Alignments for a candidate for rbsK in Planktomarina temperata RCA23

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsK in Planktomarina temperata RCA23

Align deoxyribose kinase (EC 2.7.1.15) (characterized)
to candidate WP_044050603.1 RCA23_RS12565 ribokinase

Query= reanno::BFirm:BPHYT_RS25805
         (328 letters)



>NCBI__GCF_000738435.1:WP_044050603.1
          Length = 306

 Score =  318 bits (815), Expect = 1e-91
 Identities = 162/300 (54%), Positives = 205/300 (68%)

Query: 13  VVILGIYVTDLTFRAGRMPQIGETIAGTAFAMGPGGKGSNQAVAAARVGADVVFCTRIGN 72
           +VILG++V D  +RA R P++GETI G +FA+GPGGKGSNQ+VAA   GA V F T++G 
Sbjct: 5   IVILGVFVADTAYRAQRQPRLGETILGQSFALGPGGKGSNQSVAAGMAGASVGFITKLGK 64

Query: 73  DAFGSIARATWAAEGITARASVIDGVSTGAAHIFVDDNTGMNAIIVASGAAGTMEAADVD 132
           D F  +A ATW   G+T+ A+      TGAA+IFVD+NTG NAIIV  GAA T+  +D+D
Sbjct: 65  DPFADMALATWKKAGVTSLATRHADDYTGAAYIFVDENTGDNAIIVCPGAAATINRSDID 124

Query: 133 AIEADIAAARVFVTQLEQPLAAARRGLEVARKHGVITVFNPAPAMPLDDAIFPLCDYITP 192
           +    I   +V +TQLEQP+ AA   L  ARK G  T+ NPAPA+ L  ++  LCD++TP
Sbjct: 125 SHAEVIKQCKVLMTQLEQPIDAAEYALACARKAGATTILNPAPAVELPTSMIALCDFVTP 184

Query: 193 NETEATALTGVPIANADDARRAADVLLAKGVGTAIITLGEGGALLHSANQSLLVPAYHCG 252
           NE EA  +TG+ + +  DA  AA+ LLAKG G AIITLGE G L H  + S+ VPA + G
Sbjct: 185 NEIEAETITGITVNSPKDAVAAAEALLAKGAGGAIITLGENGCLYHDGSNSVHVPAINAG 244

Query: 253 RVVETAGAGDGFTGGFAAALARGDDAITALRFGCALAGISVTRPGTAPSMPTLDEVNQVL 312
            VVET GAGD F GGFA A+A G   + A+RFG A A ISVTRPGTAPSMPT  E+  +L
Sbjct: 245 PVVETTGAGDAFNGGFAVAIAEGHSPLEAIRFGTATAAISVTRPGTAPSMPTRKEIESLL 304


Lambda     K      H
   0.318    0.133    0.384 

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: 286
Number of extensions: 11
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: 328
Length of database: 306
Length adjustment: 27
Effective length of query: 301
Effective length of database: 279
Effective search space:    83979
Effective search space used:    83979
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_044050603.1 RCA23_RS12565 (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.1979768.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    9.6e-96  306.6   4.4    1.1e-95  306.4   4.4    1.0  1  NCBI__GCF_000738435.1:WP_044050603.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000738435.1:WP_044050603.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.4   4.4   1.1e-95   1.1e-95       1     297 [.       5     301 ..       5     302 .. 0.97

  Alignments for each domain:
  == domain 1  score: 306.4 bits;  conditional E-value: 1.1e-95
                             TIGR02152   1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefgeellenlkk 73 
                                           iv++G + +D+  r++r p+ Get+ +++f +++GGKG+NQ+vaa   ga+v +i+k+GkD f++++l ++kk
  NCBI__GCF_000738435.1:WP_044050603.1   5 IVILGVFVADTAYRAQRQPRLGETILGQSFALGPGGKGSNQSVAAGMAGASVGFITKLGKDPFADMALATWKK 77 
                                           89*********************************************************************** PP

                             TIGR02152  74 egidteyvkkvkktstGvAlilvde.egeNsIvvvaGaneeltpedvkaaeekikesdlvllQlEipletvee 145
                                            g+ t+  +++++  tG A+i+vde +g+N+I+v+ Ga ++++ +d+++++e ik++++++ QlE p++++e+
  NCBI__GCF_000738435.1:WP_044050603.1  78 AGV-TSLATRHADDYTGAAYIFVDEnTGDNAIIVCPGAAATINRSDIDSHAEVIKQCKVLMTQLEQPIDAAEY 149
                                           ***.78888889999********86369********************************************* PP

                             TIGR02152 146 alkiakkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgievedledaekaaekllekgvkaviit 218
                                           al +a+kag +++lnPAPa + l++++++l+d+++pNe Eae++tgi+v++ +da +aae+ll+kg+   iit
  NCBI__GCF_000738435.1:WP_044050603.1 150 ALACARKAGATTILNPAPAVE-LPTSMIALCDFVTPNEIEAETITGITVNSPKDAVAAAEALLAKGAGGAIIT 221
                                           *******************66.99************************************************* PP

                             TIGR02152 219 lGskGallvskdekklipalkvk.avDttaAGDtFigalavaLaegksledavrfanaaaalsVtrkGaqssi 290
                                           lG++G+l+++ +++ ++pa+++  +v tt+AGD+F+g++ava+aeg+s  +a+rf++a aa+sVtr G+++s+
  NCBI__GCF_000738435.1:WP_044050603.1 222 LGENGCLYHDGSNSVHVPAINAGpVVETTGAGDAFNGGFAVAIAEGHSPLEAIRFGTATAAISVTRPGTAPSM 294
                                           ********************996368*********************************************** PP

                             TIGR02152 291 Ptkeeve 297
                                           Pt++e+e
  NCBI__GCF_000738435.1:WP_044050603.1 295 PTRKEIE 301
                                           *****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (306 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: 15.38
//
[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