Alignments for a candidate for galE in Flavobacterium sp. LM5

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Flavobacterium sp. LM5

Align UDP-glucose 4-epimerase; EC 5.1.3.2 (characterized, see rationale)
to candidate WP_078210642.1 BXU11_RS00700 UDP-glucose 4-epimerase GalE

Query= uniprot:L0FXG3
         (337 letters)



>NCBI__GCF_002017945.1:WP_078210642.1
          Length = 337

 Score =  369 bits (947), Expect = e-107
 Identities = 184/338 (54%), Positives = 249/338 (73%), Gaps = 5/338 (1%)

Query: 3   QILITGGAGYIGSHTAVALVNAGYEPIIVDNFSNSNKEVLNGLEKILGAPVKYHEGDCND 62
           QI++TGG G+IGSHT V L N GYE I++DN SNS+ +VL G+E+I G    + + D  +
Sbjct: 2   QIVVTGGLGFIGSHTVVELQNVGYEVIVIDNLSNSSIDVLGGIERITGKQPIFEQIDLRE 61

Query: 63  RKFMQAVFEE-NDLQGVIHFAASKAVGESTKIPLTYYSNNINSLIILLETMKQFGVKDIV 121
           +  +QA F +  ++ GVIHFAASKAVGES + PL YY NNI SL+ LL+ +++      +
Sbjct: 62  KAAVQAFFAKYTEVSGVIHFAASKAVGESVQNPLLYYENNIASLVYLLQELQKKPEAHFI 121

Query: 122 FSSSCTVYGQPDKLPVKETTPRKDAESPYGNTKKICEDILTDHVK-SGAPARVVALRYFN 180
           FSSSCTVYGQ + +P+ E+TP + A SPYGNTK+I E+I+ D  K SG  A  + LRYFN
Sbjct: 122 FSSSCTVYGQAEVMPIAESTPIQAAMSPYGNTKQIGEEIIADVTKVSGLNA--ILLRYFN 179

Query: 181 PIGAHPSSLIGELPLGVPANLIPFVTQTGAGIREKITVFGDDYNTPDGTCIRDYIHVMDL 240
           PIGAHPS+ IGELP+GVP NL+PF+TQTG G+R++++V+G+DY T DGTC+RDYIHV+DL
Sbjct: 180 PIGAHPSTEIGELPIGVPQNLVPFITQTGMGLRKELSVYGNDYPTVDGTCVRDYIHVVDL 239

Query: 241 ADAHVKSIQYLADQP-ENFIDLFNVGTGNGNTVMEVIKAFEKVSEKPLNYEIGPRRSGDI 299
           A AHV ++Q L D+  E  +++FN+GTG G++V+EVI AFEKVS + L Y I PRR GD+
Sbjct: 240 AKAHVVALQRLLDKKNETALEVFNLGTGKGSSVLEVITAFEKVSGQKLPYTIVPRREGDV 299

Query: 300 EKVWANTDKVSKVLGWTPQFGLEEALRDAWNWQLSLKK 337
            + +ANT+K +KVLGW     LEEA+  AW W+   +K
Sbjct: 300 TEAYANTEKANKVLGWKTAATLEEAIESAWKWEQKSRK 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: 356
Number of extensions: 16
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: 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 WP_078210642.1 BXU11_RS00700 (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.1276419.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.7e-125  401.7   0.1   1.1e-124  401.6   0.1    1.0  1  NCBI__GCF_002017945.1:WP_078210642.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002017945.1:WP_078210642.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  401.6   0.1  1.1e-124  1.1e-124       1     329 [.       2     336 ..       2     337 .] 0.96

  Alignments for each domain:
  == domain 1  score: 401.6 bits;  conditional E-value: 1.1e-124
                             TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavlee.ek 70 
                                           +i+vtGg G+iGsh+v++l++ g+ev+v+Dnls++s ++l  +e+it  +  + + dl++k++++a++++ ++
  NCBI__GCF_002017945.1:WP_078210642.1   2 QIVVTGGLGFIGSHTVVELQNVGYEVIVIDNLSNSSIDVLGGIERITgkQPIFEQIDLREKAAVQAFFAKyTE 74 
                                           589*******************************************9988889999************97268 PP

                             TIGR01179  71 idaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespln.pi 142
                                           +  viHfaa++avgEsv++Pl YYenn+ + + Ll+++qk    ++iFsss++vYg+ e +pi E++p++ ++
  NCBI__GCF_002017945.1:WP_078210642.1  75 VSGVIHFAASKAVGESVQNPLLYYENNIASLVYLLQELQKKPEAHFIFSSSCTVYGQAEVMPIAESTPIQaAM 147
                                           9*******************************************************************99899 PP

                             TIGR01179 143 npYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkrekleifG 214
                                           +pYG++k + E+i+ d++k+ ++l+ ++LRYFn++GA+++ eiGe + + + +l++ ++++ +g r++l+++G
  NCBI__GCF_002017945.1:WP_078210642.1 148 SPYGNTKQIGEEIIADVTKV-SGLNAILLRYFNPIGAHPSTEIGELPIGVPqNLVPFITQTGMGLRKELSVYG 219
                                           ********************.******************************9********************* PP

                             TIGR01179 215 tdyptkDGtcvRDyiHveDlaeaHlaalealeeg...gesevynlGagqgfsvkevieavkkvsgkdikvela 284
                                           +dypt DGtcvRDyiHv Dla+aH+ al+ l ++   +  ev+nlG+g+g sv+evi a++kvsg+++++++ 
  NCBI__GCF_002017945.1:WP_078210642.1 220 NDYPTVDGTCVRDYIHVVDLAKAHVVALQRLLDKkneTALEVFNLGTGKGSSVLEVITAFEKVSGQKLPYTIV 292
                                           *****************************9976632245689******************************* PP

                             TIGR01179 285 drRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklk 329
                                           +rR+GD+++ +a+++k++++lgwk+  + Lee i+saw+We+k +
  NCBI__GCF_002017945.1:WP_078210642.1 293 PRREGDVTEAYANTEKANKVLGWKTAAT-LEEAIESAWKWEQKSR 336
                                           **************************99.************9875 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.31
//
[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