Alignments for a candidate for deoK in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoK in Acidovorax sp. GW101-3H11

Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate Ac3H11_1839 Ribokinase (EC 2.7.1.15)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_1839
          Length = 314

 Score =  224 bits (571), Expect = 2e-63
 Identities = 135/299 (45%), Positives = 175/299 (58%), Gaps = 8/299 (2%)

Query: 2   IVIIGSVNMDLVLRVPRMPLPGETLAGDRFMTIPGGKGANQAVACARLAAPGTRVAMVAC 61
           I ++GS+NMDLVL+V   P PGET+  D    +PGGKG NQAVACAR    G +VA+   
Sbjct: 9   IAVVGSLNMDLVLQVQHAPGPGETVLADALHLVPGGKGGNQAVACAR---QGAQVALFGR 65

Query: 62  VGDDAFGGQMRQSITACGIDDRYIDEVAGEATGIASIMVDANAQNSIVIAAGANGRLDVE 121
           VGDD +G  +R  + A GID   +       TG+A+I V+A  QN IV+  GANGR  ++
Sbjct: 66  VGDDGYGHTLRAGLDADGIDHSGVQTDTATTTGVAAITVEATGQNRIVVVPGANGRFVLD 125

Query: 122 RIERARALIEQASIVLLQLEVPMATVIHSIELAHALGKTVVLNPAPAQALPRALLQKIDY 181
                 AL + A  ++LQ E P+  V+ + E+AHA G  VVLNP+P Q LP AL   +  
Sbjct: 126 ATALGAAL-QGAGGLVLQFETPLRQVLAAAEMAHAAGCPVVLNPSPIQPLPEALWPLVHT 184

Query: 182 LILNEIEAAMLAEEQ---SEDIPMLARKLHDLGARNVVVTLGEKGVYGSFADGQQRHLPA 238
           L++NE+EAA LA +      D    A+ L   G   VVVTLG  G   + A G + H P 
Sbjct: 185 LVVNEVEAAALAGQNVTTPADAAQAAQALRAKGPAQVVVTLGAAGAVAADAAGNRYH-PG 243

Query: 239 RKVQAVDTTAAGDTFIGGFIGAIAQGRDQFEAIAYAQAAAALSVTRVGAQTSIPTRDEV 297
             V+AVDTTAAGDTF+G    A+A+G      +     AAAL VT+ GAQ SIPTR  V
Sbjct: 244 LVVRAVDTTAAGDTFLGALAVALARGEPLDAGVREGIRAAALCVTQHGAQPSIPTRAAV 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: 233
Number of extensions: 11
Number of successful extensions: 5
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: 314
Length adjustment: 27
Effective length of query: 272
Effective length of database: 287
Effective search space:    78064
Effective search space used:    78064
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 Ac3H11_1839 (Ribokinase (EC 2.7.1.15))
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.31357.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-95  306.0   6.2    1.7e-95  305.8   6.2    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1839  Ribokinase (EC 2.7.1.15)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1839  Ribokinase (EC 2.7.1.15)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.8   6.2   1.7e-95   1.7e-95       1     297 [.       9     303 ..       9     304 .. 0.98

  Alignments for each domain:
  == domain 1  score: 305.8 bits;  conditional E-value: 1.7e-95
                                        TIGR02152   1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDe 62 
                                                      i+vvGS+n+Dlvl+v++ p pGetv a+ +++++GGKG NQAva+ar ga+v++ g+vG+D 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1839   9 IAVVGSLNMDLVLQVQHAPGPGETVLADALHLVPGGKGGNQAVACARQGAQVALFGRVGDDG 70 
                                                      79************************************************************ PP

                                        TIGR02152  63 fgeellenlkkegidteyvkkvkktstGvAlilvdeegeNsIvvvaGaneeltpedvkaaee 124
                                                      +g++l+  l ++gid + v++++ t+tGvA+i+v+ +g+N+Ivvv Gan ++  +  +a  +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1839  71 YGHTLRAGLDADGIDHSGVQTDTATTTGVAAITVEATGQNRIVVVPGANGRFVLD-ATALGA 131
                                                      ***************************************************9865.566789 PP

                                        TIGR02152 125 kikesdlvllQlEipletveealkiakkagvkvllnPAPaekkldeellslvdiivpNetEa 186
                                                      +++ +  ++lQ+E+pl  v +a+++a++ag  v+lnP P ++ l+e l+ lv+++v Ne Ea
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1839 132 ALQGAGGLVLQFETPLRQVLAAAEMAHAAGCPVVLNPSPIQP-LPEALWPLVHTLVVNEVEA 192
                                                      9***************************************77.99***************** PP

                                        TIGR02152 187 eiLtgievedledaekaaekllekgvkaviitlGskGallvskdekklipalkvkavDttaA 248
                                                      ++L g++v++ +da +aa++l++kg  +v++tlG+ Ga+ +++  ++  p l v+avDttaA
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1839 193 AALAGQNVTTPADAAQAAQALRAKGPAQVVVTLGAAGAVAADAAGNRYHPGLVVRAVDTTAA 254
                                                      ************************************************************** PP

                                        TIGR02152 249 GDtFigalavaLaegksledavrfanaaaalsVtrkGaqssiPtkeeve 297
                                                      GDtF galavaLa+g+ l++ vr + +aaal Vt++Gaq+siPt++ v+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1839 255 GDTFLGALAVALARGEPLDAGVREGIRAAALCVTQHGAQPSIPTRAAVA 303
                                                      *********************************************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (314 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: 7.35
//
[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