Alignments for a candidate for deoB in Marivita geojedonensis DPG-138

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoB in Marivita geojedonensis DPG-138

Align Phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_085636214.1 MGEO_RS08080 phosphopentomutase

Query= reanno::Dino:3607415
         (399 letters)



>NCBI__GCF_002115805.1:WP_085636214.1
          Length = 402

 Score =  522 bits (1345), Expect = e-153
 Identities = 261/403 (64%), Positives = 301/403 (74%), Gaps = 6/403 (1%)

Query: 1   MTRAFLIVMDSVGCGGAPDAADF-----GDEGANTLAHIAQACAAGRADAGRSGPLRMPV 55
           M+RAF++VMDSVG GGAPDA  F      D GANT+ HIAQACAAGRA+ GRSGPL +P 
Sbjct: 1   MSRAFIVVMDSVGIGGAPDADQFFNGTVPDTGANTVLHIAQACAAGRAEEGRSGPLNLPT 60

Query: 56  LDGLGLGAAIRLASGAETPGLAATPTGLWGAATEVSRGKDTPTGHWELAGVPVPWEWTTF 115
           LD LGLG A+ LASG   PGL AT TG WGAATE+S+GKDTP+GHWELAG+PVPW+WT  
Sbjct: 61  LDALGLGQAVELASGQRAPGLDATATGRWGAATEISKGKDTPSGHWELAGLPVPWDWTYL 120

Query: 116 PDTDPAFPPDLLAEMARAAGTEGTLCNTHASGTEVIERFGAEHLRTGWPICYTSVDSVLQ 175
           PDT P+FP D+   +   AGT+G L N H++G +VIE FGAEHLRTG PICYTS DSVLQ
Sbjct: 121 PDTVPSFPDDITQRICDLAGTDGILGNCHSNGVKVIEDFGAEHLRTGKPICYTSADSVLQ 180

Query: 176 IAAHEEAFGLDRLLDVCETLAPRLHAMKVGRVIARPFLGSEATGFARTQNRRDFAIAPPA 235
           IAAHEEAFGLDRLL +CE LAP  HA ++GRVIARPF+G E   F RT NR D+AIAPP 
Sbjct: 181 IAAHEEAFGLDRLLQICEDLAPMCHARRIGRVIARPFVGEEGR-FERTTNRHDYAIAPPE 239

Query: 236 PTLCDRVQAAGRRVHAIGKIKDIFSGRGIDTVAKGSDAALMEALIAAGQVAEEGSLTFAN 295
           P L + V  AG+ V AIGKI DIFS  GID V KGSD  LM  L      A EG+L FAN
Sbjct: 240 PVLTNWVHDAGQAVIAIGKIGDIFSMSGIDAVHKGSDTQLMTHLAHQIDTAPEGALIFAN 299

Query: 296 FVEFDSLYGHRRDVAGYARALEWFDAQLPRFLATLRPGDLAIFTADHGNDPTWHGTEHTR 355
           FVEFDS YGHRRDV+GYARALEWFDA++ + L  L+P DL + TADHGNDPTW GT+HTR
Sbjct: 300 FVEFDSKYGHRRDVSGYARALEWFDAEIAKLLPRLKPDDLLLITADHGNDPTWTGTDHTR 359

Query: 356 ERVPVVGYGVGVHEVGIVGFRDVGATIGAHLGVEMFDMGKAML 398
           ERVPV+  G G  E+G +GF DV A+I  HLGV     G++ L
Sbjct: 360 ERVPVLIAGAGSGEIGHIGFVDVAASIAEHLGVASKGSGRSFL 402


Lambda     K      H
   0.321    0.137    0.429 

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: 552
Number of extensions: 21
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: 399
Length of database: 402
Length adjustment: 31
Effective length of query: 368
Effective length of database: 371
Effective search space:   136528
Effective search space used:   136528
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_085636214.1 MGEO_RS08080 (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.461607.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-124  402.2   0.0   1.2e-124  402.0   0.0    1.0  1  NCBI__GCF_002115805.1:WP_085636214.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002115805.1:WP_085636214.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.0   0.0  1.2e-124  1.2e-124       1     379 [.       3     398 ..       3     400 .. 0.92

  Alignments for each domain:
  == domain 1  score: 402.0 bits;  conditional E-value: 1.2e-124
                             TIGR01696   1 rvflivldsvGiGeaedaadf.....kdeGadtlghiaealdk..........lnlpnleklGlgkiee.... 54 
                                           r+f++v+dsvGiG a+da++f      d Ga+t+ hia+a++           lnlp l+ lGlg++ e    
  NCBI__GCF_002115805.1:WP_085636214.1   3 RAFIVVMDSVGIGGAPDADQFfngtvPDTGANTVLHIAQACAAgraeegrsgpLNLPTLDALGLGQAVElasg 75 
                                           89*****************9854444599*************99***********************995555 PP

                             TIGR01696  55 ..lagvdaveevlayyaklseassGkdtmtGhweiaGlnilkefkvfs...ngfpeelldkleeragrk.vlg 121
                                              +g+da   + + ++ + e+s+Gkdt++Ghwe+aGl++  ++ + +    +fp+++ +++ + ag   +lg
  NCBI__GCF_002115805.1:WP_085636214.1  76 qrAPGLDA--TATGRWGAATEISKGKDTPSGHWELAGLPVPWDWTYLPdtvPSFPDDITQRICDLAGTDgILG 146
                                           44455554..56789*********************************77679***************99*** PP

                             TIGR01696 122 nkpasGtvildelGeehmktGklivytsadsvlqiaaheevvpleelyelcekarellkdpkyliGriiarpf 194
                                           n+++ G ++++++G eh++tGk+i ytsadsvlqiaahee ++l++l ++ce    + +     iGr+iarpf
  NCBI__GCF_002115805.1:WP_085636214.1 147 NCHSNGVKVIEDFGAEHLRTGKPICYTSADSVLQIAAHEEAFGLDRLLQICEDLAPMCHA--RRIGRVIARPF 217
                                           ****************************************************99887765..57********* PP

                             TIGR01696 195 vGeaGnfkrtsnrhdyalkpfaktvldklkdekydvisiGkiadiydgeGitkkvrtksnmdgldkvikelke 267
                                           vGe G+f+rt+nrhdya+ p+++ + + ++d++  vi+iGki di++  Gi  +v+  s  +++ ++ ++++ 
  NCBI__GCF_002115805.1:WP_085636214.1 218 VGEEGRFERTTNRHDYAIAPPEPVLTNWVHDAGQAVIAIGKIGDIFSMSGID-AVHKGSDTQLMTHLAHQIDT 289
                                           **************************************************96.677789999*********** PP

                             TIGR01696 268 dftg.isfanlvdfdalyGhrrdkeGyaaaleefdarlpellsklreddlliltadhGndptatGtdhtreyi 339
                                           + +g + fan+v+fd+ yGhrrd++Gya+ale fda + +ll +l+ ddll++tadhGndpt+tGtdhtre +
  NCBI__GCF_002115805.1:WP_085636214.1 290 APEGaLIFANFVEFDSKYGHRRDVSGYARALEWFDAEIAKLLPRLKPDDLLLITADHGNDPTWTGTDHTRERV 362
                                           *9999******************************************************************** PP

                             TIGR01696 340 pvlvyspkvkkgqalesaetfadiGatladnfntskpeyG 379
                                           pvl+ +    +    ++   f d+ a++a+++++++   G
  NCBI__GCF_002115805.1:WP_085636214.1 363 PVLIAGAGSGEI---GH-IGFVDVAASIAEHLGVASKGSG 398
                                           ****99765443...43.4688999999998888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (381 nodes)
Target sequences:                          1  (402 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 16.77
//
[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