Alignments for a candidate for uxuA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for uxuA in Paraburkholderia bryophila 376MFSha3.1

Align D-mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate H281DRAFT_02953 H281DRAFT_02953 D-mannonate dehydratase (EC 4.2.1.8)

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



>FitnessBrowser__Burk376:H281DRAFT_02953
          Length = 353

 Score =  400 bits (1028), Expect = e-116
 Identities = 195/355 (54%), Positives = 250/355 (70%), Gaps = 12/355 (3%)

Query: 1   MKLVFRWYGEKHDTVTLEQIRQIPGVEGVVGALFDIPVGEVWPFEEIMKLKETVEKAGLK 60
           +K+ FRWYG+  D V L  IRQIPG+ GVV A++D+PVG+VWP + I  LKE +E  GL 
Sbjct: 1   LKMTFRWYGDA-DPVPLAYIRQIPGMVGVVSAVYDVPVGDVWPVDTIRSLKEKIEAHGLT 59

Query: 61  LEVIESVNVHEDIKLGLPTRDRYIENYKKTIRNLAKAGVKVVCYNFMPVFDWMRTDLHKK 120
           L+VIESV VHEDIKLG PTRD  I NY +T+RNL   GVKVVCYNFMPVFDW RT L   
Sbjct: 60  LDVIESVPVHEDIKLGKPTRDTLIANYGQTLRNLGACGVKVVCYNFMPVFDWTRTSLEMP 119

Query: 121 LPDGSETMEYDHRLIEGVTPDELIKRVKEGSQGFVLPGWEWD-RLEKLRETFELYKNVDE 179
           LPDGS T+ +D + I          R  + SQG  LPGW+   R E+L+     Y+ +DE
Sbjct: 120 LPDGSTTLAFDTQAI----------RELDVSQGIQLPGWDASYRPEQLKALLREYEALDE 169

Query: 180 EKLFENLVYFLERVIPVCEECDVKLAIHPDDPPWSIFGLPRIITNKENIERMLKAVDSPY 239
             L+ NL YFL  +IPV +E  +K+AIHPDDPP  IFGLPRI+ N+ +++R+L  VD P 
Sbjct: 170 AGLWANLDYFLRAIIPVAKEAGIKMAIHPDDPPRPIFGLPRIVKNRADLQRVLAIVDDPA 229

Query: 240 NGITFCMGSLGANPENNIPEMIRYFGKMGRIHFAHVRNLKFTGEKSFYETAHPSFCGSHD 299
           NG+T C GSLGA+ +N+IP ++R FG  GRIHFAH+RN++      F+ET+H S  GS D
Sbjct: 230 NGLTLCSGSLGADLQNDIPALVREFGARGRIHFAHLRNVQTNAAGDFHETSHRSADGSLD 289

Query: 300 LFEVMKAFHDIGYEGYIRPDHGRLIWGEKARPGYGLYDRALGATYILGLWEAIDK 354
           + E++KA+ + G+EGY RPDHGR+IWGE  R GYGL+DRALGA Y+ G+WE + K
Sbjct: 290 MAEIVKAYFETGFEGYARPDHGRMIWGETGRAGYGLFDRALGAVYLNGIWEGLAK 344


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: 468
Number of extensions: 21
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: 360
Length of database: 353
Length adjustment: 29
Effective length of query: 331
Effective length of database: 324
Effective search space:   107244
Effective search space used:   107244
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 H281DRAFT_02953 H281DRAFT_02953 (D-mannonate dehydratase (EC 4.2.1.8))
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.26175.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.1e-124  402.5   0.0      3e-66  210.1   0.0    2.0  2  lcl|FitnessBrowser__Burk376:H281DRAFT_02953  H281DRAFT_02953 D-mannonate dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_02953  H281DRAFT_02953 D-mannonate dehydratase (EC 4.2.1.8)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.7   0.0   2.3e-60   2.3e-60       2     138 ..       2     139 ..       1     142 [. 0.98
   2 !  210.1   0.0     3e-66     3e-66     180     389 ..     144     344 ..     138     348 .. 0.94

  Alignments for each domain:
  == domain 1  score: 190.7 bits;  conditional E-value: 2.3e-60
                                    TIGR00695   2 eqtfrwyGrndpvsledvrqa.GakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvp 66 
                                                  ++tfrwyG  dpv l+++rq+ G+ G+v a++++p+G+vw v+ i+  ke+ie  Gl+ +v+esvp
  lcl|FitnessBrowser__Burk376:H281DRAFT_02953   2 KMTFRWYGDADPVPLAYIRQIpGMVGVVSAVYDVPVGDVWPVDTIRSLKEKIEAHGLTLDVIESVP 67 
                                                  79**************************************************************** PP

                                    TIGR00695  67 vheeiklqteeyekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkik 132
                                                  vhe+ikl++  ++  i+ny qtlrnl  cG+kvvcynfmpv+dwtrt l+ +l+dGs++l fd  +
  lcl|FitnessBrowser__Burk376:H281DRAFT_02953  68 VHEDIKLGKPTRDTLIANYGQTLRNLGACGVKVVCYNFMPVFDWTRTSLEMPLPDGSTTLAFDTQA 133
                                                  ****************************************************************99 PP

                                    TIGR00695 133 vaalel 138
                                                  +  l++
  lcl|FitnessBrowser__Burk376:H281DRAFT_02953 134 IRELDV 139
                                                  998885 PP

  == domain 2  score: 210.1 bits;  conditional E-value: 3e-66
                                    TIGR00695 180 glpGaeegekldrikelleaykdideeklrenlafflkeilpvaeevGvkmaihpddpprpilGlp 245
                                                   lpG++  ++ +++k ll  y  +de+ l+ nl +fl++i+pva+e G+kmaihpddpprpi+Glp
  lcl|FitnessBrowser__Burk376:H281DRAFT_02953 144 QLPGWDASYRPEQLKALLREYEALDEAGLWANLDYFLRAIIPVAKEAGIKMAIHPDDPPRPIFGLP 209
                                                  59**************************************************************** PP

                                    TIGR00695 246 rivstiedmkklveisdspangitlctGsyGvradndlvelakqfa..driyfahlrsvkreenpk 309
                                                  riv   +d++++ +i+d pang+tlc+Gs+G+  +nd+  l+++f+  +ri+fahlr+v+ +  + 
  lcl|FitnessBrowser__Burk376:H281DRAFT_02953 210 RIVKNRADLQRVLAIVDDPANGLTLCSGSLGADLQNDIPALVREFGarGRIHFAHLRNVQTNAAG- 274
                                                  *********************************************94457************999. PP

                                    TIGR00695 310 tfheaahlekdvdlyevvkavleeehrrkaeGkedlipvrpdhGrqllddlkkktnpGysaigrlk 375
                                                  +fhe++h + d++l   +  +++  +    eG    +  rpdhGr +++   +  + Gy++++r++
  lcl|FitnessBrowser__Burk376:H281DRAFT_02953 275 DFHETSHRSADGSLD--MAEIVKAYFETGFEG----Y-ARPDHGRMIWG---ETGRAGYGLFDRAL 330
                                                  **********99877..666677777778899....6.8**********...99************ PP

                                    TIGR00695 376 GlaelrGlelalkk 389
                                                  G ++l+G++  l k
  lcl|FitnessBrowser__Burk376:H281DRAFT_02953 331 GAVYLNGIWEGLAK 344
                                                  *********98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (353 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 3.91
//
[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