Alignments for a candidate for galE in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Pseudomonas fluorescens FW300-N1B4

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate Pf1N1B4_5092 UDP-glucose 4-epimerase (EC 5.1.3.2)

Query= curated2:Q57301
         (336 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5092
          Length = 354

 Score =  391 bits (1004), Expect = e-113
 Identities = 188/334 (56%), Positives = 243/334 (72%), Gaps = 2/334 (0%)

Query: 4   LITGGAGYIGSHTVLTLLEQGRNVVVLDNLINSSAESLARVSKICGRKPNFYHGDILDRS 63
           LITGGAGYIGSHT LTL++ GR V+VLDNL NS  ESL R+  +  ++ +F  GDI D  
Sbjct: 6   LITGGAGYIGSHTTLTLIDAGRQVLVLDNLCNSCHESLTRLEYLTRKRVDFIEGDIRDSH 65

Query: 64  CLKLIFSSHKIDSVIHFAGLKSVGESVEKPIEYYQNNVVGSITLLEEMCLANVKKLIFSS 123
            L  IFS + ID+V+HFAGLKSV ESV KP++YY NNVVG++ L   M    V KL+FSS
Sbjct: 66  LLDDIFSRYDIDAVVHFAGLKSVEESVRKPLDYYANNVVGTLNLCHAMARFEVFKLVFSS 125

Query: 124 SATVYGEPEFVPLTEKARIGGTTNPYGTSKVMVEQILKDFSLAHPDYSITALRYFNPVGA 183
           SATVYG P  +PL E    G   NPYG +K+++E++L D  L+ P +SI  LRYFNP+GA
Sbjct: 126 SATVYGAPRQIPLIEDMGAGKPINPYGRTKLLIEELLTDLCLSDPQWSIAVLRYFNPIGA 185

Query: 184 HPSGLIGEDPNGKPNNLLPFITQVAIGKLSKLLVYGNDYDTPDGSGIRDYIHVMDLAEGH 243
           H SGLIGE+PNG+PNNLLP +T+VA+ ++ +L+VYG+DY T DG+ +RDY+HV+D+A+GH
Sbjct: 186 HASGLIGENPNGRPNNLLPCLTRVAMRQVPELMVYGSDYPTVDGTCVRDYVHVLDVADGH 245

Query: 244 LSTL--INLTSGFRIYNLGTGVGYSVLHMIKEFERITGKNIPFDIVSRRPGDIAECWASP 301
           L  L  +  T+G  ++NLGTG+G+SVL +I  FE ITG  IPF    RR GDIAECWA P
Sbjct: 246 LKALRALQNTNGIHVWNLGTGIGHSVLQIIHSFENITGITIPFRFAPRRDGDIAECWADP 305

Query: 302 ELAHLELGWYAKRTLVDMLQDAWKWQKMNPNGYN 335
             A  +LGWYA+R L+ M+ D W+WQ  NP GY+
Sbjct: 306 TKAGRDLGWYAQRDLMQMIIDTWRWQLCNPYGYH 339


Lambda     K      H
   0.319    0.138    0.415 

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: 472
Number of extensions: 17
Number of successful extensions: 2
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: 336
Length of database: 354
Length adjustment: 29
Effective length of query: 307
Effective length of database: 325
Effective search space:    99775
Effective search space used:    99775
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate Pf1N1B4_5092 (UDP-glucose 4-epimerase (EC 5.1.3.2))
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.23322.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   2.8e-135  436.4   0.0   3.2e-135  436.2   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5092  UDP-glucose 4-epimerase (EC 5.1.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5092  UDP-glucose 4-epimerase (EC 5.1.3.2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  436.2   0.0  3.2e-135  3.2e-135       3     328 ..       6     334 ..       4     338 .. 0.98

  Alignments for each domain:
  == domain 1  score: 436.2 bits;  conditional E-value: 3.2e-135
                                      TIGR01179   3 LvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkeklea 64 
                                                    L+tGgaGyiGsh++ +l ++g +v+vlDnl+++ +e+l++le +t  +v ++egd++d++ l++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5092   6 LITGGAGYIGSHTTLTLIDAGRQVLVLDNLCNSCHESLTRLEYLTrkRVDFIEGDIRDSHLLDD 69 
                                                    9*****************************************998889**************** PP

                                      TIGR01179  65 vleeekidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYges 128
                                                    ++++ +idav+Hfa+l++v+Esv++Pl YY+nnvv+tl+L++am++++v+kl+Fsssa+vYg +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5092  70 IFSRYDIDAVVHFAGLKSVEESVRKPLDYYANNVVGTLNLCHAMARFEVFKLVFSSSATVYGAP 133
                                                    **************************************************************** PP

                                      TIGR01179 129 ekvpisEespln.pinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeaskn 191
                                                    +++p+ E++  + pinpYGr+kl +E++l+dl  +d+++++++LRYFn++GA+ +g iGe++++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5092 134 RQIPLIEDMGAGkPINPYGRTKLLIEELLTDLCLSDPQWSIAVLRYFNPIGAHASGLIGENPNG 197
                                                    *********9988*************************************************** PP

                                      TIGR01179 192 at.hliklvaevavgkrekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevy 254
                                                     + +l++ +++va+ + ++l+++G dypt DGtcvRDy+Hv D+a++Hl+al+al+++++ +v+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5092 198 RPnNLLPCLTRVAMRQVPELMVYGSDYPTVDGTCVRDYVHVLDVADGHLKALRALQNTNGIHVW 261
                                                    **9************************************************************* PP

                                      TIGR01179 255 nlGagqgfsvkevieavkkvsgkdikveladrRaGDpaslvadaskikrelgwkpkyddLeeii 318
                                                    nlG+g g+sv+++i+ +++++g +i++++a+rR+GD+a+++ad+ k+ r lgw +++d L ++i
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5092 262 NLGTGIGHSVLQIIHSFENITGITIPFRFAPRRDGDIAECWADPTKAGRDLGWYAQRD-LMQMI 324
                                                    *********************************************************9.***** PP

                                      TIGR01179 319 ksawdWekkl 328
                                                     ++w+W+  +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5092 325 IDTWRWQLCN 334
                                                    ******9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (354 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: 00:00:00.01
# Mc/sec: 6.15
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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