Alignments for a candidate for deoK in Rhizobium leguminosarum 3841

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoK in Rhizobium leguminosarum 3841

Align deoxyribose kinase (EC 2.7.1.15) (characterized)
to candidate WP_011652279.1 RL_RS14180 ribokinase

Query= reanno::Burk376:H281DRAFT_01116
         (320 letters)



>NCBI__GCF_000009265.1:WP_011652279.1
          Length = 310

 Score =  349 bits (895), Expect = e-101
 Identities = 177/302 (58%), Positives = 216/302 (71%)

Query: 11  VVILGIYVTDLTFRAARMPLVGETIAGSAFAMGPGGKGSNQAVAAARAGAEVVFCTRIGN 70
           V ILGI+V D  + A RMP VGETI G+ FA+GPGGKGSNQAVAAARAG  V F ++IG 
Sbjct: 5   VSILGIFVADTAYLAKRMPNVGETITGTGFAVGPGGKGSNQAVAAARAGGTVSFISKIGR 64

Query: 71  DAFGSIAQATWAREGITARASVVEGVSTGAAHIFVDDTTGMNAIIVAAGAAGTLSAADVD 130
           D FG +A  T+A  G+T +   ++ + TGAA I+V+D  G NAIIV  GAAGT+   DV+
Sbjct: 65  DTFGDMALKTYAEAGVTPKVVQMDDMPTGAAFIYVNDGNGDNAIIVYPGAAGTIGIGDVE 124

Query: 131 AIEADIAGSRVFVTQLEQPLAAARRGLEVARKHGVTTVFNPAPALPLDDDIFPLCDYITP 190
           A    I  S VFVTQLEQP  AA+R LE+A   GVTTVFNPAPA P  D I+PLCDYI P
Sbjct: 125 AARETIEQSAVFVTQLEQPAEAAQRALEIAHAAGVTTVFNPAPAEPFPDTIYPLCDYIVP 184

Query: 191 NETEAAALTGVPIANVDDARRAADVLLAKGVGTVIVTLGEGGALLHDATQSIWLPAFRCG 250
           NETEAAA+ G P+  +DDARRA D LLAKGV   ++TLG  G L H A QS+ +PA   G
Sbjct: 185 NETEAAAIVGFPLDTLDDARRAGDALLAKGVKAALITLGGRGVLYHTARQSVHVPAVSSG 244

Query: 251 AVVETAGAGDGFTGGFAAALARGEDAISAMRFGCALAGISVTRAGTAPSMPTLAEVNRVL 310
           AV++T GAGD F GGF+AAL+RG   + A+RFGCA AGI+VTR GTAP+MP + E+  +L
Sbjct: 245 AVIDTTGAGDAFVGGFSAALSRGASPVEAVRFGCATAGIAVTRRGTAPAMPKIEEIEALL 304

Query: 311 SE 312
            +
Sbjct: 305 QK 306


Lambda     K      H
   0.318    0.132    0.377 

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: 290
Number of extensions: 7
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: 320
Length of database: 310
Length adjustment: 27
Effective length of query: 293
Effective length of database: 283
Effective search space:    82919
Effective search space used:    82919
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate WP_011652279.1 RL_RS14180 (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.14599.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    7.8e-97  310.1   3.8    8.9e-97  310.0   3.8    1.0  1  lcl|NCBI__GCF_000009265.1:WP_011652279.1  RL_RS14180 ribokinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009265.1:WP_011652279.1  RL_RS14180 ribokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.0   3.8   8.9e-97   8.9e-97       1     297 [.       5     301 ..       5     302 .. 0.97

  Alignments for each domain:
  == domain 1  score: 310.0 bits;  conditional E-value: 8.9e-97
                                 TIGR02152   1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefgeelle 69 
                                               + ++G + +D+   +kr+p+ Get++++ f +++GGKG+NQAvaaar g +vs+i+k+G+D+fg+++l+
  lcl|NCBI__GCF_000009265.1:WP_011652279.1   5 VSILGIFVADTAYLAKRMPNVGETITGTGFAVGPGGKGSNQAVAAARAGGTVSFISKIGRDTFGDMALK 73 
                                               6799***************************************************************** PP

                                 TIGR02152  70 nlkkegidteyvkkvkktstGvAlilvde.egeNsIvvvaGaneeltpedvkaaeekikesdlvllQlE 137
                                               ++++ g++ + v+ +++++tG A+i v++ +g+N+I+v+ Ga  ++   dv+aa+e+i++s + + QlE
  lcl|NCBI__GCF_000009265.1:WP_011652279.1  74 TYAEAGVTPKVVQ-MDDMPTGAAFIYVNDgNGDNAIIVYPGAAGTIGIGDVEAARETIEQSAVFVTQLE 141
                                               *******666555.789**********98689************************************* PP

                                 TIGR02152 138 ipletveealkiakkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgievedledaekaaek 206
                                                p e++++al+ia++agv++++nPAPae+  +++++ l+d+ivpNetEa++++g   ++l+da++a ++
  lcl|NCBI__GCF_000009265.1:WP_011652279.1 142 QPAEAAQRALEIAHAAGVTTVFNPAPAEP-FPDTIYPLCDYIVPNETEAAAIVGFPLDTLDDARRAGDA 209
                                               ***************************76.99************************************* PP

                                 TIGR02152 207 llekgvkaviitlGskGallvskdekklipalkvka.vDttaAGDtFigalavaLaegksledavrfan 274
                                               ll+kgvka +itlG +G+l++++ ++ ++pa+   a +Dtt+AGD+F+g++++aL++g s  +avrf+ 
  lcl|NCBI__GCF_000009265.1:WP_011652279.1 210 LLAKGVKAALITLGGRGVLYHTARQSVHVPAVSSGAvIDTTGAGDAFVGGFSAALSRGASPVEAVRFGC 278
                                               *******************************9876527******************************* PP

                                 TIGR02152 275 aaaalsVtrkGaqssiPtkeeve 297
                                               a a ++Vtr G+++++P+ ee+e
  lcl|NCBI__GCF_000009265.1:WP_011652279.1 279 ATAGIAVTRRGTAPAMPKIEEIE 301
                                               *********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (310 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: 10.46
//
[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 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