GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuA in Rhizobium freirei PRF 81

Align mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate WP_037152525.1 RHSP_RS16605 mannonate dehydratase

Query= BRENDA::P24215
         (394 letters)



>NCBI__GCF_000359745.1:WP_037152525.1
          Length = 396

 Score =  418 bits (1075), Expect = e-121
 Identities = 213/396 (53%), Positives = 274/396 (69%), Gaps = 3/396 (0%)

Query: 1   MEQTWRWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWS 60
           ME+ +RWYGP+DPV LA +RQAGATG+V+ALH I +G  WS ++IL  KA+IE AG+ WS
Sbjct: 1   MEECFRWYGPDDPVPLAHIRQAGATGIVSALHQIYDGSPWSDDQILAHKALIEAAGMRWS 60

Query: 61  VVESVPIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLP 120
           VVES+P+H  IK  T +  ++I  Y+ TLR LA+ GI TVCYNFMPV+DWTRT+L   L 
Sbjct: 61  VVESIPVHNSIKLATADSARYIGWYKDTLRALARAGIATVCYNFMPVVDWTRTELMQPLA 120

Query: 121 DGSKALRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAG 180
           +G  ALRFD ++FAA+++  LKRP  E  Y+EE+I  A ERF  M      R+ RN+IAG
Sbjct: 121 NGGYALRFDAVDFAAYDLFALKRPHVEDSYSEEQILAARERFGRMDPAKIDRIERNLIAG 180

Query: 181 LPGAEEGYTLDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVHPDDPPRP 240
           LP  E  +    F   L  Y  +    L  N A FLK I+PVAEEVG+R+ +HPDDP   
Sbjct: 181 LPATERQFNRASFLAALAEYDGMTADHLHANLARFLKEIVPVAEEVGIRLCIHPDDPAFS 240

Query: 241 ILGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLR 300
           + GLPRIVST  D + ++ TV S ANG T CTGS+G RADNDL  MI++FGPRI+F HLR
Sbjct: 241 LYGLPRIVSTAADARRILATVESPANGLTFCTGSFGTRADNDLPAMIREFGPRIHFAHLR 300

Query: 301 STMREDNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKED-LIPMRPDHGHQMLDD 359
           +  RE++  +F+EA HL G  D+  V+ A+++E+ RR  EG+ D  IP+RPDHGH + DD
Sbjct: 301 NVQREED-GSFYEADHLGGSSDIPAVILALMQEQKRRLEEGRTDWQIPLRPDHGHLLADD 359

Query: 360 L-KKKTNPGYSAIGRLKGLAEVRGVELAIQRAFFSR 394
           + K+K NPGYS IGRLKGLAE+RGV   I  A   R
Sbjct: 360 IGKEKINPGYSLIGRLKGLAEIRGVMQGIATAMTER 395


Lambda     K      H
   0.320    0.136    0.410 

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: 26
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: 394
Length of database: 396
Length adjustment: 31
Effective length of query: 363
Effective length of database: 365
Effective search space:   132495
Effective search space used:   132495
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_037152525.1 RHSP_RS16605 (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.2956864.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.9e-152  493.9   0.0   2.1e-152  493.7   0.0    1.0  1  NCBI__GCF_000359745.1:WP_037152525.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000359745.1:WP_037152525.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  493.7   0.0  2.1e-152  2.1e-152       1     391 [.       1     392 [.       1     395 [. 0.98

  Alignments for each domain:
  == domain 1  score: 493.7 bits;  conditional E-value: 2.1e-152
                             TIGR00695   1 meqtfrwyGrndpvsledvrqaGakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvheeikl 73 
                                           me +frwyG++dpv l+++rqaGa+Giv alh+i  G  w+ ++i ++k+ ie aG+ +svves+pvh+ ikl
  NCBI__GCF_000359745.1:WP_037152525.1   1 MEECFRWYGPDDPVPLAHIRQAGATGIVSALHQIYDGSPWSDDQILAHKALIEAAGMRWSVVESIPVHNSIKL 73 
                                           899********************************************************************** PP

                             TIGR00695  74 qteeyekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaalelhilkrpda 146
                                            t +  +yi  yk tlr la+ Gi +vcynfmpv+dwtrt+l+++l +G  alrfd +++aa++l+ lkrp+ 
  NCBI__GCF_000359745.1:WP_037152525.1  74 ATADSARYIGWYKDTLRALARAGIATVCYNFMPVVDWTRTELMQPLANGGYALRFDAVDFAAYDLFALKRPHV 146
                                           ************************************************************************* PP

                             TIGR00695 147 ekdyteeelvraveeasdmseedkarltrniiaglpGaeegekldrikelleaykdideeklrenlafflkei 219
                                           e +y+ee++++a+e++  m    + r+ rn+iaglp +e   + + +   l+ y  +  + l+ nla flkei
  NCBI__GCF_000359745.1:WP_037152525.1 147 EDSYSEEQILAARERFGRMDPAKIDRIERNLIAGLPATERQFNRASFLAALAEYDGMTADHLHANLARFLKEI 219
                                           ************************************************************************* PP

                             TIGR00695 220 lpvaeevGvkmaihpddpprpilGlprivstiedmkklveisdspangitlctGsyGvradndlvelakqfad 292
                                           +pvaeevG+++ ihpddp   ++Glprivst +d +++ ++++spang+t+ctGs+G+radndl  ++++f++
  NCBI__GCF_000359745.1:WP_037152525.1 220 VPVAEEVGIRLCIHPDDPAFSLYGLPRIVSTAADARRILATVESPANGLTFCTGSFGTRADNDLPAMIREFGP 292
                                           ************************************************************************* PP

                             TIGR00695 293 riyfahlrsvkreenpktfheaahlekdvdlyevvkavleeehrrkaeGkedl.ipvrpdhGrqllddl.kkk 363
                                           ri+fahlr+v+ree++ +f+ea hl + +d+  v+ a+++e+ rr +eG++d  ip+rpdhG+ l dd+ k+k
  NCBI__GCF_000359745.1:WP_037152525.1 293 RIHFAHLRNVQREEDG-SFYEADHLGGSSDIPAVILALMQEQKRRLEEGRTDWqIPLRPDHGHLLADDIgKEK 364
                                           ****************.*********************************99549*************96889 PP

                             TIGR00695 364 tnpGysaigrlkGlaelrGlelalkkva 391
                                            npGys+igrlkGlae+rG+ + +  ++
  NCBI__GCF_000359745.1:WP_037152525.1 365 INPGYSLIGRLKGLAEIRGVMQGIATAM 392
                                           ********************99887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (396 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: 25.68
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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