Alignments for a candidate for galE in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Echinicola vietnamensis KMM 6221, DSM 17526

Align UDP-glucose 4-epimerase; EC 5.1.3.2 (characterized, see rationale)
to candidate Echvi_1472 Echvi_1472 UDP-glucose-4-epimerase

Query= uniprot:L0FXG3
         (337 letters)



>FitnessBrowser__Cola:Echvi_1472
          Length = 337

 Score =  685 bits (1767), Expect = 0.0
 Identities = 337/337 (100%), Positives = 337/337 (100%)

Query: 1   MQQILITGGAGYIGSHTAVALVNAGYEPIIVDNFSNSNKEVLNGLEKILGAPVKYHEGDC 60
           MQQILITGGAGYIGSHTAVALVNAGYEPIIVDNFSNSNKEVLNGLEKILGAPVKYHEGDC
Sbjct: 1   MQQILITGGAGYIGSHTAVALVNAGYEPIIVDNFSNSNKEVLNGLEKILGAPVKYHEGDC 60

Query: 61  NDRKFMQAVFEENDLQGVIHFAASKAVGESTKIPLTYYSNNINSLIILLETMKQFGVKDI 120
           NDRKFMQAVFEENDLQGVIHFAASKAVGESTKIPLTYYSNNINSLIILLETMKQFGVKDI
Sbjct: 61  NDRKFMQAVFEENDLQGVIHFAASKAVGESTKIPLTYYSNNINSLIILLETMKQFGVKDI 120

Query: 121 VFSSSCTVYGQPDKLPVKETTPRKDAESPYGNTKKICEDILTDHVKSGAPARVVALRYFN 180
           VFSSSCTVYGQPDKLPVKETTPRKDAESPYGNTKKICEDILTDHVKSGAPARVVALRYFN
Sbjct: 121 VFSSSCTVYGQPDKLPVKETTPRKDAESPYGNTKKICEDILTDHVKSGAPARVVALRYFN 180

Query: 181 PIGAHPSSLIGELPLGVPANLIPFVTQTGAGIREKITVFGDDYNTPDGTCIRDYIHVMDL 240
           PIGAHPSSLIGELPLGVPANLIPFVTQTGAGIREKITVFGDDYNTPDGTCIRDYIHVMDL
Sbjct: 181 PIGAHPSSLIGELPLGVPANLIPFVTQTGAGIREKITVFGDDYNTPDGTCIRDYIHVMDL 240

Query: 241 ADAHVKSIQYLADQPENFIDLFNVGTGNGNTVMEVIKAFEKVSEKPLNYEIGPRRSGDIE 300
           ADAHVKSIQYLADQPENFIDLFNVGTGNGNTVMEVIKAFEKVSEKPLNYEIGPRRSGDIE
Sbjct: 241 ADAHVKSIQYLADQPENFIDLFNVGTGNGNTVMEVIKAFEKVSEKPLNYEIGPRRSGDIE 300

Query: 301 KVWANTDKVSKVLGWTPQFGLEEALRDAWNWQLSLKK 337
           KVWANTDKVSKVLGWTPQFGLEEALRDAWNWQLSLKK
Sbjct: 301 KVWANTDKVSKVLGWTPQFGLEEALRDAWNWQLSLKK 337


Lambda     K      H
   0.316    0.136    0.403 

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: 577
Number of extensions: 9
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: 337
Length of database: 337
Length adjustment: 28
Effective length of query: 309
Effective length of database: 309
Effective search space:    95481
Effective search space used:    95481
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 Echvi_1472 Echvi_1472 (UDP-glucose-4-epimerase)
to HMM TIGR01179 (galE: UDP-glucose 4-epimerase GalE (EC 5.1.3.2))

# 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/TIGR01179.hmm
# target sequence database:        /tmp/gapView.22767.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01179  [M=332]
Accession:   TIGR01179
Description: galE: UDP-glucose 4-epimerase GalE
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-129  417.4   0.0   1.9e-129  417.2   0.0    1.0  1  lcl|FitnessBrowser__Cola:Echvi_1472  Echvi_1472 UDP-glucose-4-epimera


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_1472  Echvi_1472 UDP-glucose-4-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.2   0.0  1.9e-129  1.9e-129       1     328 [.       3     335 ..       3     337 .] 0.98

  Alignments for each domain:
  == domain 1  score: 417.2 bits;  conditional E-value: 1.9e-129
                            TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavleeekid 72 
                                          +iL+tGgaGyiGsh++++l ++g+e +++Dn s+++ke+l+ leki    vk+ egd +d++ ++av+ee++++
  lcl|FitnessBrowser__Cola:Echvi_1472   3 QILITGGAGYIGSHTAVALVNAGYEPIIVDNFSNSNKEVLNGLEKILgaPVKYHEGDCNDRKFMQAVFEENDLQ 76 
                                          69*******************************************99999************************ PP

                            TIGR01179  73 aviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespln.pinpY 145
                                           viHfaa++avgEs+k Pl YY+nn+++ + Lle+m+++gvk+++Fsss++vYg+++k+p++E++p + +++pY
  lcl|FitnessBrowser__Cola:Echvi_1472  77 GVIHFAASKAVGESTKIPLTYYSNNINSLIILLETMKQFGVKDIVFSSSCTVYGQPDKLPVKETTPRKdAESPY 150
                                          ******************************************************************9989**** PP

                            TIGR01179 146 GrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkrekleifGtdyp 218
                                          G++k + E il+d  k+ +  +vv+LRYFn++GA+++  iGe + + + +li+ v+++ +g rek+++fG+dy+
  lcl|FitnessBrowser__Cola:Echvi_1472 151 GNTKKICEDILTDHVKSGAPARVVALRYFNPIGAHPSSLIGELPLGVPaNLIPFVTQTGAGIREKITVFGDDYN 224
                                          ************************************************9************************* PP

                            TIGR01179 219 tkDGtcvRDyiHveDlaeaHlaalealeegge..sevynlGagqgfsvkevieavkkvsgkdikveladrRaGD 290
                                          t+DGtc+RDyiHv+Dla+aH++++++l+++ e   +++n+G+g+g+ v+evi+a++kvs k++++e+ +rR+GD
  lcl|FitnessBrowser__Cola:Echvi_1472 225 TPDGTCIRDYIHVMDLADAHVKSIQYLADQPEnfIDLFNVGTGNGNTVMEVIKAFEKVSEKPLNYEIGPRRSGD 298
                                          ****************************996622589************************************* PP

                            TIGR01179 291 paslvadaskikrelgwkpkyddLeeiiksawdWekkl 328
                                          + +++a+++k++++lgw+p+++ Lee +++aw+W+ +l
  lcl|FitnessBrowser__Cola:Echvi_1472 299 IEKVWANTDKVSKVLGWTPQFG-LEEALRDAWNWQLSL 335
                                          **********************.***********9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (337 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.35
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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