Alignments for a candidate for deoB in Lactobacillus oryzae SG293

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoB in Lactobacillus oryzae SG293

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_034529052.1 LOSG293_RS07900 phosphopentomutase

Query= BRENDA::Q818Z9
         (394 letters)



>NCBI__GCF_000740055.1:WP_034529052.1
          Length = 395

 Score =  465 bits (1197), Expect = e-136
 Identities = 230/395 (58%), Positives = 295/395 (74%), Gaps = 5/395 (1%)

Query: 3   KYKRIFLVVMDSVGIGEAPDAEQFGDLGSDTIGHIAEHMNG-LQMPNMVKLGLGNIRE-- 59
           KYKR+F +V+DSVG G APDAE+F D+GSDT+GHI EH  G LQ+PN+ K+G+ N+RE  
Sbjct: 2   KYKRVFGLVLDSVGTGAAPDAEKFDDVGSDTLGHIGEHFAGKLQIPNLQKMGISNLRETP 61

Query: 60  MKGISKVEKPLGYYTKMQEKSTGKDTMTGHWEIMGLYIDTPFQVFPEGFPKELLDELEEK 119
           ++G+  VE P+GYY KM+E S GKD+M GHWE+MGL +      FP GFPKE+LD++   
Sbjct: 62  IEGVPAVETPIGYYGKMRETSAGKDSMDGHWEMMGLPVKHALNTFPNGFPKEILDKISAF 121

Query: 120 TGRKIIGNKPASGTEILDELGQEQMETGSLIVYTSADSVLQIAAHEEVVPLDELYKICKI 179
           +GRKIIGN P SGT+I+ ELG++QM+TG LIVYTS DSV+QIAAHE+++PLDELYKIC+ 
Sbjct: 122 SGRKIIGNCPESGTKIIAELGEQQMKTGDLIVYTSGDSVIQIAAHEDIIPLDELYKICEY 181

Query: 180 ARELTLDEKYMVGRVIARPFVG-EPGNFTRTPNRHDYALKPFGRTVMNELKDSDYDVIAI 238
            R L    +Y VGR+IARP+VG +  +FTRT NRHD+ L+P G+T ++ L+++    I I
Sbjct: 182 TRTLVNGPEYTVGRIIARPYVGPDKDHFTRTANRHDFTLEPTGKTDIDYLQEAGVHTIGI 241

Query: 239 GKISDIYDGEGVTESLRTKSNMDGMDKLVDTLNMDFTGLSFLNLVDFDALFGHRRDPQGY 298
           GKI+DI+ G G+ E    +SNMDGMD +   +  DFTG  F+NLVDFDA++GHRR+P+G+
Sbjct: 242 GKINDIFSGHGIDEGYHNESNMDGMDHVDHVMAEDFTGFCFINLVDFDAMYGHRRNPEGF 301

Query: 299 GEALQEYDARLPEVFAKLKEDDLLLITADHGNDPIHPGTDHTREYVPLLAYSPSMKEGGQ 358
           G+AL ++D RL  V  ++K DDLLLITADHGNDP   G+DHTRE VPLLAYSPSM   G 
Sbjct: 302 GQALMDFDKRLGTVLDQMKPDDLLLITADHGNDPGFKGSDHTREQVPLLAYSPSMTTSG- 360

Query: 359 ELPLRQTFADIGATVAENFGVKMPEYGTSFLNELK 393
            L  R  FAD GATV ENF V     G SFL+ELK
Sbjct: 361 SLGTRSPFADFGATVLENFDVTGNGVGESFLSELK 395


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: 646
Number of extensions: 35
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: 395
Length adjustment: 31
Effective length of query: 363
Effective length of database: 364
Effective search space:   132132
Effective search space used:   132132
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_034529052.1 LOSG293_RS07900 (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.1011536.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-160  520.1   0.2   1.7e-160  519.9   0.2    1.0  1  NCBI__GCF_000740055.1:WP_034529052.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000740055.1:WP_034529052.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  519.9   0.2  1.7e-160  1.7e-160       1     379 [.       5     387 ..       5     389 .. 0.98

  Alignments for each domain:
  == domain 1  score: 519.9 bits;  conditional E-value: 1.7e-160
                             TIGR01696   1 rvflivldsvGiGeaedaadfkdeGadtlghiaealdk.lnlpnleklGlgkiee..lagvdaveevlayyak 70 
                                           rvf +vldsvG G+a+da++f+d+G+dtlghi e++++ l++pnl+k+G++++ e  ++gv ave +++yy+k
  NCBI__GCF_000740055.1:WP_034529052.1   5 RVFGLVLDSVGTGAAPDAEKFDDVGSDTLGHIGEHFAGkLQIPNLQKMGISNLREtpIEGVPAVETPIGYYGK 77 
                                           8999********************************9659*************998899************** PP

                             TIGR01696  71 lseassGkdtmtGhweiaGlnilkefkvfsngfpeelldkleeragrkvlgnkpasGtvildelGeehmktGk 143
                                           ++e+s+Gkd+m Ghwe++Gl++++  + f+ngfp+e+ldk+   +grk++gn+p sGt+i+ elGe++mktG+
  NCBI__GCF_000740055.1:WP_034529052.1  78 MRETSAGKDSMDGHWEMMGLPVKHALNTFPNGFPKEILDKISAFSGRKIIGNCPESGTKIIAELGEQQMKTGD 150
                                           ************************************************************************* PP

                             TIGR01696 144 livytsadsvlqiaaheevvpleelyelcekarellkdpkyliGriiarpfvGe.aGnfkrtsnrhdyalkpf 215
                                           livyts dsv+qiaahe+++pl+ely++ce +r l++ p+y++Griiarp+vG    +f+rt+nrhd++l+p 
  NCBI__GCF_000740055.1:WP_034529052.1 151 LIVYTSGDSVIQIAAHEDIIPLDELYKICEYTRTLVNGPEYTVGRIIARPYVGPdKDHFTRTANRHDFTLEPT 223
                                           *****************************************************7699**************** PP

                             TIGR01696 216 aktvldklkdekydvisiGkiadiydgeGitkkvrtksnmdgldkvikelkedftgisfanlvdfdalyGhrr 288
                                           +kt +d l++++ + i iGki+di++g Gi +  +  snmdg+d+v +++ edftg  f+nlvdfda+yGhrr
  NCBI__GCF_000740055.1:WP_034529052.1 224 GKTDIDYLQEAGVHTIGIGKINDIFSGHGIDEGYHNESNMDGMDHVDHVMAEDFTGFCFINLVDFDAMYGHRR 296
                                           ************************************************************************* PP

                             TIGR01696 289 dkeGyaaaleefdarlpellsklreddlliltadhGndptatGtdhtreyipvlvyspkvkkgqalesaetfa 361
                                           ++eG+++al +fd+rl  +l +++ ddll++tadhGndp ++G+dhtre +p+l+ysp + ++ +l+++  fa
  NCBI__GCF_000740055.1:WP_034529052.1 297 NPEGFGQALMDFDKRLGTVLDQMKPDDLLLITADHGNDPGFKGSDHTREQVPLLAYSPSMTTSGSLGTRSPFA 369
                                           ************************************************************************* PP

                             TIGR01696 362 diGatladnfntskpeyG 379
                                           d Gat+ +nf+++    G
  NCBI__GCF_000740055.1:WP_034529052.1 370 DFGATVLENFDVTGNGVG 387
                                           ***********9977666 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (381 nodes)
Target sequences:                          1  (395 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: 00:00:00.01
# Mc/sec: 13.85
//
[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