Alignments for a candidate for deoB in Methylocapsa aurea KYG

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoB in Methylocapsa aurea KYG

Align Phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_036262414.1 DL86_RS13415 phosphopentomutase

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



>NCBI__GCF_000746085.1:WP_036262414.1
          Length = 409

 Score =  418 bits (1074), Expect = e-121
 Identities = 202/406 (49%), Positives = 271/406 (66%), Gaps = 2/406 (0%)

Query: 1   MKRTVIMMLDSFGVGAAGDAAKFGDVGSDTFGHIAKACAEGKADTG--RKGPLALPNLAR 58
           M R +I++LDS G G A DAA +GD G+DT GH+A ACA G+ D    R+G L  PNL  
Sbjct: 1   MPRALILVLDSVGCGGAQDAALYGDAGADTLGHLAVACATGRGDRNGVRQGLLNAPNLDA 60

Query: 59  LGLAHAAMESTGAFAPGFADNVDLIGAYGHAQELSSGKDTPSGHWEMAGVPVLFEWGYFS 118
           LGL   A+ S+G   PGF+   +    +G+  E + GKDTPSGHWEMAG P L  WGYF 
Sbjct: 61  LGLGLVALASSGMMPPGFSLPAEPKALWGYGVECAQGKDTPSGHWEMAGAPALAPWGYFP 120

Query: 119 EHQNSFPKELTDKILARAGLDGFLGNCHASGTTILEELGEEHMRSGKPIFYTSADSVFQI 178
           +    FP +LT  ++A  GL G LG+CHA G  I+E LG EH+R+G PI YTSADSVFQI
Sbjct: 121 KAAPCFPPKLTQALIAEGGLPGILGDCHAPGIEIIERLGAEHIRTGMPICYTSADSVFQI 180

Query: 179 ACHEGTFGLENLYRLCEIAREELEPYNIGRVIARPFDGTGPSDFARTGNRKDYSLEPPAK 238
           A HE  FGLE LY LC++AR   +   IGRVIARPF G     F RT  RKD+++ PP  
Sbjct: 181 AAHEEHFGLERLYDLCKVARRLCDALAIGRVIARPFVGDARQGFVRTPRRKDFAIPPPPG 240

Query: 239 TVLDKLKAAGGEVVSVGKIADIYAYCGITKKVKANGLEALFDATLAEVKSAGENTIVFTN 298
            +L+++  AG  + S+GK+ DI+A+C   +++K +G  A FDATL  ++   +  ++ TN
Sbjct: 241 NLLERVAQAGRAMASIGKVGDIFAHCFTGQEIKRDGNMAHFDATLEALRDLPDGGLIITN 300

Query: 299 FVDFDSHYGHRRDVAGYAKGLEYFDARLPEMLALLDEDDLLILTADHGCDPTWQGTDHTR 358
           F+DFD+ +GHRRD+AGYA  LE FD+R+PE+ A +   DL ++++DHG DPTW GTDHTR
Sbjct: 301 FLDFDTDFGHRRDIAGYAHCLEIFDSRMPELFAAMRPGDLAVISSDHGNDPTWTGTDHTR 360

Query: 359 EYVPVLAYGAGLKAGSLGRRNSFADIGQSIASYFKLEPMEYGESFI 404
           E+ P+L +G  +  G +GRR SFADIG S+A++ +L     G SF+
Sbjct: 361 EHAPILCFGPRVAGGPIGRRESFADIGASLAAHLELPATASGSSFL 406


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: 580
Number of extensions: 23
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: 409
Length adjustment: 31
Effective length of query: 373
Effective length of database: 378
Effective search space:   140994
Effective search space used:   140994
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_036262414.1 DL86_RS13415 (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.2102856.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.1e-124  400.6   0.0   3.5e-124  400.4   0.0    1.0  1  NCBI__GCF_000746085.1:WP_036262414.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000746085.1:WP_036262414.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.4   0.0  3.5e-124  3.5e-124       1     373 [.       3     396 ..       3     404 .. 0.96

  Alignments for each domain:
  == domain 1  score: 400.4 bits;  conditional E-value: 3.5e-124
                             TIGR01696   1 rvflivldsvGiGeaedaadfkdeGadtlghiaealdk............lnlpnleklGlgkiee......l 55 
                                           r+ ++vldsvG G a+daa ++d Gadtlgh+a a++             ln pnl+ lGlg +        +
  NCBI__GCF_000746085.1:WP_036262414.1   3 RALILVLDSVGCGGAQDAALYGDAGADTLGHLAVACATgrgdrngvrqglLNAPNLDALGLGLVALassgmmP 75 
                                           789**********************************99***********************99877789989 PP

                             TIGR01696  56 agvdaveevlayyaklseassGkdtmtGhweiaGlnilkefkvfs...ngfpeelldkleeragrk.vlgnkp 124
                                           +g    +e+ a ++   e ++Gkdt++Ghwe+aG + l ++++f+     fp +l + l    g++ +lg+++
  NCBI__GCF_000746085.1:WP_036262414.1  76 PGFSLPAEPKALWGYGVECAQGKDTPSGHWEMAGAPALAPWGYFPkaaPCFPPKLTQALIAEGGLPgILGDCH 148
                                           99*******************************************66668****************9****** PP

                             TIGR01696 125 asGtvildelGeehmktGklivytsadsvlqiaaheevvpleelyelcekarellkdpkyliGriiarpfvGe 197
                                           a G  i+++lG eh++tG +i ytsadsv+qiaahee ++le+ly+lc++ar l       iGr+iarpfvG+
  NCBI__GCF_000746085.1:WP_036262414.1 149 APGIEIIERLGAEHIRTGMPICYTSADSVFQIAAHEEHFGLERLYDLCKVARRLCD--ALAIGRVIARPFVGD 219
                                           ****************************************************9874..589************ PP

                             TIGR01696 198 aGn.fkrtsnrhdyalkpfaktvldklkdekydvisiGkiadiydgeGitkkvrtksnmdgldkvikelkedf 269
                                           a + f rt+ r+d+a+ p+   +l+++ +++  + siGk+ di++ +   ++++  +nm+ +d++++ l++  
  NCBI__GCF_000746085.1:WP_036262414.1 220 ARQgFVRTPRRKDFAIPPPPGNLLERVAQAGRAMASIGKVGDIFAHCFTGQEIKRDGNMAHFDATLEALRDLP 292
                                           6544*******************************************************************99 PP

                             TIGR01696 270 tg.isfanlvdfdalyGhrrdkeGyaaaleefdarlpellsklreddlliltadhGndptatGtdhtreyipv 341
                                           +g +  +n++dfd+ +Ghrrd +Gya++le fd+r+pel++ +r  dl ++++dhGndpt+tGtdhtre+ p+
  NCBI__GCF_000746085.1:WP_036262414.1 293 DGgLIITNFLDFDTDFGHRRDIAGYAHCLEIFDSRMPELFAAMRPGDLAVISSDHGNDPTWTGTDHTREHAPI 365
                                           998********************************************************************** PP

                             TIGR01696 342 lvyspkvkkgqalesaetfadiGatladnfnt 373
                                           l ++p+v +g  ++++e+fadiGa+la +++ 
  NCBI__GCF_000746085.1:WP_036262414.1 366 LCFGPRVAGG-PIGRRESFADIGASLAAHLEL 396
                                           ********99.9***************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (381 nodes)
Target sequences:                          1  (409 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: 24.83
//
[ok]

This GapMind analysis is from Apr 09 2024. 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