective search space:    77832
Effective search space used:    77832
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 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate 199996 SO0810 (ribokinase (NCBI ptt file))
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.7634.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   4.2e-120  386.5   1.1   4.7e-120  386.4   1.1    1.0  1  lcl|FitnessBrowser__MR1:199996  SO0810 ribokinase (NCBI ptt file


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199996  SO0810 ribokinase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  386.4   1.1  4.7e-120  4.7e-120       1     297 [.       4     302 ..       4     303 .] 0.99

  Alignments for each domain:
  == domain 1  score: 386.4 bits;  conditional E-value: 4.7e-120
                       TIGR02152   1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlg...aevsmigkvGkDefgeellenlkkegi 76 
                                     i+v+GS+n+D+v+++++lp+pG+t+k++++++ +GGKGANQAva+arl+   ++v++i+++G+D++g+e+++++ k+gi
  lcl|FitnessBrowser__MR1:199996   4 ILVIGSANADHVMNFEYLPVPGQTLKSRSYRLEHGGKGANQAVACARLClpdSRVDFICHLGQDSIGNEMRDSWLKDGI 82 
                                     89************************************************999************************** PP

                       TIGR02152  77 dteyvkkvkktstGvAlilvdeegeNsIvvvaGaneeltpedvkaaeekikesdlvllQlEipletveealkiakkagv 155
                                     ++e ++ v+++stG+A+i+v+++geN+I ++aGan++ltp +++++ + +++++++l+QlE+p+etv++al++ak+ g+
  lcl|FitnessBrowser__MR1:199996  83 QAEGITLVDNVSTGTAMIFVADNGENAIGIAAGANAHLTPLELEKHYALFANAQYLLIQLETPTETVSNALQMAKRLGI 161
                                     ******************************************************************************* PP

                       TIGR02152 156 kvllnPAPaekkldeellslvdiivpNetEaeiLtgievedledaekaaekllekgvkaviitlGskGallvskdekkl 234
                                     +++lnPAPa++ ++ ++l++vdii+pNetEae+Ltgiev+++eda+ aa++l+++g+++v+itlGskGa+++s + + l
  lcl|FitnessBrowser__MR1:199996 162 TTVLNPAPAAT-QELDYLKWVDIITPNETEAEALTGIEVKHEEDAKLAAQWLHQQGITTVVITLGSKGAFISSPGFTGL 239
                                     *********65.789**************************************************************** PP

                       TIGR02152 235 ipalkvkavDttaAGDtFigalavaLaegksledavrfanaaaalsVtrkGaqssiPtkeeve 297
                                     ipal+v+a+Dt+aAGDtF+gal+v L+eg+s+++av+fanaa+a++Vtr+Gaq++iP+++ev+
  lcl|FitnessBrowser__MR1:199996 240 IPALTVQAIDTVAAGDTFNGALVVGLSEGMSIAAAVSFANAASAITVTREGAQRAIPYRSEVS 302
                                     *************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (303 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: 11.26
//
[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
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