Alignments for a candidate for uxuA in Salinicoccus carnicancri Crm

GapMind for catabolism of small carbon sources

Alignments for a candidate for uxuA in Salinicoccus carnicancri Crm

Align mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate WP_017549910.1 C792_RS0113080 mannonate dehydratase

Query= BRENDA::A4VVI4
         (366 letters)



>NCBI__GCF_000330705.1:WP_017549910.1
          Length = 343

 Score =  386 bits (992), Expect = e-112
 Identities = 189/347 (54%), Positives = 239/347 (68%), Gaps = 5/347 (1%)

Query: 1   MKMSFRWYGKKDPVTLEEIKAIPGMQGIVTAVYDVPVGQAWPLENILELKKMVEEAGLEI 60
           M+MSFRWYG  DPVTLE I+ IP M+GIV+A+YD+P G+ WP E I+EL+  +   G+ +
Sbjct: 1   MEMSFRWYGNDDPVTLENIRQIPQMKGIVSAIYDIPAGEVWPYERIVELRDQIAAHGMRL 60

Query: 61  TVIESIPVHEDIKQGKPNRDALIENYKTSIRNVGAAGIPVVCYNFMPVFDWTRSDLHHPL 120
            VIES+PVHEDIK G+  RD LIENYK +IRN+  AGI  VCYNFMPVFDWTR +L  PL
Sbjct: 61  NVIESVPVHEDIKMGRGRRDELIENYKETIRNLSKAGIKTVCYNFMPVFDWTRIELDAPL 120

Query: 121 PDGSTSLAFLKSDLAGVDPVADDLNLPGWDSSYSKEEMKAIIENYRQNISEEDLWANLEY 180
            DGS SL + ++ + G+DP++ +L LPGWD SY  +++K II+ Y Q ISE+ L+ NL Y
Sbjct: 121 ADGSNSLKYDEAKVKGIDPLSGELTLPGWDLSYQTDDLKEIIDAY-QEISEDQLFGNLIY 179

Query: 181 FIKAILPTAEEAGVKMAIHPDDPPYGIFGLPRIITGQEAVERFLNLYDSEHNGITMCVGS 240
           F++ I+P AEE  V MAIHPDDPP+ IFGLPRIITG  A+ R  +   S HNGIT C GS
Sbjct: 180 FLERIIPVAEEEDVLMAIHPDDPPWSIFGLPRIITGAAALRRLFDAVPSMHNGITFCTGS 239

Query: 241 YASDPKNDVLAMTEYALKRNRINFMHTRNVT-AGAWGFQETAHLSQAGDIDMNAVVKLLV 299
           Y S P ND+  + + A    RI+F+H RNV   G   FQE +H    G +DM  ++  LV
Sbjct: 240 YGSSPTNDLFEIIDAA--AGRIHFVHARNVKWTGELSFQEVSHSVHDGSLDMVGIIDKLV 297

Query: 300 DYDWQGSLRPDHGRRIWGDQTKTPGYGLYDRALGATYFNGLYEANMR 346
                  +RPDHGR IWG +T  PGYGLYDRALGA Y NG+ +   R
Sbjct: 298 ASGVDVPIRPDHGRMIWG-ETGRPGYGLYDRALGAAYLNGILDTLKR 343


Lambda     K      H
   0.317    0.136    0.416 

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: 450
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: 366
Length of database: 343
Length adjustment: 29
Effective length of query: 337
Effective length of database: 314
Effective search space:   105818
Effective search space used:   105818
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_017549910.1 C792_RS0113080 (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.1292178.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.9e-121  390.8   0.0    1.2e-64  204.9   0.0    2.0  2  NCBI__GCF_000330705.1:WP_017549910.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000330705.1:WP_017549910.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.3   0.0     2e-58     2e-58       1     137 [.       1     138 [.       1     143 [. 0.99
   2 !  204.9   0.0   1.2e-64   1.2e-64     180     388 ..     145     342 ..     140     343 .] 0.95

  Alignments for each domain:
  == domain 1  score: 184.3 bits;  conditional E-value: 2e-58
                             TIGR00695   1 meqtfrwyGrndpvsledvrqa.GakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvheeik 72 
                                           me++frwyG++dpv+le++rq+  +kGiv a+++ip Gevw  e i + +++i   G+  +v+esvpvhe+ik
  NCBI__GCF_000330705.1:WP_017549910.1   1 MEMSFRWYGNDDPVTLENIRQIpQMKGIVSAIYDIPAGEVWPYERIVELRDQIAAHGMRLNVIESVPVHEDIK 73 
                                           9*********************99************************************************* PP

                             TIGR00695  73 lqteeyekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaale 137
                                           ++ + +++ ienyk+t+rnl++ Gik+vcynfmpv+dwtr +l  +l dGs++l++d++kv+ ++
  NCBI__GCF_000330705.1:WP_017549910.1  74 MGRGRRDELIENYKETIRNLSKAGIKTVCYNFMPVFDWTRIELDAPLADGSNSLKYDEAKVKGID 138
                                           ************************************************************99876 PP

  == domain 2  score: 204.9 bits;  conditional E-value: 1.2e-64
                             TIGR00695 180 glpGaeegekldrikelleaykdideeklrenlafflkeilpvaeevGvkmaihpddpprpilGlprivstie 252
                                            lpG++  ++ d++ke ++ay++i+e++l  nl +fl+ i+pvaee  v maihpddpp+ i+Glpri+++ +
  NCBI__GCF_000330705.1:WP_017549910.1 145 TLPGWDLSYQTDDLKEIIDAYQEISEDQLFGNLIYFLERIIPVAEEEDVLMAIHPDDPPWSIFGLPRIITGAA 217
                                           59*********************************************************************** PP

                             TIGR00695 253 dmkklveisdspangitlctGsyGvradndlvelakqfadriyfahlrsvkreenpktfheaahlekdvdlye 325
                                            +++l + ++s+ ngit+ctGsyG  + ndl e+++  a+ri+f h r+vk  ++  +f+e +h   d++l  
  NCBI__GCF_000330705.1:WP_017549910.1 218 ALRRLFDAVPSMHNGITFCTGSYGSSPTNDLFEIIDAAAGRIHFVHARNVKWTGEL-SFQEVSHSVHDGSLD- 288
                                           ***************************************************99986.*************99. PP

                             TIGR00695 326 vvkavleeehrrkaeGkedlipvrpdhGrqllddlkkktnpGysaigrlkGlaelrGlelalk 388
                                            + ++++++    a G    +p+rpdhGr +++   +  +pGy++++r++G a+l+G+ ++lk
  NCBI__GCF_000330705.1:WP_017549910.1 289 -MVGIIDKLV---ASG--VDVPIRPDHGRMIWG---ETGRPGYGLYDRALGAAYLNGILDTLK 342
                                           .668888765...556..3469***********...99********************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (343 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.85
//
[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