Alignments for a candidate for deoK in Trichodesmium erythraeum IMS101

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoK in Trichodesmium erythraeum IMS101

Align ribokinase (characterized)
to candidate WP_011610662.1 TERY_RS04075 ribokinase

Query= CharProtDB::CH_024905
         (309 letters)



>NCBI__GCF_000014265.1:WP_011610662.1
          Length = 305

 Score =  232 bits (592), Expect = 7e-66
 Identities = 127/301 (42%), Positives = 181/301 (60%), Gaps = 1/301 (0%)

Query: 6   SLVVLGSINADHILNLQSFPTPGETVTGNHYQVAFGGKGANQAVAAGRSGANIAFIACTG 65
           S+++ GS+N D I      PTPGET+ GN++  A GGKGANQAVAA   G     +   G
Sbjct: 2   SIIIFGSVNIDLIATTPRLPTPGETINGNNFFTAGGGKGANQAVAAAGLGIPTKIVGRVG 61

Query: 66  DDSIGESVRQQLATDNIDITPVSVIKGESTGVALIFVNGEGENVIGIHAGANAALSPALV 125
           +DS G+ +   L+T N+D T V V +   TGVA+I V   GEN I +  GAN +++   V
Sbjct: 62  NDSFGQQLLVSLSTANVDTTDVLVDENTHTGVAVIAVGASGENNIIVVPGANHSINNTDV 121

Query: 126 EAQRERIANASALLMQLESPLESVMAAAKIAHQNKTIVALNPAP-ARELPDELLALVDII 184
           E  +  +++ +ALL+QLE P+E  ++AAK+A +    V L+PAP     P++   L+DII
Sbjct: 122 ERLKNLLSDVTALLLQLEIPVEVAISAAKVAQEMGVKVILDPAPMPANFPNDFYNLIDII 181

Query: 185 TPNETEAEKLTGIRVENDEDAAKAAQVLHEKGIRTVLITLGSRGVWASVNGEGQRVPGFR 244
           TPNE EA +L G  V N E A +AA  L  +G++  ++ +G RGV  +   E    P F 
Sbjct: 182 TPNEIEASQLVGFEVNNQETAMEAAVELCHRGVKNAVVKIGDRGVICATKEEAFFQPAFV 241

Query: 245 VQAVDTIAAGDTFNGALITALLEEKPLPEAIRFAHAAAAIAVTRKGAQPSVPWREEIDAF 304
           V+ +DT+AAGD FNG L  AL     L EA+++  AA A+  T+ GAQP++P R+  D F
Sbjct: 242 VKTIDTVAAGDAFNGGLAAALDTGLSLKEAVKWGAAAGALCTTKPGAQPAMPDRKTFDNF 301

Query: 305 L 305
           L
Sbjct: 302 L 302


Lambda     K      H
   0.314    0.131    0.363 

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: 282
Number of extensions: 17
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: 305
Length adjustment: 27
Effective length of query: 282
Effective length of database: 278
Effective search space:    78396
Effective search space used:    78396
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_011610662.1 TERY_RS04075 (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.4025684.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-100  322.4   7.7   1.7e-100  322.2   7.7    1.0  1  NCBI__GCF_000014265.1:WP_011610662.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000014265.1:WP_011610662.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  322.2   7.7  1.7e-100  1.7e-100       1     295 [.       3     297 ..       3     300 .. 0.99

  Alignments for each domain:
  == domain 1  score: 322.2 bits;  conditional E-value: 1.7e-100
                             TIGR02152   1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefgeellenlkk 73 
                                           i+++GS+n+Dl+++++rlp pGet+++++f +a GGKGANQAvaaa lg  ++++g+vG+D+fg++ll +l++
  NCBI__GCF_000014265.1:WP_011610662.1   3 IIIFGSVNIDLIATTPRLPTPGETINGNNFFTAGGGKGANQAVAAAGLGIPTKIVGRVGNDSFGQQLLVSLST 75 
                                           89*********************************************************************** PP

                             TIGR02152  74 egidteyvkkvkktstGvAlilvdeegeNsIvvvaGaneeltpedvkaaeekikesdlvllQlEipletveea 146
                                            ++dt+ v  +++t+tGvA+i v  +geN+I+vv Gan++++++dv++ ++ +++ + +llQlEip+e++++a
  NCBI__GCF_000014265.1:WP_011610662.1  76 ANVDTTDVLVDENTHTGVAVIAVGASGENNIIVVPGANHSINNTDVERLKNLLSDVTALLLQLEIPVEVAISA 148
                                           ************************************************************************* PP

                             TIGR02152 147 lkiakkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgievedledaekaaekllekgvkaviitl 219
                                           +k+a++ gvkv+l+PAP  ++ ++++++l+dii+pNe Ea++L+g ev+++e+a +aa +l ++gvk+ ++++
  NCBI__GCF_000014265.1:WP_011610662.1 149 AKVAQEMGVKVILDPAPMPANFPNDFYNLIDIITPNEIEASQLVGFEVNNQETAMEAAVELCHRGVKNAVVKI 221
                                           ************************************************************************* PP

                             TIGR02152 220 GskGallvskdekklipalkvkavDttaAGDtFigalavaLaegksledavrfanaaaalsVtrkGaqssiPt 292
                                           G++G+++++k+e  + pa+ vk++Dt+aAGD+F+g+la+aL++g sl++av+ ++aa al  t+ Gaq+++P 
  NCBI__GCF_000014265.1:WP_011610662.1 222 GDRGVICATKEEAFFQPAFVVKTIDTVAAGDAFNGGLAAALDTGLSLKEAVKWGAAAGALCTTKPGAQPAMPD 294
                                           ************************************************************************9 PP

                             TIGR02152 293 kee 295
                                           ++ 
  NCBI__GCF_000014265.1:WP_011610662.1 295 RKT 297
                                           986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (305 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: 20.41
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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