Alignments for a candidate for galE in Paludibacter propionicigenes WB4

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Paludibacter propionicigenes WB4

Align UDP-glucose 4-epimerase; EC 5.1.3.2 (characterized, see rationale)
to candidate WP_013444597.1 PALPR_RS05370 UDP-glucose 4-epimerase GalE

Query= uniprot:L0FXG3
         (337 letters)



>NCBI__GCF_000183135.1:WP_013444597.1
          Length = 344

 Score =  385 bits (990), Expect = e-112
 Identities = 193/339 (56%), Positives = 245/339 (72%), Gaps = 2/339 (0%)

Query: 1   MQQILITGGAGYIGSHTAVALVNAGYEPIIVDNFSNSNKEVLNGLEKILGAPVKYHEGDC 60
           M +IL+TGG GYIGSHT V L   G+E ++VDN SNSN +VLNG+EKI G    +   DC
Sbjct: 1   MAKILVTGGTGYIGSHTVVELQKVGFEVVVVDNLSNSNIDVLNGIEKITGIRPAFENIDC 60

Query: 61  NDRKFMQAVFEE-NDLQGVIHFAASKAVGESTKIPLTYYSNNINSLIILLETMKQFGVKD 119
            D   M  +FE+   +  +IHFAASKAVGES + PL YY NN+ SLI LL+ M    VK+
Sbjct: 61  ADYVSMDRMFEKYKGIDAIIHFAASKAVGESVEKPLLYYRNNLVSLINLLQLMPIHKVKN 120

Query: 120 IVFSSSCTVYGQPDKLPVKETTPRKDAESPYGNTKKICEDILTDHVKSGAPARVVALRYF 179
           IVFSSSCTVYGQPD LPV E  P K A SPYGNTK+ICE+I+ D + S    + + LRYF
Sbjct: 121 IVFSSSCTVYGQPDVLPVTEDAPIKPALSPYGNTKQICEEIIHDTIHSNPCYQSIILRYF 180

Query: 180 NPIGAHPSSLIGELPLGVPANLIPFVTQTGAGIREKITVFGDDYNTPDGTCIRDYIHVMD 239
           NPIGAHPS+ IGELP GVP NL+PFVTQT  G+R+++ V+GDDYNTPDG+CIRDYIHV+D
Sbjct: 181 NPIGAHPSAEIGELPNGVPNNLLPFVTQTAIGLRKQLQVYGDDYNTPDGSCIRDYIHVVD 240

Query: 240 LADAHVKSIQ-YLADQPENFIDLFNVGTGNGNTVMEVIKAFEKVSEKPLNYEIGPRRSGD 298
           LA AHV ++Q  L +Q ++ ++ FN+GTG G +V+E+I+ FEKV+   + Y++ PRR GD
Sbjct: 241 LAKAHVIAVQRMLNNQTKHHVETFNLGTGRGLSVLEIIETFEKVNGVKIPYKLAPRREGD 300

Query: 299 IEKVWANTDKVSKVLGWTPQFGLEEALRDAWNWQLSLKK 337
           IEKVWA+    +  LGWT    +EE LR AW W+ +L K
Sbjct: 301 IEKVWADPSYANDELGWTANETVEETLRSAWVWEQNLAK 339


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: 389
Number of extensions: 10
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: 337
Length of database: 344
Length adjustment: 28
Effective length of query: 309
Effective length of database: 316
Effective search space:    97644
Effective search space used:    97644
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_013444597.1 PALPR_RS05370 (UDP-glucose 4-epimerase GalE)
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.2562247.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-128  414.6   0.0   1.4e-128  414.4   0.0    1.0  1  NCBI__GCF_000183135.1:WP_013444597.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000183135.1:WP_013444597.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  414.4   0.0  1.4e-128  1.4e-128       1     329 [.       3     338 ..       3     341 .. 0.96

  Alignments for each domain:
  == domain 1  score: 414.4 bits;  conditional E-value: 1.4e-128
                             TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavleeek. 70 
                                           kiLvtGg+GyiGsh+v++l++ g+evvv+Dnls+++ ++l+ +ekit  + ++ + d ad  ++++++e+ k 
  NCBI__GCF_000183135.1:WP_013444597.1   3 KILVTGGTGYIGSHTVVELQKVGFEVVVVDNLSNSNIDVLNGIEKITgiRPAFENIDCADYVSMDRMFEKYKg 75 
                                           79*********************************************99999*****************8655 PP

                             TIGR01179  71 idaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespln.pi 142
                                           ida+iHfaa++avgEsv++Pl YY+nn+v+ ++Ll++m  ++vk+++Fsss++vYg+++ +p++E++p++ + 
  NCBI__GCF_000183135.1:WP_013444597.1  76 IDAIIHFAASKAVGESVEKPLLYYRNNLVSLINLLQLMPIHKVKNIVFSSSCTVYGQPDVLPVTEDAPIKpAL 148
                                           **********************************************************************678 PP

                             TIGR01179 143 npYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkrekleifG 214
                                           +pYG++k + E+i++d+ ++++ ++ +iLRYFn++GA+++ eiGe +++ + +l++ v+++a+g r++l+++G
  NCBI__GCF_000183135.1:WP_013444597.1 149 SPYGNTKQICEEIIHDTIHSNPCYQSIILRYFNPIGAHPSAEIGELPNGVPnNLLPFVTQTAIGLRKQLQVYG 221
                                           ***************************************************9********************* PP

                             TIGR01179 215 tdyptkDGtcvRDyiHveDlaeaHlaalealeeg...gesevynlGagqgfsvkevieavkkvsgkdikvela 284
                                           +dy+t+DG c+RDyiHv Dla+aH+ a++ + ++   +++e++nlG+g+g sv+e+ie+++kv g++i+++la
  NCBI__GCF_000183135.1:WP_013444597.1 222 DDYNTPDGSCIRDYIHVVDLAKAHVIAVQRMLNNqtkHHVETFNLGTGRGLSVLEIIETFEKVNGVKIPYKLA 294
                                           ****************************98766422256778******************************* PP

                             TIGR01179 285 drRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklk 329
                                           +rR+GD+ +++ad+s++++elgw+++ + +ee ++saw We++l 
  NCBI__GCF_000183135.1:WP_013444597.1 295 PRREGDIEKVWADPSYANDELGWTANET-VEETLRSAWVWEQNLA 338
                                           *************************999.************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (344 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.45
//
[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