Alignments for a candidate for deoB in Rhodanobacter denitrificans 2APBS1

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoB in Rhodanobacter denitrificans 2APBS1

Align Phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_015448445.1 R2APBS1_RS14130 phosphopentomutase

Query= reanno::MR1:200397
         (404 letters)



>NCBI__GCF_000230695.2:WP_015448445.1
          Length = 402

 Score =  452 bits (1164), Expect = e-132
 Identities = 226/404 (55%), Positives = 286/404 (70%), Gaps = 5/404 (1%)

Query: 1   MKRTVIMMLDSFGVGAAGDAAKFGDVGSDTFGHIAKACAEGKADTGRKGPLALPNLARLG 60
           M R + ++ DS G+GAA DAA +GD+G+DTFGHIA AC         +GPL LP  +RLG
Sbjct: 1   MTRAIWLVCDSLGLGAAPDAAAYGDLGADTFGHIAAACV-----AAARGPLRLPQFSRLG 55

Query: 61  LAHAAMESTGAFAPGFADNVDLIGAYGHAQELSSGKDTPSGHWEMAGVPVLFEWGYFSEH 120
           L  A     G  APGF       G +GHA E + GKDTPSGHWE AGV +   +G F + 
Sbjct: 56  LPQAHAAIHGQAAPGFVGLPAPEGLWGHAVERARGKDTPSGHWETAGVVLTQPFGVFGQA 115

Query: 121 QNSFPKELTDKILARAGLDGFLGNCHASGTTILEELGEEHMRSGKPIFYTSADSVFQIAC 180
           ++SFP  L   ++ +  + G LGNCHASGT I++ LG EH+R+G PI YTSADSVFQIA 
Sbjct: 116 EHSFPPALLQALVTQGDVPGVLGNCHASGTEIIQRLGAEHLRNGCPIVYTSADSVFQIAA 175

Query: 181 HEGTFGLENLYRLCEIAREELEPYNIGRVIARPFDGTGPSDFARTGNRKDYSLEPPAKTV 240
           HE  FGLE LYRLCE+AR  L  Y+IGRVIARPF G   + F+RT +R+DY+L PPA T+
Sbjct: 176 HEQAFGLERLYRLCELARALLADYHIGRVIARPFVGDAETGFSRTVHRRDYALPPPAPTL 235

Query: 241 LDKLKAAGGEVVSVGKIADIYAYCGITKKVKANGLEALFDATLAEVKSAGENTIVFTNFV 300
            D L+AAGGEV+++GKI DI+A+ G+++ V A G +ALFDATLA +  AG ++++ TNFV
Sbjct: 236 FDALQAAGGEVIAIGKIDDIFAHRGVSRVVHAYGHDALFDATLAAMAQAGAHSLIATNFV 295

Query: 301 DFDSHYGHRRDVAGYAKGLEYFDARLPEMLALLDEDDLLILTADHGCDPTWQGTDHTREY 360
           DFD  YGHRRDV GYA  LE  DARLPE+L  L   DLL+++ADHGCDP W G+DHTRE 
Sbjct: 296 DFDMLYGHRRDVLGYAAALEALDARLPELLQALQPGDLLVVSADHGCDPVWPGSDHTREC 355

Query: 361 VPVLAYGAGLKAGSLGRRNSFADIGQSIASYFKLEPMEYGESFI 404
           +PVLA+  GL   +LGRR+SFADIGQS+AS+  L P+  G SF+
Sbjct: 356 IPVLAFAPGLAPRALGRRDSFADIGQSMASHLGLPPLAAGRSFL 399


Lambda     K      H
   0.318    0.137    0.412 

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: 567
Number of extensions: 21
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: 404
Length of database: 402
Length adjustment: 31
Effective length of query: 373
Effective length of database: 371
Effective search space:   138383
Effective search space used:   138383
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: 50 (23.9 bits)

Align candidate WP_015448445.1 R2APBS1_RS14130 (phosphopentomutase)
to HMM TIGR01696 (deoB: phosphopentomutase (EC 5.4.2.7))

# 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/TIGR01696.hmm
# target sequence database:        /tmp/gapView.1374553.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01696  [M=381]
Accession:   TIGR01696
Description: deoB: phosphopentomutase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.3e-134  432.1   0.0   9.2e-134  432.0   0.0    1.0  1  NCBI__GCF_000230695.2:WP_015448445.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000230695.2:WP_015448445.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  432.0   0.0  9.2e-134  9.2e-134       1     373 [.       3     389 ..       3     397 .. 0.96

  Alignments for each domain:
  == domain 1  score: 432.0 bits;  conditional E-value: 9.2e-134
                             TIGR01696   1 rvflivldsvGiGeaedaadfkdeGadtlghiaealdk.....lnlpnleklGlgkiee......lagvdave 62 
                                           r+  +v ds+G+G+a+daa ++d Gadt+ghia a+       l+lp++++lGl +++        +g  +  
  NCBI__GCF_000230695.2:WP_015448445.1   3 RAIWLVCDSLGLGAAPDAAAYGDLGADTFGHIAAACVAaargpLRLPQFSRLGLPQAHAaihgqaAPGFVGLP 75 
                                           66779******************************98889999*************99988888888999999 PP

                             TIGR01696  63 evlayyaklseassGkdtmtGhweiaGlnilkefkvfs...ngfpeelldkleeragrk.vlgnkpasGtvil 131
                                            +++ ++++ e + Gkdt++Ghwe aG+ ++++f+vf    ++fp  ll+ l+ + + + vlgn++asGt i+
  NCBI__GCF_000230695.2:WP_015448445.1  76 APEGLWGHAVERARGKDTPSGHWETAGVVLTQPFGVFGqaeHSFPPALLQALVTQGDVPgVLGNCHASGTEII 148
                                           *************************************988889****************9************* PP

                             TIGR01696 132 delGeehmktGklivytsadsvlqiaaheevvpleelyelcekarellkdpkyliGriiarpfvGe.aGnfkr 203
                                           ++lG eh++ G +ivytsadsv+qiaahe+ ++le+ly+lce ar ll d  y iGr+iarpfvG+    f r
  NCBI__GCF_000230695.2:WP_015448445.1 149 QRLGAEHLRNGCPIVYTSADSVFQIAAHEQAFGLERLYRLCELARALLAD--YHIGRVIARPFVGDaETGFSR 219
                                           **********************************************9976..**************6678*** PP

                             TIGR01696 204 tsnrhdyalkpfaktvldklkdekydvisiGkiadiydgeGitkkvrtksnmdgldkvikelkedftg.isfa 275
                                           t  r dyal p+a+t++d l+ ++ +vi+iGki di++  G+++ v++ + ++++d+++  + +++   +  +
  NCBI__GCF_000230695.2:WP_015448445.1 220 TVHRRDYALPPPAPTLFDALQAAGGEVIAIGKIDDIFAHRGVSRVVHAYGHDALFDATLAAMAQAGAHsLIAT 292
                                           *****************************************************************9888**** PP

                             TIGR01696 276 nlvdfdalyGhrrdkeGyaaaleefdarlpellsklreddlliltadhGndptatGtdhtreyipvlvyspkv 348
                                           n+vdfd lyGhrrd+ Gyaaale +darlpell  l+  dll+++adhG+dp+++G+dhtre ipvl+++p  
  NCBI__GCF_000230695.2:WP_015448445.1 293 NFVDFDMLYGHRRDVLGYAAALEALDARLPELLQALQPGDLLVVSADHGCDPVWPGSDHTRECIPVLAFAPGL 365
                                           ************************************************************************* PP

                             TIGR01696 349 kkgqalesaetfadiGatladnfnt 373
                                            +  al+++++fadiG+++a +++ 
  NCBI__GCF_000230695.2:WP_015448445.1 366 APR-ALGRRDSFADIGQSMASHLGL 389
                                           998.****************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (381 nodes)
Target sequences:                          1  (402 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 25.37
//
[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 2024 update 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