GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaA in Hafnia paralvei ATCC 29927

Align L-rhamnose isomerase (EC 5.3.1.14) (characterized)
to candidate WP_064574663.1 M988_RS14420 L-rhamnose isomerase

Query= BRENDA::P32170
         (419 letters)



>NCBI__GCF_001655005.1:WP_064574663.1
          Length = 418

 Score =  752 bits (1941), Expect = 0.0
 Identities = 357/418 (85%), Positives = 394/418 (94%)

Query: 1   MTTQLEQAWELAKQRFAAVGIDVEEALRQLDRLPVSMHCWQGDDVSGFENPEGSLTGGIQ 60
           MTT ++QAWELAKQRF+AVG+DVE AL+ +++LPVSMHCWQGDDV+GFENPEGSLTGGIQ
Sbjct: 1   MTTLIDQAWELAKQRFSAVGVDVENALKTMEQLPVSMHCWQGDDVAGFENPEGSLTGGIQ 60

Query: 61  ATGNYPGKARNASELRADLEQAMRLIPGPKRLNLHAIYLESDTPVSRDQIKPEHFKNWVE 120
           ATGNYPGKARNA+ELR+DLE A+ LIPGPKRLNLHAIYLESDTPV+R++I+P HF +WVE
Sbjct: 61  ATGNYPGKARNAAELRSDLEMALSLIPGPKRLNLHAIYLESDTPVARNKIEPRHFAHWVE 120

Query: 121 WAKANQLGLDFNPSCFSHPLSADGFTLSHADDSIRQFWIDHCKASRRVSAYFGEQLGTPS 180
           WAK + LGLDFNPSCFSHPLSADGFTLS +D  IRQFWI+HC+ASRR+SAYFGEQLGTPS
Sbjct: 121 WAKKHHLGLDFNPSCFSHPLSADGFTLSSSDPEIRQFWIEHCQASRRISAYFGEQLGTPS 180

Query: 181 VMNIWIPDGMKDITVDRLAPRQRLLAALDEVISEKLNPAHHIDAVESKLFGIGAESYTVG 240
           VMNIWIPDGMKD  +DRLAPRQRL +ALDEVISEKLNPAHHIDAVESKLFGIGAESYTVG
Sbjct: 181 VMNIWIPDGMKDTPIDRLAPRQRLASALDEVISEKLNPAHHIDAVESKLFGIGAESYTVG 240

Query: 241 SNEFYMGYATSRQTALCLDAGHFHPTEVISDKISAAMLYVPQLLLHVSRPVRWDSDHVVL 300
           SNEFY+GYA SRQTALCLDAGHFHPTEVISDKIS+AMLYVP+LLLHVSRPVRWDSDHVVL
Sbjct: 241 SNEFYLGYAASRQTALCLDAGHFHPTEVISDKISSAMLYVPRLLLHVSRPVRWDSDHVVL 300

Query: 301 LDDETQAIASEIVRHDLFDRVHIGLDFFDASINRIAAWVIGTRNMKKALLRALLEPTAEL 360
           LDDETQAIA+EIVRHDLFDRVHIGLDFFDASINRIAAWVIGTRNMKKALLRALLEPT  L
Sbjct: 301 LDDETQAIANEIVRHDLFDRVHIGLDFFDASINRIAAWVIGTRNMKKALLRALLEPTEHL 360

Query: 361 RKLEAAGDYTARLALLEEQKSLPWQAVWEMYCQRHDTPAGSEWLESVRAYEKEILSRR 418
           R+LE +GDYTARLALLEEQKSLPWQAVWEMYCQR+D PA + WL +VR YE+++LS+R
Sbjct: 361 RELEESGDYTARLALLEEQKSLPWQAVWEMYCQRNDVPADARWLNAVREYEEQVLSQR 418


Lambda     K      H
   0.319    0.134    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: 701
Number of extensions: 18
Number of successful extensions: 1
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: 419
Length of database: 418
Length adjustment: 32
Effective length of query: 387
Effective length of database: 386
Effective search space:   149382
Effective search space used:   149382
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_064574663.1 M988_RS14420 (L-rhamnose isomerase)
to HMM TIGR01748 (rhaA: L-rhamnose isomerase (EC 5.3.1.14))

# 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/TIGR01748.hmm
# target sequence database:        /tmp/gapView.2756172.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01748  [M=414]
Accession:   TIGR01748
Description: rhaA: L-rhamnose isomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-242  790.8   0.0   1.9e-242  790.6   0.0    1.0  1  NCBI__GCF_001655005.1:WP_064574663.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001655005.1:WP_064574663.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  790.6   0.0  1.9e-242  1.9e-242       1     414 []       5     418 .]       5     418 .] 1.00

  Alignments for each domain:
  == domain 1  score: 790.6 bits;  conditional E-value: 1.9e-242
                             TIGR01748   1 iekayevakqryeavgidveealrqledvkislhcwqgddvegfenpegeltggiqatgnypgkartaeelrr 73 
                                           i++a+e+akqr++avg+dve+al+++e++++s+hcwqgddv gfenpeg+ltggiqatgnypgkar+a elr 
  NCBI__GCF_001655005.1:WP_064574663.1   5 IDQAWELAKQRFSAVGVDVENALKTMEQLPVSMHCWQGDDVAGFENPEGSLTGGIQATGNYPGKARNAAELRS 77 
                                           789********************************************************************** PP

                             TIGR01748  74 dlekalslipgkkrlnlhaiyvetdekverdeikpkhfknwvewakeqglgldfnptlfshelaadgltlsha 146
                                           dle alslipg+krlnlhaiy+e+d++v r++i+p+hf  wvewak++ lgldfnp++fsh+l+adg+tls++
  NCBI__GCF_001655005.1:WP_064574663.1  78 DLEMALSLIPGPKRLNLHAIYLESDTPVARNKIEPRHFAHWVEWAKKHHLGLDFNPSCFSHPLSADGFTLSSS 150
                                           ************************************************************************* PP

                             TIGR01748 147 dkeirefwiehckasrriseyfgkelgtpsvtniwipdglkdipvdrltprkrllealdevlsekldekytld 219
                                           d+eir+fwiehc+asrris+yfg++lgtpsv+niwipdg+kd p+drl+pr+rl  aldev+sekl++++++d
  NCBI__GCF_001655005.1:WP_064574663.1 151 DPEIRQFWIEHCQASRRISAYFGEQLGTPSVMNIWIPDGMKDTPIDRLAPRQRLASALDEVISEKLNPAHHID 223
                                           ************************************************************************* PP

                             TIGR01748 220 avesklfglgaesytvgshefylgyaltrdklllldaghfhptevisnkisslllyskklllhvsrpvrwdsd 292
                                           avesklfg+gaesytvgs+efylgya +r+++l+ldaghfhptevis+kiss++ly+++lllhvsrpvrwdsd
  NCBI__GCF_001655005.1:WP_064574663.1 224 AVESKLFGIGAESYTVGSNEFYLGYAASRQTALCLDAGHFHPTEVISDKISSAMLYVPRLLLHVSRPVRWDSD 296
                                           ************************************************************************* PP

                             TIGR01748 293 hvvvlddelreiaseivrndllekvaigldffdasinriaawvigtrnmkkallkalleptadlkkleeegdy 365
                                           hvv+ldde+++ia+eivr+dl+++v+igldffdasinriaawvigtrnmkkall+allept +l++lee gdy
  NCBI__GCF_001655005.1:WP_064574663.1 297 HVVLLDDETQAIANEIVRHDLFDRVHIGLDFFDASINRIAAWVIGTRNMKKALLRALLEPTEHLRELEESGDY 369
                                           ************************************************************************* PP

                             TIGR01748 366 terlalleelkslpfgavwesycerkgvpvgeewlkevkayekevllkr 414
                                           t+rlallee+kslp++avwe+yc+r++vp++  wl+ v++ye++vl++r
  NCBI__GCF_001655005.1:WP_064574663.1 370 TARLALLEEQKSLPWQAVWEMYCQRNDVPADARWLNAVREYEEQVLSQR 418
                                           **********************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (414 nodes)
Target sequences:                          1  (418 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: 15.55
//
[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:

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