Alignments for a candidate for galE in Jannaschia aquimarina GSW-M26

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Jannaschia aquimarina GSW-M26

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_043917800.1 jaqu_RS04770 UDP-glucose 4-epimerase GalE

Query= curated2:P55180
         (339 letters)



>NCBI__GCF_000877395.1:WP_043917800.1
          Length = 340

 Score =  348 bits (892), Expect = e-100
 Identities = 178/334 (53%), Positives = 226/334 (67%), Gaps = 2/334 (0%)

Query: 3   ILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLLDR 62
           IL+TGGAGYIGSHTCV L  +G+E V+LD+ SN+    + R+  I G         +LD 
Sbjct: 4   ILLTGGAGYIGSHTCVALHEAGHEAVILDDFSNADESVVERIGRIIGAPPPVVNGSILDG 63

Query: 63  EAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIVFS 122
           EAV   FAE+ I+ VIHFA  KAVGESVA PL Y+ NN+ G+  L  AM +  V  +VFS
Sbjct: 64  EAVRRAFAEHAIDGVIHFAAFKAVGESVANPLAYFENNIAGSIALARAMREAQVWPLVFS 123

Query: 123 SSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRDLHTADNEWSVALLRYFNPFGA 182
           S+ATVYG P+  PI E  P G T+PY  TK+ +EQIL     AD  + +  LRYFNP GA
Sbjct: 124 STATVYGEPDAFPIPETAPTGYTSPYAFTKITVEQILAQAAAAD-PFVIGALRYFNPVGA 182

Query: 183 HPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLAEGH 242
           H S  IGEDP GIP+NLMPY+A+VA+G+LEQLSVFG+DY T DGTG+RDYIHV+DLAE H
Sbjct: 183 HESALIGEDPRGIPDNLMPYMAKVAMGELEQLSVFGDDYDTPDGTGLRDYIHVMDLAEAH 242

Query: 243 VKALEKVLNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCFADP 302
           V ++  +L    A   N+GTG   SVL+M +A+ +  G+E+P R   RRPGD+    ADP
Sbjct: 243 VLSMNALLEGR-AHTLNIGTGIPTSVLQMHEAYSRAVGRELPMRVVPRRPGDVPRLDADP 301

Query: 303 AKAKRELGWEAKRGLEEMCADSWRWQSSNVNGYK 336
           A+A   LG+EAKR L+ MC DSWRW  +   G++
Sbjct: 302 ARALEVLGFEAKRDLDAMCRDSWRWVRAQAAGWR 335


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: 398
Number of extensions: 14
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: 340
Length adjustment: 28
Effective length of query: 311
Effective length of database: 312
Effective search space:    97032
Effective search space used:    97032
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_043917800.1 jaqu_RS04770 (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.2039834.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.2e-120  386.9   0.0     4e-120  386.6   0.0    1.0  1  NCBI__GCF_000877395.1:WP_043917800.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000877395.1:WP_043917800.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  386.6   0.0    4e-120    4e-120       1     328 [.       3     330 ..       3     333 .. 0.98

  Alignments for each domain:
  == domain 1  score: 386.6 bits;  conditional E-value: 4e-120
                             TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavleeeki 71 
                                           +iL+tGgaGyiGsh++++l e+g+e v+lD+ s++ +++++++ +i      +v+g + d e+++++++e++i
  NCBI__GCF_000877395.1:WP_043917800.1   3 RILLTGGAGYIGSHTCVALHEAGHEAVILDDFSNADESVVERIGRIIgaPPPVVNGSILDGEAVRRAFAEHAI 75 
                                           69*******************************************9988899********************* PP

                             TIGR01179  72 daviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinp 144
                                           d viHfaa++avgEsv++Pl Y+enn+ +++ L +am++a+v  l+Fss+a+vYge+++ pi E++p++ ++p
  NCBI__GCF_000877395.1:WP_043917800.1  76 DGVIHFAAFKAVGESVANPLAYFENNIAGSIALARAMREAQVWPLVFSSTATVYGEPDAFPIPETAPTGYTSP 148
                                           ************************************************************************* PP

                             TIGR01179 145 YGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkrekleifGtd 216
                                           Y  +k++vE+il +++ a   + + +LRYFn++GA+e+  iGe++++++ +l++++a+va+g++e+l++fG+d
  NCBI__GCF_000877395.1:WP_043917800.1 149 YAFTKITVEQILAQAAAA-DPFVIGALRYFNPVGAHESALIGEDPRGIPdNLMPYMAKVAMGELEQLSVFGDD 220
                                           ***************999.88**************************************************** PP

                             TIGR01179 217 yptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaG 289
                                           y+t+DGt++RDyiHv+DlaeaH+ +++al e g ++++n+G+g   sv+++ ea ++++g+++++++ +rR+G
  NCBI__GCF_000877395.1:WP_043917800.1 221 YDTPDGTGLRDYIHVMDLAEAHVLSMNALLE-GRAHTLNIGTGIPTSVLQMHEAYSRAVGRELPMRVVPRRPG 292
                                           ******************************8.789************************************** PP

                             TIGR01179 290 DpaslvadaskikrelgwkpkyddLeeiiksawdWekkl 328
                                           D+++l ad++++ ++lg+++k+d L+ +++++w+W + +
  NCBI__GCF_000877395.1:WP_043917800.1 293 DVPRLDADPARALEVLGFEAKRD-LDAMCRDSWRWVRAQ 330
                                           **********************9.***********9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (340 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: 17.16
//
[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