Alignments for a candidate for galE in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Dinoroseobacter shibae DFL-12

Align UDP-glucose 4-epimerase (EC 5.1.3.7; EC 5.1.3.2) (characterized)
to candidate 3610487 Dshi_3868 UDP-glucose 4-epimerase (RefSeq)

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



>FitnessBrowser__Dino:3610487
          Length = 359

 Score =  357 bits (917), Expect = e-103
 Identities = 179/325 (55%), Positives = 227/325 (69%)

Query: 3   ILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLLDR 62
           IL+TGGAGYIGSHT V L  +G+E+V+LD+ SN++ +  +R++ ITG  +  YE  +LDR
Sbjct: 5   ILLTGGAGYIGSHTYVALKAAGFEVVILDDFSNAARDVPDRLELITGAPVRLYEGSVLDR 64

Query: 63  EAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIVFS 122
             +  +F E  I+AV+HFA  KAVGESVA+PL Y+  N TG   L + ME   V ++VFS
Sbjct: 65  GLLARLFTETRIDAVVHFAARKAVGESVAMPLAYFETNCTGLVGLLQEMEAACVHRLVFS 124

Query: 123 SSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRDLHTADNEWSVALLRYFNPFGA 182
           SSATVYG+P+ +P  E  P    NPYG TK+  E IL  L T+D +W+   LRYFNP GA
Sbjct: 125 SSATVYGIPDVTPTPETAPHRHMNPYGLTKITGELILDALATSDPKWAFGTLRYFNPAGA 184

Query: 183 HPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLAEGH 242
           H S  IGEDP+ IPNNLMPY+AQVA+G+   L VFG+DYPT DGTGVRDYIHV DLAEGH
Sbjct: 185 HGSALIGEDPSDIPNNLMPYIAQVAMGQRPHLQVFGDDYPTPDGTGVRDYIHVEDLAEGH 244

Query: 243 VKALEKVLNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCFADP 302
           V +L+ +L +  +   NLGTG GYSVLEMV A+    G+ +PYR  DRRPGD+    A  
Sbjct: 245 VLSLKSLLETGESHLVNLGTGRGYSVLEMVAAYSAACGRALPYRIVDRRPGDVPIYCATV 304

Query: 303 AKAKRELGWEAKRGLEEMCADSWRW 327
            +A+  LG+EAKR L +MCA SW W
Sbjct: 305 ERARALLGFEAKRDLAQMCASSWAW 329


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: 410
Number of extensions: 12
Number of successful extensions: 1
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: 359
Length adjustment: 29
Effective length of query: 310
Effective length of database: 330
Effective search space:   102300
Effective search space used:   102300
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 3610487 Dshi_3868 (UDP-glucose 4-epimerase (RefSeq))
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.5719.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   5.7e-122  392.6   0.0   6.6e-122  392.4   0.0    1.0  1  lcl|FitnessBrowser__Dino:3610487  Dshi_3868 UDP-glucose 4-epimeras


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3610487  Dshi_3868 UDP-glucose 4-epimerase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  392.4   0.0  6.6e-122  6.6e-122       2     330 ..       5     335 ..       4     337 .. 0.99

  Alignments for each domain:
  == domain 1  score: 392.4 bits;  conditional E-value: 6.6e-122
                         TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavleeekidaviH 76 
                                       iL+tGgaGyiGsh+ ++l+++g+evv+lD+ s++ +++  +le it   v l+eg + d+  l+++++e++idav+H
  lcl|FitnessBrowser__Dino:3610487   5 ILLTGGAGYIGSHTYVALKAAGFEVVILDDFSNAARDVPDRLELITgaPVRLYEGSVLDRGLLARLFTETRIDAVVH 81 
                                       9******************************************999999**************************** PP

                         TIGR01179  77 faaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYGrsklmvE 153
                                       faa++avgEsv+ Pl Y+e n ++ + Ll++m++a v++l+Fsssa+vYg ++ +p  E++p   +npYG +k++ E
  lcl|FitnessBrowser__Dino:3610487  82 FAARKAVGESVAMPLAYFETNCTGLVGLLQEMEAACVHRLVFSSSATVYGIPDVTPTPETAPHRHMNPYGLTKITGE 158
                                       ***************************************************************************** PP

                         TIGR01179 154 rilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkrekleifGtdyptkDGtcvRDyi 229
                                        il++l+++d+++ +  LRYFn+aGA+ +  iGe++++++ +l++++a+va+g+r++l++fG+dypt+DGt+vRDyi
  lcl|FitnessBrowser__Dino:3610487 159 LILDALATSDPKWAFGTLRYFNPAGAHGSALIGEDPSDIPnNLMPYIAQVAMGQRPHLQVFGDDYPTPDGTGVRDYI 235
                                       ****************************************9************************************ PP

                         TIGR01179 230 HveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpaslvadaskikrelg 306
                                       HveDlae+H+ +l+ l e+ges++ nlG+g+g+sv+e++ a ++++g+ +++++ drR+GD++ ++a+ +++++ lg
  lcl|FitnessBrowser__Dino:3610487 236 HVEDLAEGHVLSLKSLLETGESHLVNLGTGRGYSVLEMVAAYSAACGRALPYRIVDRRPGDVPIYCATVERARALLG 312
                                       ***************************************************************************** PP

                         TIGR01179 307 wkpkyddLeeiiksawdWekklke 330
                                       +++k+d L+++++s+w+W + + +
  lcl|FitnessBrowser__Dino:3610487 313 FEAKRD-LAQMCASSWAWIQARAQ 335
                                       *****9.***********987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (359 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.89
//
[ok]

This GapMind analysis is from Sep 17 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