Alignments for a candidate for uxuA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for uxuA in Burkholderia phytofirmans PsJN

Align D-mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate BPHYT_RS28515 BPHYT_RS28515 mannonate dehydratase

Query= metacyc::MONOMER-17955
         (360 letters)



>FitnessBrowser__BFirm:BPHYT_RS28515
          Length = 350

 Score =  399 bits (1025), Expect = e-116
 Identities = 195/353 (55%), Positives = 248/353 (70%), Gaps = 12/353 (3%)

Query: 3   LVFRWYGEKHDTVTLEQIRQIPGVEGVVGALFDIPVGEVWPFEEIMKLKETVEKAGLKLE 62
           + FRWYG+  D V L  IRQIPG+ GVV A++D+PVGEVWP + I  LKE +E  GL LE
Sbjct: 1   MTFRWYGDT-DPVPLAYIRQIPGMVGVVSAIYDVPVGEVWPIDRIRSLKEKIEAHGLTLE 59

Query: 63  VIESVNVHEDIKLGLPTRDRYIENYKKTIRNLAKAGVKVVCYNFMPVFDWMRTDLHKKLP 122
           VIESV VHEDIKLG PTRD  I NY +T+RNL   GVKVVCYNFMPVFDW RT L   LP
Sbjct: 60  VIESVPVHEDIKLGKPTRDTLIVNYGQTLRNLGACGVKVVCYNFMPVFDWTRTSLEMPLP 119

Query: 123 DGSETMEYDHRLIEGVTPDELIKRVKEGSQGFVLPGWEWD-RLEKLRETFELYKNVDEEK 181
           DGS T+ +D + I          R  + S+G  LPGW+   R E+L+     Y+ +DE  
Sbjct: 120 DGSTTLAFDTQAI----------RELDVSEGIQLPGWDASYRPEQLKALLRDYEALDEAG 169

Query: 182 LFENLVYFLERVIPVCEECDVKLAIHPDDPPWSIFGLPRIITNKENIERMLKAVDSPYNG 241
           L+ NL YFL  +IPV +E  +K+AIHPDDPP  IFGLPRI+ N+ +++R+L  VD P NG
Sbjct: 170 LWANLDYFLRAIIPVAKEAGIKMAIHPDDPPRPIFGLPRIVKNRADLQRVLDIVDDPANG 229

Query: 242 ITFCMGSLGANPENNIPEMIRYFGKMGRIHFAHVRNLKFTGEKSFYETAHPSFCGSHDLF 301
           +T C GSLGA+ +N+IP ++R FG  GRIHFAH+RN++      F+ET+H S  GS D+ 
Sbjct: 230 LTLCSGSLGADLQNDIPALVREFGARGRIHFAHLRNVQTNAAGDFHETSHRSADGSLDMA 289

Query: 302 EVMKAFHDIGYEGYIRPDHGRLIWGEKARPGYGLYDRALGATYILGLWEAIDK 354
           E++KA+ + G+EGY RPDHGR+IWGE  R GYGL+DRALGA Y+ G+WE + K
Sbjct: 290 EIVKAYFETGFEGYARPDHGRMIWGETGRAGYGLFDRALGAVYLNGIWEGLAK 342


Lambda     K      H
   0.322    0.142    0.448 

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: 467
Number of extensions: 20
Number of successful extensions: 2
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: 360
Length of database: 350
Length adjustment: 29
Effective length of query: 331
Effective length of database: 321
Effective search space:   106251
Effective search space used:   106251
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: 49 (23.5 bits)

Align candidate BPHYT_RS28515 BPHYT_RS28515 (mannonate dehydratase)
to HMM TIGR00695 (uxuA: mannonate dehydratase (EC 4.2.1.8))

# 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/TIGR00695.hmm
# target sequence database:        /tmp/gapView.3450.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00695  [M=394]
Accession:   TIGR00695
Description: uxuA: mannonate dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   4.2e-124  400.6   0.0    3.1e-66  210.0   0.0    2.0  2  lcl|FitnessBrowser__BFirm:BPHYT_RS28515  BPHYT_RS28515 mannonate dehydrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS28515  BPHYT_RS28515 mannonate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.7   0.0   9.4e-60   9.4e-60       3     138 ..       1     137 [.       1     139 [. 0.98
   2 !  210.0   0.0   3.1e-66   3.1e-66     180     389 ..     142     342 ..     138     346 .. 0.94

  Alignments for each domain:
  == domain 1  score: 188.7 bits;  conditional E-value: 9.4e-60
                                TIGR00695   3 qtfrwyGrndpvsledvrqa.GakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvheei 71 
                                              +tfrwyG  dpv l+++rq+ G+ G+v a++++p+Gevw ++ i+  ke+ie  Gl+ +v+esvpvhe+i
  lcl|FitnessBrowser__BFirm:BPHYT_RS28515   1 MTFRWYGDTDPVPLAYIRQIpGMVGVVSAIYDVPVGEVWPIDRIRSLKEKIEAHGLTLEVIESVPVHEDI 70 
                                              79******************************************************************** PP

                                TIGR00695  72 klqteeyekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaalel 138
                                              kl++  ++  i ny qtlrnl  cG+kvvcynfmpv+dwtrt l+ +l+dGs++l fd  ++  l++
  lcl|FitnessBrowser__BFirm:BPHYT_RS28515  71 KLGKPTRDTLIVNYGQTLRNLGACGVKVVCYNFMPVFDWTRTSLEMPLPDGSTTLAFDTQAIRELDV 137
                                              ***********************************************************99998875 PP

  == domain 2  score: 210.0 bits;  conditional E-value: 3.1e-66
                                TIGR00695 180 glpGaeegekldrikelleaykdideeklrenlafflkeilpvaeevGvkmaihpddpprpilGlprivs 249
                                               lpG++  ++ +++k ll  y  +de+ l+ nl +fl++i+pva+e G+kmaihpddpprpi+Glpriv 
  lcl|FitnessBrowser__BFirm:BPHYT_RS28515 142 QLPGWDASYRPEQLKALLRDYEALDEAGLWANLDYFLRAIIPVAKEAGIKMAIHPDDPPRPIFGLPRIVK 211
                                              59******************************************************************** PP

                                TIGR00695 250 tiedmkklveisdspangitlctGsyGvradndlvelakqfa..driyfahlrsvkreenpktfheaahl 317
                                                +d++++ +i+d pang+tlc+Gs+G+  +nd+  l+++f+  +ri+fahlr+v+ +  + +fhe++h 
  lcl|FitnessBrowser__BFirm:BPHYT_RS28515 212 NRADLQRVLDIVDDPANGLTLCSGSLGADLQNDIPALVREFGarGRIHFAHLRNVQTNAAG-DFHETSHR 280
                                              *****************************************94457************999.******** PP

                                TIGR00695 318 ekdvdlyevvkavleeehrrkaeGkedlipvrpdhGrqllddlkkktnpGysaigrlkGlaelrGlelal 387
                                              + d++l   +  +++  +    eG    +  rpdhGr +++   +  + Gy++++r++G ++l+G++  l
  lcl|FitnessBrowser__BFirm:BPHYT_RS28515 281 SADGSLD--MAEIVKAYFETGFEG----Y-ARPDHGRMIWG---ETGRAGYGLFDRALGAVYLNGIWEGL 340
                                              **99877..666677777778899....6.8**********...99*********************987 PP

                                TIGR00695 388 kk 389
                                               k
  lcl|FitnessBrowser__BFirm:BPHYT_RS28515 341 AK 342
                                              65 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (350 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 3.06
//
[ok]

This GapMind analysis is from Sep 17 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 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