Alignments for a candidate for rbsK in Oceanisphaera arctica V1-41

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsK in Oceanisphaera arctica V1-41

Align ribokinase (characterized)
to candidate WP_104486314.1 UN63_RS08330 ribokinase

Query= CharProtDB::CH_024905
         (309 letters)



>NCBI__GCF_002936955.1:WP_104486314.1
          Length = 303

 Score =  337 bits (863), Expect = 3e-97
 Identities = 174/301 (57%), Positives = 222/301 (73%), Gaps = 1/301 (0%)

Query: 6   SLVVLGSINADHILNLQSFPTPGETVTGNHYQVAFGGKGANQAVAAGRSGANIAFIACTG 65
           +L V+GSIN DH++ L  FP PGET+TG+ Y++  GGKGANQAVAA R+GA   FIAC G
Sbjct: 2   TLTVVGSINIDHVIRLPQFPRPGETLTGSDYRIVPGGKGANQAVAAARAGAATRFIACVG 61

Query: 66  DDSIGESVRQQLATDNIDITPVSVIKGESTGVALIFVNGEGENVIGIHAGANAALSPALV 125
           DD++ +S+    A D ID   +  I G +TGVALI VNGEGEN I + AGAN  L+P  +
Sbjct: 62  DDALAQSLVDGFAADGIDTGAIDRITGINTGVALIQVNGEGENTISLAAGANGRLTPEQL 121

Query: 126 EAQRERIANASALLMQLESPLESVMAAAKIAHQNKTIVALNPAPARELPDELLALVDIIT 185
               E + N   LL+QLE PL++ +AAA  A      V LNPAPA+ LPD LL+LVD+IT
Sbjct: 122 NRHSEGL-NCEQLLLQLEIPLDTNIAAASQAKAQGARVVLNPAPAQALPDALLSLVDMIT 180

Query: 186 PNETEAEKLTGIRVENDEDAAKAAQVLHEKGIRTVLITLGSRGVWASVNGEGQRVPGFRV 245
           PNETEAE+LTG+ V +D  AA AAQ LH+KGI TV+ITLG+RGVW S  GEG+ +PGF+V
Sbjct: 181 PNETEAERLTGVAVNDDAGAAAAAQALHDKGIATVIITLGARGVWLSEQGEGRVIPGFKV 240

Query: 246 QAVDTIAAGDTFNGALITALLEEKPLPEAIRFAHAAAAIAVTRKGAQPSVPWREEIDAFL 305
           +AVDT AAGDTFNGAL+ AL +++PL +A+RFA AAAA++VT+ GAQ SVP++ EI A L
Sbjct: 241 KAVDTTAAGDTFNGALLAALQQQQPLEQAVRFAQAAAALSVTKPGAQTSVPYQAEIVALL 300

Query: 306 D 306
           +
Sbjct: 301 E 301


Lambda     K      H
   0.314    0.131    0.363 

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: 352
Number of extensions: 13
Number of successful extensions: 2
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: 309
Length of database: 303
Length adjustment: 27
Effective length of query: 282
Effective length of database: 276
Effective search space:    77832
Effective search space used:    77832
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: 42 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate WP_104486314.1 UN63_RS08330 (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.294735.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.8e-114  365.6   6.8   1.1e-113  365.5   6.8    1.0  1  NCBI__GCF_002936955.1:WP_104486314.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002936955.1:WP_104486314.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  365.5   6.8  1.1e-113  1.1e-113       2     296 ..       4     296 ..       3     298 .. 0.98

  Alignments for each domain:
  == domain 1  score: 365.5 bits;  conditional E-value: 1.1e-113
                             TIGR02152   2 vvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefgeellenlkke 74 
                                           +vvGSin+D+v+r +++p+pGet+++++++i++GGKGANQAvaaar ga++++i++vG+D+ +++l++ ++++
  NCBI__GCF_002936955.1:WP_104486314.1   4 TVVGSINIDHVIRLPQFPRPGETLTGSDYRIVPGGKGANQAVAAARAGAATRFIACVGDDALAQSLVDGFAAD 76 
                                           8************************************************************************ PP

                             TIGR02152  75 gidteyvkkvkktstGvAlilvdeegeNsIvvvaGaneeltpedvkaaeekikesdlvllQlEipletveeal 147
                                           gidt  + +++  +tGvAli+v+ egeN+I ++aGan +ltpe++++++e + +++ +llQlEipl+t+++a+
  NCBI__GCF_002936955.1:WP_104486314.1  77 GIDTGAIDRITGINTGVALIQVNGEGENTISLAAGANGRLTPEQLNRHSEGL-NCEQLLLQLEIPLDTNIAAA 148
                                           ***********************************************97766.79999*************** PP

                             TIGR02152 148 kiakkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgievedledaekaaekllekgvkaviitlG 220
                                           + ak++g  v+lnPAPa++ l++ llslvd+i+pNetEae Ltg++v+d + a +aa++l++kg+ +viitlG
  NCBI__GCF_002936955.1:WP_104486314.1 149 SQAKAQGARVVLNPAPAQA-LPDALLSLVDMITPNETEAERLTGVAVNDDAGAAAAAQALHDKGIATVIITLG 220
                                           *****************55.99*************************************************** PP

                             TIGR02152 221 skGallvskdekklipalkvkavDttaAGDtFigalavaLaegksledavrfanaaaalsVtrkGaqssiPtk 293
                                           ++G+ l++++e ++ip +kvkavDttaAGDtF+gal +aL++++ le+avrfa+aaaalsVt+ Gaq+s+P++
  NCBI__GCF_002936955.1:WP_104486314.1 221 ARGVWLSEQGEGRVIPGFKVKAVDTTAAGDTFNGALLAALQQQQPLEQAVRFAQAAAALSVTKPGAQTSVPYQ 293
                                           ************************************************************************* PP

                             TIGR02152 294 eev 296
                                           +e+
  NCBI__GCF_002936955.1:WP_104486314.1 294 AEI 296
                                           *98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (303 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 18.40
//
[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