Alignments for a candidate for rbsK in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsK in Dyella japonica UNC79MFTsu3.2

Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate N515DRAFT_3101 N515DRAFT_3101 ribokinase

Query= reanno::pseudo5_N2C3_1:AO356_00950
         (304 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3101
          Length = 297

 Score =  225 bits (573), Expect = 1e-63
 Identities = 135/301 (44%), Positives = 179/301 (59%), Gaps = 11/301 (3%)

Query: 3   AKVVVIGSLNMDLVTRAPRLPRGGETLIGESFATIPGGKGANQAVAAARLGAQVSMVGCV 62
           A+VVV+GS+NMDLVT APR    GET++GE F T+PGGKGANQAVAAARLGA+V+++G +
Sbjct: 2   ARVVVVGSINMDLVTLAPRFAGPGETVLGERFLTVPGGKGANQAVAAARLGAEVTLIGAL 61

Query: 63  GDDAYGEQLRGALLAEGIDCQAV-RVEQGSSGVALIVVDDNSQNAIVIVAGANGALTAEV 121
           GDD +GEQLR  L  EGI    V R++   SG A I V    +N I++V  AN  +T   
Sbjct: 62  GDDTFGEQLREGLAREGIALDYVSRIDDCGSGTASITV-AGGENEIIVVPAANARVTPAQ 120

Query: 122 LDGVDDVLQSADVIICQLEVPDATVGHALKRGRALGKIVILNPAPASHALPADWYACIDY 181
           ++   D +  AD ++ Q+E+P  +V   L+ G  LG  VILNPAPA   LP +W     Y
Sbjct: 121 VEAATDAIARADAVLVQMEIPLESVEATLRLGHRLGVPVILNPAPA-QKLPTEWLKLARY 179

Query: 182 LIPNESEAAVLSGLAVDSLETAEAAAAHLIAAGAGKVIVTLGAQGLMFANGASFEHFPAP 241
           + PN+ E A+L  L  D+ +   A    L+    G V++T G +G  +       H    
Sbjct: 180 VTPNQHELAIL--LGADAQQDFRA----LMRQAPGPVVLTRGGEGAWYREDGEPTHQSGF 233

Query: 242 RVKAVDTTAAGDTFVGGFAAALACGKSEVDAIRFGQVAAALSVTRAGAQPSIPTLLEVQA 301
            V  VDTT AGDTF G  A  L  G  +  A+R    AAALSVTR GAQ  +PT +E+ A
Sbjct: 234 AVDVVDTTGAGDTFNGALAVFLHEGLPQ--AVRKACAAAALSVTRLGAQGGMPTRVELDA 291

Query: 302 F 302
           +
Sbjct: 292 W 292


Lambda     K      H
   0.318    0.133    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: 309
Number of extensions: 20
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: 304
Length of database: 297
Length adjustment: 27
Effective length of query: 277
Effective length of database: 270
Effective search space:    74790
Effective search space used:    74790
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 N515DRAFT_3101 N515DRAFT_3101 (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.12921.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   6.1e-100  320.3   0.1   6.9e-100  320.2   0.1    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_3101  N515DRAFT_3101 ribokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_3101  N515DRAFT_3101 ribokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.2   0.1  6.9e-100  6.9e-100       1     297 [.       4     290 ..       4     291 .. 0.98

  Alignments for each domain:
  == domain 1  score: 320.2 bits;  conditional E-value: 6.9e-100
                                    TIGR02152   1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefgee 66 
                                                  +vvvGSin+Dlv+ ++r++ pGetv +e f +++GGKGANQAvaaarlgaev++ig++G+D+fge+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3101   4 VVVVGSINMDLVTLAPRFAGPGETVLGERFLTVPGGKGANQAVAAARLGAEVTLIGALGDDTFGEQ 69 
                                                  79**************************************************************** PP

                                    TIGR02152  67 llenlkkegidteyvkkvkktstGvAlilvdeegeNsIvvvaGaneeltpedvkaaeekikesdlv 132
                                                  l+e l++egi  +yv++++++ +G+A i+v+  geN+I+vv  an+++tp++v+aa+++i+++d v
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3101  70 LREGLAREGIALDYVSRIDDCGSGTASITVAG-GENEIIVVPAANARVTPAQVEAATDAIARADAV 134
                                                  *******************************9.********************************* PP

                                    TIGR02152 133 llQlEipletveealkiakkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgievedle 198
                                                  l+Q+Eiple+ve+ l++ ++ gv v+lnPAPa+k l++e+l+l+ +++pN++E++iL+g       
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3101 135 LVQMEIPLESVEATLRLGHRLGVPVILNPAPAQK-LPTEWLKLARYVTPNQHELAILLGA------ 193
                                                  ********************************66.9***********************9...... PP

                                    TIGR02152 199 daekaaekllekgvkaviitlGskGallvskdekklipalkvkavDttaAGDtFigalavaLaegk 264
                                                  da++  ++l++++   v++t G +Ga + + +e ++ + + v++vDtt+AGDtF+galav L+eg 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3101 194 DAQQDFRALMRQAPGPVVLTRGGEGAWYREDGEPTHQSGFAVDVVDTTGAGDTFNGALAVFLHEG- 258
                                                  68899999999999*************************************************99. PP

                                    TIGR02152 265 sledavrfanaaaalsVtrkGaqssiPtkeeve 297
                                                   l +avr+a aaaalsVtr+Gaq ++Pt+ e++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3101 259 -LPQAVRKACAAAALSVTRLGAQGGMPTRVELD 290
                                                  .8899************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (297 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: 7.02
//
[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