Alignments for a candidate for rbsK in Collimonas pratensis Ter91

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsK in Collimonas pratensis Ter91

Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate WP_061944912.1 CPter91_RS23405 ribokinase

Query= reanno::HerbieS:HSERO_RS11500
         (299 letters)



>NCBI__GCF_001584185.1:WP_061944912.1
          Length = 304

 Score =  357 bits (916), Expect = e-103
 Identities = 189/303 (62%), Positives = 234/303 (77%), Gaps = 7/303 (2%)

Query: 1   MIVIIGSVNMDLVLRVPRMPLPGETLAGDRFMTIPGGKGANQAVACARLAAPGTRVAMVA 60
           MIVIIGS+NMDLVLRVPRMP PGETL+G +F TIPGGKGANQAVA ARL+A   +VAM+A
Sbjct: 1   MIVIIGSINMDLVLRVPRMPHPGETLSGGQFRTIPGGKGANQAVAAARLSADSVKVAMIA 60

Query: 61  CVGDDAFGGQMRQSITACGIDDRYIDEVAGEATGIASIMVDANAQNSIVIAAGANGRLDV 120
           C+GDDAFG ++R ++ + GIDD ++  V+G A+G+ASI+VDA  QNSIV+AAGAN  L  
Sbjct: 61  CLGDDAFGAELRAALRSDGIDDSHVSTVSGSASGVASILVDAGGQNSIVLAAGANDALSP 120

Query: 121 ERIERARALIEQASIVLLQLEVPMATVIHSIELAHALGKTVVLNPAPAQALPRALLQKID 180
             I+ ARALIEQA I++LQLE P+ T+ H+I+LAH LGKTVVLNPAPAQ LP  LL +++
Sbjct: 121 AHIDAARALIEQARIIVLQLETPLPTIRHAIKLAHQLGKTVVLNPAPAQVLPADLLAQVE 180

Query: 181 YLILNEIEAAMLA--EEQSED----IPMLARKLHDLGARNVVVTLGEKGVYGSFADGQQR 234
           YLI NEIEAAMLA   E S D    I     KL   G+ NV+VTLG KGVY + + G + 
Sbjct: 181 YLIPNEIEAAMLAGLPEVSLDNDAAIDAAVAKLRANGSANVLVTLGSKGVYAALSSGSE- 239

Query: 235 HLPARKVQAVDTTAAGDTFIGGFIGAIAQGRDQFEAIAYAQAAAALSVTRVGAQTSIPTR 294
           H  A+ V+A+DTTAAGDTFIGGF+ A+A+GR + +AIA+ Q AAALSV R+GAQTSIP R
Sbjct: 240 HFAAQPVKAIDTTAAGDTFIGGFVAALAEGRSEADAIAFGQRAAALSVARIGAQTSIPYR 299

Query: 295 DEV 297
            E+
Sbjct: 300 HEL 302


Lambda     K      H
   0.320    0.135    0.374 

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: 251
Number of extensions: 8
Number of successful extensions: 3
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: 299
Length of database: 304
Length adjustment: 27
Effective length of query: 272
Effective length of database: 277
Effective search space:    75344
Effective search space used:    75344
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate WP_061944912.1 CPter91_RS23405 (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.1441183.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-111  358.0   3.7   2.3e-111  357.9   3.7    1.0  1  NCBI__GCF_001584185.1:WP_061944912.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001584185.1:WP_061944912.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  357.9   3.7  2.3e-111  2.3e-111       1     297 [.       2     303 ..       2     304 .] 0.97

  Alignments for each domain:
  == domain 1  score: 357.9 bits;  conditional E-value: 2.3e-111
                             TIGR02152   1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlg...aevsmigkvGkDefgeellen 70 
                                           iv++GSin+Dlvlrv+r+p+pGet+ + +f++++GGKGANQAvaaarl+    +v+mi+++G+D+fg+el+ +
  NCBI__GCF_001584185.1:WP_061944912.1   2 IVIIGSINMDLVLRVPRMPHPGETLSGGQFRTIPGGKGANQAVAAARLSadsVKVAMIACLGDDAFGAELRAA 74 
                                           89**********************************************977778******************* PP

                             TIGR02152  71 lkkegidteyvkkvkktstGvAlilvdeegeNsIvvvaGaneeltpedvkaaeekikesdlvllQlEipletv 143
                                           l+++gid ++v++v+ +++GvA ilvd  g+NsIv++aGan+ l+p++++aa++ i+++++++lQlE+pl t+
  NCBI__GCF_001584185.1:WP_061944912.1  75 LRSDGIDDSHVSTVSGSASGVASILVDAGGQNSIVLAAGANDALSPAHIDAARALIEQARIIVLQLETPLPTI 147
                                           ************************************************************************* PP

                             TIGR02152 144 eealkiakkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgie...vedledaekaaekllekgvk 213
                                           ++a+k+a++ g++v+lnPAPa + l+++ll++v++++pNe Ea++L g      ++ +++++a +kl+++g  
  NCBI__GCF_001584185.1:WP_061944912.1 148 RHAIKLAHQLGKTVVLNPAPA-QVLPADLLAQVEYLIPNEIEAAMLAGLPevsLDNDAAIDAAVAKLRANGSA 219
                                           *********************.56**********************99764447888999************* PP

                             TIGR02152 214 aviitlGskGallvskdekklipalkvkavDttaAGDtFigalavaLaegksledavrfanaaaalsVtrkGa 286
                                           +v++tlGskG++ + ++ ++++ a  vka+DttaAGDtFig++++aLaeg+s +da+ f+++aaalsV r+Ga
  NCBI__GCF_001584185.1:WP_061944912.1 220 NVLVTLGSKGVYAALSSGSEHFAAQPVKAIDTTAAGDTFIGGFVAALAEGRSEADAIAFGQRAAALSVARIGA 292
                                           ************************************************************************* PP

                             TIGR02152 287 qssiPtkeeve 297
                                           q+siP+++e+e
  NCBI__GCF_001584185.1:WP_061944912.1 293 QTSIPYRHELE 303
                                           *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (304 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 13.05
//
[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