Alignments for a candidate for deoB in Rhizobium leguminosarum bv. trifolii WSM1325

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoB in Rhizobium leguminosarum bv. trifolii WSM1325

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_012759723.1 RLEG_RS22180 phosphopentomutase

Query= BRENDA::P0A6K6
         (407 letters)



>NCBI__GCF_000023185.1:WP_012759723.1
          Length = 406

 Score =  473 bits (1218), Expect = e-138
 Identities = 232/408 (56%), Positives = 297/408 (72%), Gaps = 7/408 (1%)

Query: 1   MKRAFIMVLDSFGIGATEDAERFGDVGADTLGHIAEACAKGEADNG--RKGPLNLPNLTR 58
           M RAF+ VLDSFGIG   DA  +GD GADTLGHIAE CA G  D    R+GPL+LPN++ 
Sbjct: 1   MARAFLFVLDSFGIGGAPDAAAYGDEGADTLGHIAEFCAAGAGDRAGLREGPLSLPNMSE 60

Query: 59  LGLAKAHEGSTGFIPAGMDGNAEVIGAYAWAHEMSSGKDTPSGHWEIAGVPVLFEWGYFS 118
           LGL +    ++G  PAGM    +V G Y  A E+S GKDTPSGHWEIAG PV F+WGYF 
Sbjct: 61  LGLMQIARSASGRFPAGMPVPEKVYGIYGAATEISRGKDTPSGHWEIAGTPVSFDWGYFP 120

Query: 119 DHENSFPQELLDKLVERANLPGYLGNCHSSGTVILDQLGEEHMKTGKPIFYTSADSVFQI 178
              ++FP E ++ L   A++PG LGNCH+SGT I+ +LGE+H++TGKPI YTS+DSVFQ+
Sbjct: 121 IEGDAFPAEFIEALCREADVPGILGNCHASGTEIIARLGEDHIRTGKPICYTSSDSVFQV 180

Query: 179 ACHEETFGLDKLYELCEIAREELTNGGYNIGRVIARPFIGDKAGNFQRTGNRHDLAVEPP 238
           A HEE FGLD+L   C +AR  L    YNIGRVIARPFIG  A  FQRTGNR D +V PP
Sbjct: 181 AAHEEHFGLDRLLAFCRLARGLL--DPYNIGRVIARPFIGQSASTFQRTGNRRDFSVVPP 238

Query: 239 APTVLQKLVDEKHGQ-VVSVGKIADIYANCGITKKVKATGLDALFDATIKEMKEAGDNTI 297
            PT+L +L++  HG+ V +VGKI DI+A+ GI+K +KA G +AL DA++  + EAGD  +
Sbjct: 239 EPTLLDRLIE--HGRHVHAVGKIDDIFAHQGISKVIKANGNEALMDASLAALDEAGDGDL 296

Query: 298 VFTNFVDFDSSWGHRRDVAGYAAGLELFDRRLPELMSLLRDDDILILTADHGCDPTWTGT 357
           VFTNFVDFD  +GHRRDV GYAA LE FD RLPE+   L+  D+++LTADHGCDPTW GT
Sbjct: 297 VFTNFVDFDMIYGHRRDVPGYAAALEAFDARLPEVHKKLKPGDLVVLTADHGCDPTWRGT 356

Query: 358 DHTREHIPVLVYGPKVKPGSLGHRETFADIGQTLAKYFGTSDMEYGKA 405
           DHTRE +PV+ YGP ++  S+G R ++ADIG+++A++ G     +G++
Sbjct: 357 DHTRERVPVIAYGPGIRSRSIGVRRSYADIGESIARHLGIPAGPHGRS 404


Lambda     K      H
   0.318    0.138    0.422 

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: 630
Number of extensions: 35
Number of successful extensions: 4
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: 407
Length of database: 406
Length adjustment: 31
Effective length of query: 376
Effective length of database: 375
Effective search space:   141000
Effective search space used:   141000
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_012759723.1 RLEG_RS22180 (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.3127696.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.6e-148  478.0   0.0   1.1e-147  477.8   0.0    1.0  1  NCBI__GCF_000023185.1:WP_012759723.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000023185.1:WP_012759723.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  477.8   0.0  1.1e-147  1.1e-147       1     379 [.       3     402 ..       3     404 .. 0.98

  Alignments for each domain:
  == domain 1  score: 477.8 bits;  conditional E-value: 1.1e-147
                             TIGR01696   1 rvflivldsvGiGeaedaadfkdeGadtlghiaealdk............lnlpnleklGlgkiee......l 55 
                                           r+fl+vlds+GiG a+daa ++deGadtlghiae ++             l+lpn++ lGl +i        +
  NCBI__GCF_000023185.1:WP_012759723.1   3 RAFLFVLDSFGIGGAPDAAAYGDEGADTLGHIAEFCAAgagdraglregpLSLPNMSELGLMQIARsasgrfP 75 
                                           89**********************************999*************************999999999 PP

                             TIGR01696  56 agvdaveevlayyaklseassGkdtmtGhweiaGlnilkefkvfs...ngfpeelldkleeragrk.vlgnkp 124
                                           ag+   e+v + y+ + e+s Gkdt++GhweiaG ++ +++++f+   ++fp e+++ l + a+ + +lgn++
  NCBI__GCF_000023185.1:WP_012759723.1  76 AGMPVPEKVYGIYGAATEISRGKDTPSGHWEIAGTPVSFDWGYFPiegDAFPAEFIEALCREADVPgILGNCH 148
                                           **********************************************9999****************9****** PP

                             TIGR01696 125 asGtvildelGeehmktGklivytsadsvlqiaaheevvpleelyelcekarellkdpkyliGriiarpfvGe 197
                                           asGt i+ +lGe+h++tGk+i yts+dsv+q+aahee ++l++l  +c  ar ll d  y+iGr+iarpf+G+
  NCBI__GCF_000023185.1:WP_012759723.1 149 ASGTEIIARLGEDHIRTGKPICYTSSDSVFQVAAHEEHFGLDRLLAFCRLARGLL-D-PYNIGRVIARPFIGQ 219
                                           ****************************************************987.4.4************** PP

                             TIGR01696 198 .aGnfkrtsnrhdyalkpfaktvldklkdekydvisiGkiadiydgeGitkkvrtksnmdgldkvikelkedf 269
                                            a  f+rt+nr d+++ p+++t+ld+l + + +v ++Gki di++ +Gi+k +++++n++++d+ +  l+e++
  NCBI__GCF_000023185.1:WP_012759723.1 220 sASTFQRTGNRRDFSVVPPEPTLLDRLIEHGRHVHAVGKIDDIFAHQGISKVIKANGNEALMDASLAALDEAG 292
                                           999********************************************************************** PP

                             TIGR01696 270 tg.isfanlvdfdalyGhrrdkeGyaaaleefdarlpellsklreddlliltadhGndptatGtdhtreyipv 341
                                           +g ++f+n+vdfd +yGhrrd++Gyaaale fdarlpe+  kl+  dl++ltadhG+dpt++Gtdhtre +pv
  NCBI__GCF_000023185.1:WP_012759723.1 293 DGdLVFTNFVDFDMIYGHRRDVPGYAAALEAFDARLPEVHKKLKPGDLVVLTADHGCDPTWRGTDHTRERVPV 365
                                           **9********************************************************************** PP

                             TIGR01696 342 lvyspkvkkgqalesaetfadiGatladnfntskpeyG 379
                                           ++y+p +++  +++ + ++adiG+++a ++++    +G
  NCBI__GCF_000023185.1:WP_012759723.1 366 IAYGPGIRSR-SIGVRRSYADIGESIARHLGIPAGPHG 402
                                           *******987.****************99987766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (381 nodes)
Target sequences:                          1  (406 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: 26.69
//
[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