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.22261.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.29
//
[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:

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:

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:

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:

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