Aligments for a candidate for galE in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Aligments for a candidate for galE in Paraburkholderia bryophila 376MFSha3.1

Align UDP-glucose 4-epimerase (EC 5.1.3.7; EC 5.1.3.2) (characterized)
to candidate H281DRAFT_00074 H281DRAFT_00074 UDP-galactose 4-epimerase

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



>FitnessBrowser__Burk376:H281DRAFT_00074
          Length = 340

 Score =  440 bits (1131), Expect = e-128
 Identities = 211/334 (63%), Positives = 254/334 (76%)

Query: 3   ILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLLDR 62
           ILVTGGAG+IGSHTCVELLN GY++VV+DNL +S+ E+L RV+ I G+ + FYEAD  D 
Sbjct: 7   ILVTGGAGFIGSHTCVELLNGGYDVVVIDNLVHSNRESLQRVERIAGRGVAFYEADARDE 66

Query: 63  EAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIVFS 122
            A++ VF  + I   IHFA LKAVGESVA P++YY NN+     L   M    VK+ VFS
Sbjct: 67  AALNRVFDAHPITGAIHFAALKAVGESVAKPIEYYSNNVGSLLALLGVMRDRNVKQFVFS 126

Query: 123 SSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRDLHTADNEWSVALLRYFNPFGA 182
           SSATVYGVP++SPI E FPL ATNPYGQ+KL+ EQ+LRDL  AD  W +A LRYFNP GA
Sbjct: 127 SSATVYGVPKSSPIDESFPLSATNPYGQSKLIAEQVLRDLEVADPSWRIATLRYFNPVGA 186

Query: 183 HPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLAEGH 242
           H SG IGEDP G+PNNLMPYVAQVAVGKL++L VFG DY T DGTGVRDYIHVVDLA GH
Sbjct: 187 HESGLIGEDPAGVPNNLMPYVAQVAVGKLDKLRVFGGDYETPDGTGVRDYIHVVDLARGH 246

Query: 243 VKALEKVLNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCFADP 302
           + AL+ ++    +   NLGTG GYSV+++VKAFEK SG+ VPY    RRPGD+A+CFADP
Sbjct: 247 LAALDALVKRDASFVVNLGTGQGYSVIDVVKAFEKASGRPVPYEIVARRPGDVASCFADP 306

Query: 303 AKAKRELGWEAKRGLEEMCADSWRWQSSNVNGYK 336
             A   LGW A+ G+E MCAD WRWQS+N +G++
Sbjct: 307 RAALELLGWRAEFGIERMCADHWRWQSANPDGFR 340


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: 433
Number of extensions: 7
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: 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 H281DRAFT_00074 H281DRAFT_00074 (UDP-galactose 4-epimerase)
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.11637.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   7.3e-136  438.3   0.0   8.2e-136  438.1   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_00074  H281DRAFT_00074 UDP-galactose 4-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_00074  H281DRAFT_00074 UDP-galactose 4-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.1   0.0  8.2e-136  8.2e-136       2     330 ..       7     337 ..       6     339 .. 0.99

  Alignments for each domain:
  == domain 1  score: 438.1 bits;  conditional E-value: 8.2e-136
                                    TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleav 65 
                                                  iLvtGgaG+iGsh++++ll+ g++vvv+Dnl+++++e+l+++e+i    v+++e+d +d+++l++v
  lcl|FitnessBrowser__Burk376:H281DRAFT_00074   7 ILVTGGAGFIGSHTCVELLNGGYDVVVIDNLVHSNRESLQRVERIAgrGVAFYEADARDEAALNRV 72 
                                                  9********************************************9989***************** PP

                                    TIGR01179  66 leeekidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekv 131
                                                  ++++ i   iHfaal+avgEsv++P++YY+nnv + l Ll +m++ +vk+++Fsssa+vYg ++++
  lcl|FitnessBrowser__Burk376:H281DRAFT_00074  73 FDAHPITGAIHFAALKAVGESVAKPIEYYSNNVGSLLALLGVMRDRNVKQFVFSSSATVYGVPKSS 138
                                                  ****************************************************************** PP

                                    TIGR01179 132 pisEesplnpinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hli 196
                                                  pi E++pl+++npYG+skl++E++l+dl+ ad++++++ LRYFn++GA+e+g iGe++ + + +l+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00074 139 PIDESFPLSATNPYGQSKLIAEQVLRDLEVADPSWRIATLRYFNPVGAHESGLIGEDPAGVPnNLM 204
                                                  **************************************************************9*** PP

                                    TIGR01179 197 klvaevavgkrekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgf 262
                                                  ++va+vavgk++kl++fG+dy+t+DGt+vRDyiHv Dla +Hlaal+al + + s v nlG+gqg+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00074 205 PYVAQVAVGKLDKLRVFGGDYETPDGTGVRDYIHVVDLARGHLAALDALVKRDASFVVNLGTGQGY 270
                                                  ****************************************************************** PP

                                    TIGR01179 263 svkevieavkkvsgkdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekkl 328
                                                  sv +v++a++k+sg+++++e+ +rR+GD+as++ad+  + + lgw+++++ +e ++++ w+W++ +
  lcl|FitnessBrowser__Burk376:H281DRAFT_00074 271 SVIDVVKAFEKASGRPVPYEIVARRPGDVASCFADPRAALELLGWRAEFG-IERMCADHWRWQSAN 335
                                                  **************************************************.************998 PP

                                    TIGR01179 329 ke 330
                                                  ++
  lcl|FitnessBrowser__Burk376:H281DRAFT_00074 336 PD 337
                                                  76 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.91
//
[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, or view the source code.

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