Alignments for a candidate for deoB in Lactobacillus silagei IWT126

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoB in Lactobacillus silagei IWT126

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_054656178.1 CES79_RS03075 phosphopentomutase

Query= BRENDA::Q818Z9
         (394 letters)



>NCBI__GCF_002217945.1:WP_054656178.1
          Length = 396

 Score =  464 bits (1193), Expect = e-135
 Identities = 220/395 (55%), Positives = 300/395 (75%), Gaps = 6/395 (1%)

Query: 4   YKRIFLVVMDSVGIGEAPDAEQFGDLGSDTIGHIAEHMNG-LQMPNMVKLGLGNIRE--- 59
           +KRIF +V+DSVGIGEA DA +F D+G+DT+GHI E   G L +PN+ K+GL NIR    
Sbjct: 3   FKRIFGIVIDSVGIGEASDANKFDDVGADTLGHIGEFYKGQLNLPNLAKMGLSNIRPDNP 62

Query: 60  MKGISKVEKPLGYYTKMQEKSTGKDTMTGHWEIMGLYIDTPFQVFPEGFPKELLDELEEK 119
           ++G++  E+P+GY+ KM E S GKD+M GHWE+MGL +  P   FP+GFP EL+ ++E+ 
Sbjct: 63  IEGVAVAEEPIGYFGKMHEVSVGKDSMDGHWEMMGLPVTEPLGFFPQGFPAELIKQIEDF 122

Query: 120 TGRKIIGNKPASGTEILDELGQEQMETGSLIVYTSADSVLQIAAHEEVVPLDELYKICKI 179
           +GR +I NKP SGT+++ + G+ Q+ETG LIVYTS DSVLQIAAH +V+PL ELYKIC+ 
Sbjct: 123 SGRHVIVNKPYSGTDVIHDYGEHQLETGDLIVYTSGDSVLQIAAHTDVIPLKELYKICEY 182

Query: 180 ARELTLDEKYMVGRVIARPFVG-EPGNFTRTPNRHDYALKPFGRTVMNELKDSDYDVIAI 238
           AR +T+D+ Y +GR+IARP+VG +  +FTRT +RHD+ L P G T ++ LK++  DV+A+
Sbjct: 183 ARSITIDKPYRIGRIIARPYVGPDKDHFTRTSDRHDFTLAPTGETDLDRLKNAGLDVLAV 242

Query: 239 GKISDIYDGEGVTESLRTKSNMDGMDKLVDTLNMDFTGLSFLNLVDFDALFGHRRDPQGY 298
           GKI+DI+ G+G+T+ + T SN DGMD+ +     DFTG SF NLVDFDA++GHRR+P+GY
Sbjct: 243 GKINDIFSGQGITKGVHTTSNADGMDQTLANAEKDFTGFSFTNLVDFDAMYGHRRNPEGY 302

Query: 299 GEALQEYDARLPEVFAKLKEDDLLLITADHGNDPIHPGTDHTREYVPLLAYSPSMKEGGQ 358
           G+AL  +D +L ++ A L++ DL++ITADHGNDP + GTDHTREYVPLLAYSP +K+ G 
Sbjct: 303 GQALMAFDKQLGDLLATLQDGDLVMITADHGNDPTYKGTDHTREYVPLLAYSPGLKQSG- 361

Query: 359 ELPLRQTFADIGATVAENFGVKMPEYGTSFLNELK 393
            L +R+T+AD GATV +NF V     GTSFL  LK
Sbjct: 362 SLGIRRTYADFGATVLDNFNVSGNPTGTSFLQTLK 396


Lambda     K      H
   0.316    0.138    0.398 

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: 30
Number of successful extensions: 5
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: 394
Length of database: 396
Length adjustment: 31
Effective length of query: 363
Effective length of database: 365
Effective search space:   132495
Effective search space used:   132495
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_054656178.1 CES79_RS03075 (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.4143757.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-164  533.4   0.3   1.5e-164  533.3   0.3    1.0  1  NCBI__GCF_002217945.1:WP_054656178.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002217945.1:WP_054656178.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  533.3   0.3  1.5e-164  1.5e-164       1     376 [.       5     385 ..       5     390 .. 0.98

  Alignments for each domain:
  == domain 1  score: 533.3 bits;  conditional E-value: 1.5e-164
                             TIGR01696   1 rvflivldsvGiGeaedaadfkdeGadtlghiaealdk.lnlpnleklGlgkiee...lagvdaveevlayya 69 
                                           r+f iv+dsvGiGea da++f+d+Gadtlghi e +++ lnlpnl+k+Gl++i     ++gv  +ee+++y++
  NCBI__GCF_002217945.1:WP_054656178.1   5 RIFGIVIDSVGIGEASDANKFDDVGADTLGHIGEFYKGqLNLPNLAKMGLSNIRPdnpIEGVAVAEEPIGYFG 77 
                                           7899******************************998758*************8767899************* PP

                             TIGR01696  70 klseassGkdtmtGhweiaGlnilkefkvfsngfpeelldkleeragrkvlgnkpasGtvildelGeehmktG 142
                                           k++e+s+Gkd+m Ghwe++Gl+++++ ++f++gfp el++++e+ +gr+v+ nkp sGt ++ ++Ge++++tG
  NCBI__GCF_002217945.1:WP_054656178.1  78 KMHEVSVGKDSMDGHWEMMGLPVTEPLGFFPQGFPAELIKQIEDFSGRHVIVNKPYSGTDVIHDYGEHQLETG 150
                                           ************************************************************************* PP

                             TIGR01696 143 klivytsadsvlqiaaheevvpleelyelcekarellkdpkyliGriiarpfvGe.aGnfkrtsnrhdyalkp 214
                                           +livyts dsvlqiaah +v+pl+ely++ce ar  + d  y iGriiarp+vG    +f+rts+rhd++l p
  NCBI__GCF_002217945.1:WP_054656178.1 151 DLIVYTSGDSVLQIAAHTDVIPLKELYKICEYARSITIDKPYRIGRIIARPYVGPdKDHFTRTSDRHDFTLAP 223
                                           ******************************************************7699*************** PP

                             TIGR01696 215 faktvldklkdekydvisiGkiadiydgeGitkkvrtksnmdgldkvikelkedftgisfanlvdfdalyGhr 287
                                            ++t ld+lk++++dv+++Gki+di++g+Gitk v+t+sn dg+d+++ + ++dftg sf+nlvdfda+yGhr
  NCBI__GCF_002217945.1:WP_054656178.1 224 TGETDLDRLKNAGLDVLAVGKINDIFSGQGITKGVHTTSNADGMDQTLANAEKDFTGFSFTNLVDFDAMYGHR 296
                                           ************************************************************************* PP

                             TIGR01696 288 rdkeGyaaaleefdarlpellsklreddlliltadhGndptatGtdhtreyipvlvyspkvkkgqalesaetf 360
                                           r++eGy++al  fd++l +ll+ l++ dl+++tadhGndpt++Gtdhtrey+p+l+ysp  k++ +l+ + t+
  NCBI__GCF_002217945.1:WP_054656178.1 297 RNPEGYGQALMAFDKQLGDLLATLQDGDLVMITADHGNDPTYKGTDHTREYVPLLAYSPGLKQSGSLGIRRTY 369
                                           ************************************************************************* PP

                             TIGR01696 361 adiGatladnfntskp 376
                                           ad Gat+ dnfn+s  
  NCBI__GCF_002217945.1:WP_054656178.1 370 ADFGATVLDNFNVSGN 385
                                           ************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (381 nodes)
Target sequences:                          1  (396 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: 25.55
//
[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