Alignments for a candidate for rbsK in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsK in Herbaspirillum seropedicae SmR1

Align deoxyribose kinase (EC 2.7.1.15) (characterized)
to candidate HSERO_RS05105 HSERO_RS05105 ribokinase

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



>FitnessBrowser__HerbieS:HSERO_RS05105
          Length = 319

 Score =  340 bits (873), Expect = 2e-98
 Identities = 183/314 (58%), Positives = 216/314 (68%), Gaps = 1/314 (0%)

Query: 1   MSSQPQQSGRVVILGIYVTDLTFRAARMPLVGETIAGSAFAMGPGGKGSNQAVAAARAGA 60
           M+S P + G V +LGIYV DL FRA  MP +G+TIAG+ FAMGPGGKGSNQAVAAAR GA
Sbjct: 1   MTSFPHKQG-VAVLGIYVADLAFRAPNMPGLGQTIAGTGFAMGPGGKGSNQAVAAARVGA 59

Query: 61  EVVFCTRIGNDAFGSIAQATWAREGITARASVVEGVSTGAAHIFVDDTTGMNAIIVAAGA 120
            V F + IG DAFG  A + W RE I     V++G  TGAA I+V+D +G NAIIV  GA
Sbjct: 60  PVRFISAIGKDAFGDFALSLWRRETIAPHVRVIDGAPTGAAFIYVNDASGDNAIIVVPGA 119

Query: 121 AGTLSAADVDAIEADIAGSRVFVTQLEQPLAAARRGLEVARKHGVTTVFNPAPALPLDDD 180
           A  LS  DV+     I  ++VFVTQLEQP  AA  GL++AR  G TTVFNPAPAL     
Sbjct: 120 ASQLSEQDVERERQAIEAAKVFVTQLEQPPEAALAGLQIARAAGTTTVFNPAPALAFPAQ 179

Query: 181 IFPLCDYITPNETEAAALTGVPIANVDDARRAADVLLAKGVGTVIVTLGEGGALLHDATQ 240
           ++ LCD+ITPNE EAA LTG+ I ++DDARRAADVLL +GVG  ++TLG  G+LLH  +Q
Sbjct: 180 VYGLCDFITPNEHEAALLTGIEIHHIDDARRAADVLLERGVGCALITLGAQGSLLHSRSQ 239

Query: 241 SIWLPAFRCGAVVETAGAGDGFTGGFAAALARGEDAISAMRFGCALAGISVTRAGTAPSM 300
           S+ LPA   G VVETAGAGD F G FAA LA G  A  A R   A+A ISVTR GTAPSM
Sbjct: 240 SLHLPALCAGTVVETAGAGDAFNGAFAAGLAEGMSAEEAARLATAVAAISVTRPGTAPSM 299

Query: 301 PTLAEVNRVLSESA 314
           P+  E   +L   A
Sbjct: 300 PSRQEALALLDTHA 313


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: 273
Number of extensions: 10
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: 319
Length adjustment: 28
Effective length of query: 292
Effective length of database: 291
Effective search space:    84972
Effective search space used:    84972
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 HSERO_RS05105 HSERO_RS05105 (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.7921.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    7.6e-97  310.2   0.7    8.6e-97  310.0   0.7    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS05105  HSERO_RS05105 ribokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS05105  HSERO_RS05105 ribokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.0   0.7   8.6e-97   8.6e-97       1     295 [.      10     304 ..      10     307 .. 0.97

  Alignments for each domain:
  == domain 1  score: 310.0 bits;  conditional E-value: 8.6e-97
                                  TIGR02152   1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefgeell 68 
                                                ++v+G + +Dl +r++++p  G+t++++ f +++GGKG+NQAvaaar+ga v++i+++GkD+fg+ +l
  lcl|FitnessBrowser__HerbieS:HSERO_RS05105  10 VAVLGIYVADLAFRAPNMPGLGQTIAGTGFAMGPGGKGSNQAVAAARVGAPVRFISAIGKDAFGDFAL 77 
                                                78****************************************************************** PP

                                  TIGR02152  69 enlkkegidteyvkkvkktstGvAlilvde.egeNsIvvvaGaneeltpedvkaaeekikesdlvllQ 135
                                                + +++e i + +v+ ++ ++tG A+i v++ +g+N+I+vv Ga ++l+++dv++++++i+++++ + Q
  lcl|FitnessBrowser__HerbieS:HSERO_RS05105  78 SLWRRETI-APHVRVIDGAPTGAAFIYVNDaSGDNAIIVVPGAASQLSEQDVERERQAIEAAKVFVTQ 144
                                                ********.789****************97368*********************************** PP

                                  TIGR02152 136 lEipletveealkiakkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgievedledaeka 203
                                                lE p e++ + l+ia++ag+++++nPAPa  + +++++ l+d+i+pNe+Ea++Ltgie+++++da++a
  lcl|FitnessBrowser__HerbieS:HSERO_RS05105 145 LEQPPEAALAGLQIARAAGTTTVFNPAPAL-AFPAQVYGLCDFITPNEHEAALLTGIEIHHIDDARRA 211
                                                *****************************5.599********************************** PP

                                  TIGR02152 204 aekllekgvkaviitlGskGallvskdekklipalkv.kavDttaAGDtFigalavaLaegksledav 270
                                                a+ lle+gv   +itlG++G+ll+s++++ ++pal + ++v t++AGD+F+ga+a+ Laeg+s+e+a 
  lcl|FitnessBrowser__HerbieS:HSERO_RS05105 212 ADVLLERGVGCALITLGAQGSLLHSRSQSLHLPALCAgTVVETAGAGDAFNGAFAAGLAEGMSAEEAA 279
                                                **********************************98736789************************** PP

                                  TIGR02152 271 rfanaaaalsVtrkGaqssiPtkee 295
                                                r a+a+aa+sVtr G+++s+P+++e
  lcl|FitnessBrowser__HerbieS:HSERO_RS05105 280 RLATAVAAISVTRPGTAPSMPSRQE 304
                                                ***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (319 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: 8.11
//
[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