Alignments for a candidate for galE in Methylovulum miyakonense HT12

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Methylovulum miyakonense HT12

Align UDP-glucose 4-epimerase (EC 5.1.3.7; EC 5.1.3.2) (characterized)
to candidate WP_019867605.1 METMI_RS0117540 UDP-glucose 4-epimerase GalE

Query= metacyc::BSU38860-MONOMER
         (339 letters)



>NCBI__GCF_000384075.1:WP_019867605.1
          Length = 353

 Score =  461 bits (1186), Expect = e-134
 Identities = 222/345 (64%), Positives = 270/345 (78%), Gaps = 10/345 (2%)

Query: 3   ILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLLDR 62
           ILVTGGAGYIGSH CVELL +GY+IVV DNLSNS  E+L RV++ITGK+L FY+AD+ D+
Sbjct: 7   ILVTGGAGYIGSHACVELLQAGYDIVVADNLSNSKTESLARVQQITGKNLKFYQADIRDK 66

Query: 63  EAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIVFS 122
            A+D +F +N I+ VIHFAGLKAVGES + P  YYHNN+ GT +L EAM+  GVK++VFS
Sbjct: 67  AALDEIFDQNPIDTVIHFAGLKAVGESCSKPHLYYHNNVYGTLVLTEAMQAAGVKRLVFS 126

Query: 123 SSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRDLHTAD------NEWSVALLRY 176
           SSATVYG  +T    EDFPLGA NPYG++K M+E ILRDL  AD      + W +ALLRY
Sbjct: 127 SSATVYGESDTPQYAEDFPLGAINPYGRSKAMIEDILRDLSAADHINQDPSPWKIALLRY 186

Query: 177 FNPFGAHPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVV 236
           FNP GAH SG IGEDPNGIPNNLMPY++QVAVGKL QLSVFGNDYPT DGTG+RDYIHVV
Sbjct: 187 FNPIGAHASGLIGEDPNGIPNNLMPYISQVAVGKLAQLSVFGNDYPTPDGTGIRDYIHVV 246

Query: 237 DLAEGHVKALEKV----LNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRP 292
           DL +GH+KA+E +        G  AYNLGTG GYSVLEM++AFE+V+GK + Y+   RR 
Sbjct: 247 DLVKGHIKAIETLDSDAFGPGGCKAYNLGTGRGYSVLEMIQAFERVTGKAINYQIVGRRA 306

Query: 293 GDIATCFADPAKAKRELGWEAKRGLEEMCADSWRWQSSNVNGYKS 337
           GD+A CFA+P +A +ELGW+A++ L++M AD+W WQS N  GY S
Sbjct: 307 GDLAECFANPKRALQELGWQAEKNLDDMVADTWNWQSKNPQGYGS 351


Lambda     K      H
   0.315    0.134    0.395 

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: 466
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: 339
Length of database: 353
Length adjustment: 29
Effective length of query: 310
Effective length of database: 324
Effective search space:   100440
Effective search space used:   100440
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_019867605.1 METMI_RS0117540 (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.20086.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-140  454.2   0.0   1.2e-140  454.0   0.0    1.0  1  lcl|NCBI__GCF_000384075.1:WP_019867605.1  METMI_RS0117540 UDP-glucose 4-ep


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000384075.1:WP_019867605.1  METMI_RS0117540 UDP-glucose 4-epimerase GalE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  454.0   0.0  1.2e-140  1.2e-140       1     331 [.       6     348 ..       6     349 .. 0.97

  Alignments for each domain:
  == domain 1  score: 454.0 bits;  conditional E-value: 1.2e-140
                                 TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavle 67 
                                               kiLvtGgaGyiGsh +++ll++g+++vv Dnls++++e+l ++++it  ++k++++d++dk++l+++++
  lcl|NCBI__GCF_000384075.1:WP_019867605.1   6 KILVTGGAGYIGSHACVELLQAGYDIVVADNLSNSKTESLARVQQITgkNLKFYQADIRDKAALDEIFD 74 
                                               79********************************************9999******************* PP

                                 TIGR01179  68 eekidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEe 136
                                               ++ id+viHfa+l+avgEs ++P  YY+nnv +tl+L eamq+agvk+l+Fsssa+vYges++  + E+
  lcl|NCBI__GCF_000384075.1:WP_019867605.1  75 QNPIDTVIHFAGLKAVGESCSKPHLYYHNNVYGTLVLTEAMQAAGVKRLVFSSSATVYGESDTPQYAED 143
                                               ********************************************************************* PP

                                 TIGR01179 137 splnpinpYGrsklmvErilkdlkkadk......elkvviLRYFnvaGAdeegeiGeasknat.hlikl 198
                                               +pl++inpYGrsk+m+E il+dl+ ad+       +k+++LRYFn++GA+ +g iGe++++++ +l+++
  lcl|NCBI__GCF_000384075.1:WP_019867605.1 144 FPLGAINPYGRSKAMIEDILRDLSAADHinqdpsPWKIALLRYFNPIGAHASGLIGEDPNGIPnNLMPY 212
                                               ***********************999743333336****************************9***** PP

                                 TIGR01179 199 vaevavgkrekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeg....gesevynlGagqgfs 263
                                               + +vavgk+ +l++fG+dypt+DGt++RDyiHv Dl ++H++a+e+l +     g+ ++ynlG+g+g+s
  lcl|NCBI__GCF_000384075.1:WP_019867605.1 213 ISQVAVGKLAQLSVFGNDYPTPDGTGIRDYIHVVDLVKGHIKAIETLDSDafgpGGCKAYNLGTGRGYS 281
                                               ***********************************************9864555799************ PP

                                 TIGR01179 264 vkevieavkkvsgkdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklkeg 331
                                               v+e+i+a+++v+gk i++++  rRaGD+a+++a+++++ +elgw+++ + L+++++++w+W++k+++g
  lcl|NCBI__GCF_000384075.1:WP_019867605.1 282 VLEMIQAFERVTGKAINYQIVGRRAGDLAECFANPKRALQELGWQAEKN-LDDMVADTWNWQSKNPQG 348
                                               ***********************************************99.***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (353 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: 00:00:00.00
# Mc/sec: 11.78
//
[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 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