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.734208.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.64
//
[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:

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:

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:

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:

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