Alignments for a candidate for deoB in Methylobacterium nodulans ORS 2060

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoB in Methylobacterium nodulans ORS 2060

Align Phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_015931598.1 MNOD_RS24240 phosphopentomutase

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



>NCBI__GCF_000022085.1:WP_015931598.1
          Length = 407

 Score =  450 bits (1157), Expect = e-131
 Identities = 228/400 (57%), Positives = 279/400 (69%), Gaps = 4/400 (1%)

Query: 1   MKRTVIMMLDSFGVGAAGDAAKFGDVGSDTFGHIAKACAEGKADTG--RKGPLALPNLAR 58
           M R ++++LDS G+G A DAA +GD G+DT GHIA +CA G  D    R+GPL LP+LA 
Sbjct: 1   MSRALLIVLDSVGIGGAPDAASYGDEGADTVGHIAASCARGAGDRAGLRQGPLRLPHLAA 60

Query: 59  LGLAHAAMESTGAFAPGFADNVDLIGAYGHAQELSSGKDTPSGHWEMAGVPVLFEWGYFS 118
           LGL  AA  +TG   PG A    + GA+GHA E + GKDT SGHWE+AGVPV F+WG F 
Sbjct: 61  LGLGLAAEAATGRMPPGLAPAGSVTGAWGHAVETARGKDTVSGHWEIAGVPVDFDWGRFP 120

Query: 119 EHQNSFPKELTDKILARAGLDGFLGNCHASGTTILEELGEEHMRSGKPIFYTSADSVFQI 178
             + SFP ELT  ++A AGL G LG+CHASGT I+EELG E +R+GKPI YTS DSVFQI
Sbjct: 121 ATEPSFPPELTQALIAEAGLPGILGDCHASGTAIIEELGAEQVRTGKPICYTSVDSVFQI 180

Query: 179 ACHEGTFGLENLYRLCEIAREELEPYNIGRVIARPFDGTGPSDFARTGNRKDYSLEPPAK 238
           A HE  FGLE L  +C +AR   +PY IGRVIARPF G     F RT NR+D++  PP+ 
Sbjct: 181 AAHEEAFGLERLSAVCAVARRLCDPYRIGRVIARPFTGDARRGFVRTANRRDFATPPPSD 240

Query: 239 TVLDKLKAAGGEVVSVGKIADIYAYCGITKKVKANGLEALFDATLAEVKSA--GENTIVF 296
           T+LD+L AAG  VVSVGKI DI+A+     +VK  G EA  DA LA    +  G   +VF
Sbjct: 241 TLLDRLVAAGRPVVSVGKIGDIFAHRSTGSEVKPAGNEACLDAALAAFAESGLGPGGLVF 300

Query: 297 TNFVDFDSHYGHRRDVAGYAKGLEYFDARLPEMLALLDEDDLLILTADHGCDPTWQGTDH 356
            N VDFD+ YGHRRDV GYA  LE FDAR+PE+ A L   DL ++TADHG DPTW GTDH
Sbjct: 301 VNLVDFDTEYGHRRDVPGYAAALERFDARIPEIRAGLAPGDLCVITADHGNDPTWSGTDH 360

Query: 357 TREYVPVLAYGAGLKAGSLGRRNSFADIGQSIASYFKLEP 396
           TRE VPVL++G GL+ G LGRR++FADIG ++A++  L P
Sbjct: 361 TREQVPVLSFGPGLRPGPLGRRDTFADIGAALAAHLGLPP 400


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: 590
Number of extensions: 25
Number of successful extensions: 3
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: 407
Length adjustment: 31
Effective length of query: 373
Effective length of database: 376
Effective search space:   140248
Effective search space used:   140248
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_015931598.1 MNOD_RS24240 (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.2942430.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     4e-135  436.4   0.0   4.9e-135  436.2   0.0    1.0  1  NCBI__GCF_000022085.1:WP_015931598.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000022085.1:WP_015931598.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  436.2   0.0  4.9e-135  4.9e-135       1     371 [.       3     396 ..       3     402 .. 0.97

  Alignments for each domain:
  == domain 1  score: 436.2 bits;  conditional E-value: 4.9e-135
                             TIGR01696   1 rvflivldsvGiGeaedaadfkdeGadtlghiaealdk............lnlpnleklGlgkiee......l 55 
                                           r+ livldsvGiG a+daa ++deGadt+ghia ++++            l+lp l+ lGlg + e      +
  NCBI__GCF_000022085.1:WP_015931598.1   3 RALLIVLDSVGIGGAPDAASYGDEGADTVGHIAASCARgagdraglrqgpLRLPHLAALGLGLAAEaatgrmP 75 
                                           789**********************************99*************************999999999 PP

                             TIGR01696  56 agvdaveevlayyaklseassGkdtmtGhweiaGlnilkefkvfs...ngfpeelldkleeragrk.vlgnkp 124
                                           +g+  +  v ++++++ e++ Gkdt++GhweiaG++++++++ f+    +fp el + l   ag++ +lg+++
  NCBI__GCF_000022085.1:WP_015931598.1  76 PGLAPAGSVTGAWGHAVETARGKDTVSGHWEIAGVPVDFDWGRFPatePSFPPELTQALIAEAGLPgILGDCH 148
                                           9********************************************88779*********************** PP

                             TIGR01696 125 asGtvildelGeehmktGklivytsadsvlqiaaheevvpleelyelcekarellkdpkyliGriiarpfvGe 197
                                           asGt+i++elG e+++tGk+i yts dsv+qiaahee ++le+l  +c +ar l  dp y iGr+iarpf G+
  NCBI__GCF_000022085.1:WP_015931598.1 149 ASGTAIIEELGAEQVRTGKPICYTSVDSVFQIAAHEEAFGLERLSAVCAVARRLC-DP-YRIGRVIARPFTGD 219
                                           ****************************************************875.54.************** PP

                             TIGR01696 198 .aGnfkrtsnrhdyalkpfaktvldklkdekydvisiGkiadiydgeGitkkvrtksnmdgldkvikelkedf 269
                                               f rt+nr d+a  p++ t+ld+l+ ++  v+s+Gki di++     ++v+  +n++ ld+ +  + e++
  NCBI__GCF_000022085.1:WP_015931598.1 220 aRRGFVRTANRRDFATPPPSDTLLDRLVAAGRPVVSVGKIGDIFAHRSTGSEVKPAGNEACLDAALAAFAESG 292
                                           5567*******************************************************************98 PP

                             TIGR01696 270 tg...isfanlvdfdalyGhrrdkeGyaaaleefdarlpellsklreddlliltadhGndptatGtdhtreyi 339
                                            g   ++f+nlvdfd+ yGhrrd++Gyaaale fdar+pe+ + l   dl ++tadhGndpt++Gtdhtre +
  NCBI__GCF_000022085.1:WP_015931598.1 293 LGpggLVFVNLVDFDTEYGHRRDVPGYAAALERFDARIPEIRAGLAPGDLCVITADHGNDPTWSGTDHTREQV 365
                                           65556******************************************************************** PP

                             TIGR01696 340 pvlvyspkvkkgqalesaetfadiGatladnf 371
                                           pvl ++p  ++g  l++++tfadiGa+la ++
  NCBI__GCF_000022085.1:WP_015931598.1 366 PVLSFGPGLRPG-PLGRRDTFADIGAALAAHL 396
                                           ************.9**************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (381 nodes)
Target sequences:                          1  (407 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: 21.51
//
[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