Alignments for a candidate for galE in Lacinutrix algicola AKS293

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Lacinutrix algicola AKS293

Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_055437079.1 ASC41_RS12290 UDP-glucose 4-epimerase GalE

Query= BRENDA::Q9W0P5
         (350 letters)



>NCBI__GCF_001418085.1:WP_055437079.1
          Length = 343

 Score =  347 bits (889), Expect = e-100
 Identities = 172/342 (50%), Positives = 228/342 (66%), Gaps = 8/342 (2%)

Query: 6   VLVTGGAGYIGSHTVLEMLNAGYNVICVDNLCNAYSSGAKLPEALSRVQEITGKKVNFYR 65
           ++VTGG GYIGSHTV+E++   + V+  D+L N+        + +SR+ +ITG K  F +
Sbjct: 5   IIVTGGCGYIGSHTVIELIENDFEVVIFDDLSNSTE------KTISRIHKITGVKPTFIK 58

Query: 66  VDITDREQVRSVFQEHKIDM-VAHFAALKAVGESCRIPLQYYHNNMTGTNVLLEAMADNN 124
           VD+ ++E     F+ HK  + V HFAA KAVGES   PL YY NN+     +LE+  +NN
Sbjct: 59  VDLKNQEATSKAFEAHKDTLGVIHFAAHKAVGESVEKPLMYYKNNLYSLLNVLESQNENN 118

Query: 125 VFKFVYSSSATVYGEPKFLPVTEEHPTGNCTSPYGKTKYFTEEILKDLCKSDKRWAVVSL 184
           +  F++SSSATVYG P  LP+TE++ T    SPYG TK   EEIL D  KS + ++ +SL
Sbjct: 119 INNFIFSSSATVYGTPNTLPITEKNETQRPFSPYGNTKKIAEEILDDFTKSSQDFSAISL 178

Query: 185 RYFNPVGAHISGRIGEDPNGEPNNLMPYIAQVAVGRRPSLSVYGSDFPTHDGTGVRDYIH 244
           RYFNP+GAH SG IGE PNG PNNLMPYI Q A G R  L VYG+D+PT DGT +RDYIH
Sbjct: 179 RYFNPIGAHESGEIGELPNGIPNNLMPYITQTAAGVRDKLMVYGNDYPTKDGTPIRDYIH 238

Query: 245 IVDLAEGHVKALDK-LRNIAETGFFAYNLGTGVGYSVLDMVKAFEKASGKKVNYTLVDRR 303
           +VDLA+ HV A+ + L+   ET    +NLGTG+GYSVLD++K FEK +  K+NY + DRR
Sbjct: 239 VVDLAKAHVLAVKRLLKKEQETALEYFNLGTGLGYSVLDVIKTFEKVTESKLNYEITDRR 298

Query: 304 SGDVATCYADATLADKKLGWKAERGIDKMCEDTWRWQSQNPN 345
            GDV   YA   LA +KLGW A+R +++M   +W W+    N
Sbjct: 299 DGDVPQLYASTDLAKEKLGWSADRALEEMISSSWTWEQNLRN 340


Lambda     K      H
   0.318    0.135    0.408 

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: 396
Number of extensions: 17
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: 350
Length of database: 343
Length adjustment: 29
Effective length of query: 321
Effective length of database: 314
Effective search space:   100794
Effective search space used:   100794
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_055437079.1 ASC41_RS12290 (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.2809195.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-129  417.9   0.1   1.4e-129  417.7   0.1    1.0  1  NCBI__GCF_001418085.1:WP_055437079.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001418085.1:WP_055437079.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.7   0.1  1.4e-129  1.4e-129       1     330 [.       4     340 ..       4     342 .. 0.96

  Alignments for each domain:
  == domain 1  score: 417.7 bits;  conditional E-value: 1.4e-129
                             TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavleeek. 70 
                                           ki+vtGg+GyiGsh+v +l e+++evv++D+ls+++++++++++kit  + ++++ dl+++e+ ++++e++k 
  NCBI__GCF_001418085.1:WP_055437079.1   4 KIIVTGGCGYIGSHTVIELIENDFEVVIFDDLSNSTEKTISRIHKITgvKPTFIKVDLKNQEATSKAFEAHKd 76 
                                           699********************************************9999*****************96652 PP

                             TIGR01179  71 idaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespln.pi 142
                                              viHfaa +avgEsv++Pl YY+nn+ + l++le+ ++ +++++iFsssa+vYg+++++pi+E+ +++ p 
  NCBI__GCF_001418085.1:WP_055437079.1  77 TLGVIHFAAHKAVGESVEKPLMYYKNNLYSLLNVLESQNENNINNFIFSSSATVYGTPNTLPITEKNETQrPF 149
                                           789***************************************************************99988** PP

                             TIGR01179 143 npYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkrekleifG 214
                                           +pYG++k ++E+il+d++k+ ++++ ++LRYFn++GA+e+geiGe +++++ +l+++++++a+g r+kl+++G
  NCBI__GCF_001418085.1:WP_055437079.1 150 SPYGNTKKIAEEILDDFTKSSQDFSAISLRYFNPIGAHESGEIGELPNGIPnNLMPYITQTAAGVRDKLMVYG 222
                                           ***************************************************9********************* PP

                             TIGR01179 215 tdyptkDGtcvRDyiHveDlaeaHlaalealeeg...gesevynlGagqgfsvkevieavkkvsgkdikvela 284
                                           +dyptkDGt +RDyiHv Dla+aH+ a++ l ++   +  e +nlG+g g+sv++vi++++kv+  ++++e++
  NCBI__GCF_001418085.1:WP_055437079.1 223 NDYPTKDGTPIRDYIHVVDLAKAHVLAVKRLLKKeqeTALEYFNLGTGLGYSVLDVIKTFEKVTESKLNYEIT 295
                                           ****************************99987732234578******************************* PP

                             TIGR01179 285 drRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklke 330
                                           drR+GD+++l+a+++ +k++lgw++ +  Lee+i+s+w+We++l++
  NCBI__GCF_001418085.1:WP_055437079.1 296 DRRDGDVPQLYASTDLAKEKLGWSADRA-LEEMISSSWTWEQNLRN 340
                                           ***************************9.************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 16.41
//
[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