GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoK in Bacillus altitudinis 41KF2b

Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate WP_035702262.1 BA79_RS08560 ribokinase

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



>NCBI__GCF_000691145.1:WP_035702262.1
          Length = 292

 Score =  201 bits (512), Expect = 1e-56
 Identities = 124/299 (41%), Positives = 176/299 (58%), Gaps = 12/299 (4%)

Query: 3   AKVVVIGSLNMDLVTRAPRLPRGGETLIGESFATIPGGKGANQAVAAARLGAQVSMVGCV 62
           +++VV+GS +MDLV  + + P  GET++GESF T+PGGKGANQAVA+ARLGA V M+G V
Sbjct: 2   SQIVVVGSCSMDLVVTSNKRPSAGETVLGESFKTVPGGKGANQAVASARLGADVYMIGRV 61

Query: 63  GDDAYGEQLRGALLAEGIDCQAVR-VEQGSSGVALIVVDDNSQNAIVIVAGANGALTAEV 121
           GDDAYG+ +   L A+G+    ++ V +  SG A I++ +   N+IV+V GAN  +T   
Sbjct: 62  GDDAYGQDIMSNLQAQGVRTTYMKPVTEMESGTAHIILAE-GDNSIVVVKGANNEVTPHY 120

Query: 122 LDGVDDVLQSADVIICQLEVPDATVGHALKRGRALGKIVILNPAPASHALPADWYACIDY 181
           +      +++  +++ Q E+P+ TV          G  VILNPAPA   +         Y
Sbjct: 121 VKDALSSIENIGIVLIQQEIPEETVEAVCAICSEKGIPVILNPAPA-RKVSQQILDQAAY 179

Query: 182 LIPNESEAAVLSGLAVDSLETAEAAAAHLIAAGAGKVIVTLGAQGLMFANGASFEHFPAP 241
           + PNE EAA    L  D L  AEA   +       K+++T G  G+ + +G+     P  
Sbjct: 180 ITPNEHEAA----LMFDGLTIAEALRQY-----PNKLLITEGKNGVRYFDGSKEVLVPGY 230

Query: 242 RVKAVDTTAAGDTFVGGFAAALACGKSEVDAIRFGQVAAALSVTRAGAQPSIPTLLEVQ 300
            VKAVDTT AGDTF G  A AL  GKS  DA+ F  +AA++SVT+ GAQ  +P   E++
Sbjct: 231 PVKAVDTTGAGDTFNGALAVALTEGKSLYDALAFANLAASISVTKFGAQGGMPAREELE 289


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: 236
Number of extensions: 12
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: 292
Length adjustment: 26
Effective length of query: 278
Effective length of database: 266
Effective search space:    73948
Effective search space used:    73948
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_035702262.1 BA79_RS08560 (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.1219118.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-109  349.5   3.5     9e-109  349.3   3.5    1.0  1  NCBI__GCF_000691145.1:WP_035702262.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000691145.1:WP_035702262.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  349.3   3.5    9e-109    9e-109       1     297 [.       4     289 ..       4     290 .. 0.97

  Alignments for each domain:
  == domain 1  score: 349.3 bits;  conditional E-value: 9e-109
                             TIGR02152   1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefgeellenlkk 73 
                                           ivvvGS+++Dlv++ ++ p++Getv +e+fk+++GGKGANQAva arlga+v mig+vG+D++g+++++nl++
  NCBI__GCF_000691145.1:WP_035702262.1   4 IVVVGSCSMDLVVTSNKRPSAGETVLGESFKTVPGGKGANQAVASARLGADVYMIGRVGDDAYGQDIMSNLQA 76 
                                           89*********************************************************************** PP

                             TIGR02152  74 egidteyvkkvkktstGvAlilvdeegeNsIvvvaGaneeltpedvkaaeekikesdlvllQlEipletveea 146
                                           +g++t+y+k v+++++G+A+i+++e g+NsIvvv+Gan+e+tp++vk+a + i++  +vl+Q+Eip+etve++
  NCBI__GCF_000691145.1:WP_035702262.1  77 QGVRTTYMKPVTEMESGTAHIILAE-GDNSIVVVKGANNEVTPHYVKDALSSIENIGIVLIQQEIPEETVEAV 148
                                           ***********************99.*********************************************** PP

                             TIGR02152 147 lkiakkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgievedledaekaaekllekgvkaviitl 219
                                           + i++++g+ v+lnPAPa+k +++++l+++ +i+pNe+Ea+++++       ++ +a +++ +k    ++it 
  NCBI__GCF_000691145.1:WP_035702262.1 149 CAICSEKGIPVILNPAPARK-VSQQILDQAAYITPNEHEAALMFDGL-----TIAEALRQYPNK----LLITE 211
                                           ******************66.889*******************9985.....666777777666....***** PP

                             TIGR02152 220 GskGallvskdekklipalkvkavDttaAGDtFigalavaLaegksledavrfanaaaalsVtrkGaqssiPt 292
                                           G++G+ + + +++ l+p + vkavDtt+AGDtF+galavaL+egksl da+ fan aa++sVt++Gaq ++P+
  NCBI__GCF_000691145.1:WP_035702262.1 212 GKNGVRYFDGSKEVLVPGYPVKAVDTTGAGDTFNGALAVALTEGKSLYDALAFANLAASISVTKFGAQGGMPA 284
                                           ************************************************************************* PP

                             TIGR02152 293 keeve 297
                                           +ee+e
  NCBI__GCF_000691145.1:WP_035702262.1 285 REELE 289
                                           ***97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (292 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: 18.19
//
[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:

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:

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:

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:

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