Alignments for a candidate for uxuA in Leeuwenhoekiella blandensis MED217

GapMind for catabolism of small carbon sources

Alignments for a candidate for uxuA in Leeuwenhoekiella blandensis MED217

Align mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate WP_009780933.1 MED217_RS12715 mannonate dehydratase

Query= BRENDA::Q1QT83
         (391 letters)



>NCBI__GCF_000152985.1:WP_009780933.1
          Length = 393

 Score =  365 bits (937), Expect = e-105
 Identities = 185/385 (48%), Positives = 250/385 (64%), Gaps = 5/385 (1%)

Query: 2   EHTWRWFGPDDPITLDEIRQTGATGIVTALHEIPNGEIWPEAAIAERKRLIEASGLAWSV 61
           + + RWFGP D I LD+++  G +G+VTALHEIP GE+W   AI ER+  I++ GL W+V
Sbjct: 5   QQSMRWFGPSDAIRLDDLKAAGVSGVVTALHEIPVGEVWSIKAIQERQEYIDSFGLRWNV 64

Query: 62  VESVPVHEDIKQGRGDCETHIARYQQTLRNLAACGIDVVCYNFMPVLDWTRTDLAWPLPG 121
           VES+PV E IKQ RGD E HI  Y+ +L NLA CGI  V YNFMPVLDW RTD  +    
Sbjct: 65  VESLPVSEAIKQRRGDFERHIVNYKTSLENLAQCGIYTVTYNFMPVLDWVRTDHRFENSD 124

Query: 122 GGTALRFDQTAFAAFDLYLLERPGAEADYDATERDAARAYLDGLDESARQRLIDTIIAGL 181
           G  AL +D  AF  FD++LL+RPGA+  Y   E  AARAY + L +  +  L    + GL
Sbjct: 125 GTLALAYDHIAFVFFDVHLLQRPGAKLSYTEDELQAARAYGERLSDEEQNELFKNALLGL 184

Query: 182 PGAEEHYSLARFREVIAEYAEIDAERLRDNLGHFLRAVVPVAEEVGIRLAIHPDDPPRPL 241
           PG++ H++  +  E++A+YA ID  +LR NL  FL  ++PVA+   +++AIHPDDPP  +
Sbjct: 185 PGSKGHFTAKQILELLADYAHIDEHQLRKNLICFLEEIIPVAKSCNVQMAIHPDDPPFSV 244

Query: 242 LGLPRVVSTPRDVQWILDAAPSPANGLTFCTGSYGVSAAIDLVAMGERFAERIYFAHLRA 301
           LGLPRVV    D++ I +A P  ANGL +CTGS G     DL+ + E F ERI+F HLR 
Sbjct: 245 LGLPRVVRNYDDLKQIFEAVPDQANGLCYCTGSLGADPETDLIQVLETFKERIHFLHLRN 304

Query: 302 TQRENDPRSFHESAHLDGDVDMVGVIKALVGEERRRERDGGPRLPLRPDHGHHLLDDLSR 361
            +R  D + F ESAHLDGD  M  +++ ++   ++R+ +    LPLRPDHG     + + 
Sbjct: 305 IKR-YDAKLFQESAHLDGDHPMAAIMQGVLSIMQQRKIN----LPLRPDHGFLFRSEWNS 359

Query: 362 DTRPGYPLIGRLKGLAELRGVETAI 386
           ++ PGY  IGRLK LAELRG+E  +
Sbjct: 360 ESYPGYSYIGRLKALAELRGLELGL 384


Lambda     K      H
   0.321    0.139    0.430 

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: 383
Number of extensions: 11
Number of successful extensions: 3
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: 391
Length of database: 393
Length adjustment: 31
Effective length of query: 360
Effective length of database: 362
Effective search space:   130320
Effective search space used:   130320
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_009780933.1 MED217_RS12715 (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.1011055.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.6e-135  435.9   0.0   9.4e-135  435.6   0.0    1.0  1  NCBI__GCF_000152985.1:WP_009780933.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000152985.1:WP_009780933.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.6   0.0  9.4e-135  9.4e-135       2     386 ..       5     383 ..       4     389 .. 0.98

  Alignments for each domain:
  == domain 1  score: 435.6 bits;  conditional E-value: 9.4e-135
                             TIGR00695   2 eqtfrwyGrndpvsledvrqaGakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvheeiklq 74 
                                           +q++rw+G+ d++ l+d++ aG+ G+vtalh+ip+Gevw+++ i++r+e+i++ Gl ++vves+pv e+ik +
  NCBI__GCF_000152985.1:WP_009780933.1   5 QQSMRWFGPSDAIRLDDLKAAGVSGVVTALHEIPVGEVWSIKAIQERQEYIDSFGLRWNVVESLPVSEAIKQR 77 
                                           5899********************************************************************* PP

                             TIGR00695  75 teeyekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaalelhilkrpdae 147
                                            +++e++i nyk +l nlaqcGi +v ynfmpvldw rtd  +e  dG+ al +d+i++  +++h+l+rp+a+
  NCBI__GCF_000152985.1:WP_009780933.1  78 RGDFERHIVNYKTSLENLAQCGIYTVTYNFMPVLDWVRTDHRFENSDGTLALAYDHIAFVFFDVHLLQRPGAK 150
                                           ************************************************************************* PP

                             TIGR00695 148 kdyteeelvraveeasdmseedkarltrniiaglpGaeegekldrikelleaykdideeklrenlafflkeil 220
                                            +yte+el +a+ + + +s+e++ +l +n + glpG +   + ++i ell+ y  ide++lr+nl  fl+ei+
  NCBI__GCF_000152985.1:WP_009780933.1 151 LSYTEDELQAARAYGERLSDEEQNELFKNALLGLPGSKGHFTAKQILELLADYAHIDEHQLRKNLICFLEEII 223
                                           ************************************************************************* PP

                             TIGR00695 221 pvaeevGvkmaihpddpprpilGlprivstiedmkklveisdspangitlctGsyGvradndlvelakqfadr 293
                                           pva+   v+maihpddpp  +lGlpr+v   +d+k++ e ++  ang+  ctGs+G+ ++ dl+++ ++f +r
  NCBI__GCF_000152985.1:WP_009780933.1 224 PVAKSCNVQMAIHPDDPPFSVLGLPRVVRNYDDLKQIFEAVPDQANGLCYCTGSLGADPETDLIQVLETFKER 296
                                           ************************************************************************* PP

                             TIGR00695 294 iyfahlrsvkreenpktfheaahlekdvdlyevvkavleeehrrkaeGkedlipvrpdhGrqllddlkkktnp 366
                                           i+f hlr++kr++    f+e+ahl++d  +  ++++vl    +rk +      p+rpdhG  +  + + ++ p
  NCBI__GCF_000152985.1:WP_009780933.1 297 IHFLHLRNIKRYDAK-LFQESAHLDGDHPMAAIMQGVLSIMQQRKINL-----PLRPDHGFLFRSEWNSESYP 363
                                           ************987.9**********************999998875.....******************** PP

                             TIGR00695 367 GysaigrlkGlaelrGlela 386
                                           Gys igrlk laelrGlel 
  NCBI__GCF_000152985.1:WP_009780933.1 364 GYSYIGRLKALAELRGLELG 383
                                           *****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (393 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: 20.38
//
[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:

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 2024 update 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