Alignments for a candidate for galE in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Pseudomonas stutzeri RCH2

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate GFF69 Psest_0069 UDP-glucose-4-epimerase

Query= curated2:P55180
         (339 letters)



>FitnessBrowser__psRCH2:GFF69
          Length = 354

 Score =  418 bits (1075), Expect = e-122
 Identities = 202/334 (60%), Positives = 257/334 (76%), Gaps = 1/334 (0%)

Query: 3   ILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLLDR 62
           ILVTGGAGYIGSH  +ELL +G+E++VLDNL NSS  AL+RV+++ G+ L F + D+ +R
Sbjct: 2   ILVTGGAGYIGSHAVLELLQAGHEVLVLDNLCNSSQLALDRVEQLAGRPLHFVKGDVRNR 61

Query: 63  EAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIVFS 122
             + ++FA   + AV+HFAGLKAVGESV  PL+YY  N+ G+  LC+AM + GV K+VFS
Sbjct: 62  ALLKALFAAYPVTAVMHFAGLKAVGESVREPLRYYETNVGGSIALCQAMAEAGVFKLVFS 121

Query: 123 SSATVYGVPETSPITEDFPLGA-TNPYGQTKLMLEQILRDLHTADNEWSVALLRYFNPFG 181
           SSATVYG     PITED P G  TNPYGQ+KLM E +L+ L  +D  WS+ LLRYFNP G
Sbjct: 122 SSATVYGESPVMPITEDRPTGVPTNPYGQSKLMAENVLKGLADSDPRWSIGLLRYFNPIG 181

Query: 182 AHPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLAEG 241
           AH SG IGEDPNG+PNNL+PY+ QVAVG+ +QL+V+GNDYPT DGTGVRDYIHVVDLA+G
Sbjct: 182 AHESGLIGEDPNGVPNNLLPYMLQVAVGRRKQLNVYGNDYPTLDGTGVRDYIHVVDLAKG 241

Query: 242 HVKALEKVLNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCFAD 301
           H+KALE++    G   +NLGTG G+SV EM+ AFE+V+G+ +P+    RR GDIA C++D
Sbjct: 242 HLKALERLQLIHGVSTWNLGTGKGHSVREMITAFEEVTGRSLPHVIKPRRSGDIAQCWSD 301

Query: 302 PAKAKRELGWEAKRGLEEMCADSWRWQSSNVNGY 335
           P+KA+RELGW A++ L  M AD+WRWQS N  GY
Sbjct: 302 PSKAERELGWRAEKDLTSMLADAWRWQSRNPRGY 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: 441
Number of extensions: 9
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: 354
Length adjustment: 29
Effective length of query: 310
Effective length of database: 325
Effective search space:   100750
Effective search space used:   100750
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 GFF69 Psest_0069 (UDP-glucose-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.7334.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   8.9e-141  454.4   0.0     1e-140  454.3   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF69  Psest_0069 UDP-glucose-4-epimera


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF69  Psest_0069 UDP-glucose-4-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  454.3   0.0    1e-140    1e-140       1     331 [.       1     334 [.       1     335 [. 0.99

  Alignments for each domain:
  == domain 1  score: 454.3 bits;  conditional E-value: 1e-140
                         TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavleeekidavi 75 
                                       +iLvtGgaGyiGsh v +ll++g+ev+vlDnl+++s+ al ++e++    +++v+gd+++++ l+a++++  + av+
  lcl|FitnessBrowser__psRCH2:GFF69   1 MILVTGGAGYIGSHAVLELLQAGHEVLVLDNLCNSSQLALDRVEQLAgrPLHFVKGDVRNRALLKALFAAYPVTAVM 77 
                                       59*******************************************99989*************************** PP

                         TIGR01179  76 HfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespln.pinpYGrsklm 151
                                       Hfa+l+avgEsv+ePl+YYe nv +++ L++am++agv+kl+Fsssa+vYges  +pi+E+ p++ p+npYG+sklm
  lcl|FitnessBrowser__psRCH2:GFF69  78 HFAGLKAVGESVREPLRYYETNVGGSIALCQAMAEAGVFKLVFSSSATVYGESPVMPITEDRPTGvPTNPYGQSKLM 154
                                       *****************************************************************9*********** PP

                         TIGR01179 152 vErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkrekleifGtdyptkDGtcvRD 227
                                       +E++lk l+++d+++++ +LRYFn++GA+e+g iGe++++ + +l++++++vavg+r++l+++G+dypt DGt+vRD
  lcl|FitnessBrowser__psRCH2:GFF69 155 AENVLKGLADSDPRWSIGLLRYFNPIGAHESGLIGEDPNGVPnNLLPYMLQVAVGRRKQLNVYGNDYPTLDGTGVRD 231
                                       ******************************************9********************************** PP

                         TIGR01179 228 yiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpaslvadaskikre 304
                                       yiHv Dla++Hl+ale l+  ++++++nlG+g+g+sv+e+i a+++v+g++++  +++rR+GD+a++++d+sk++re
  lcl|FitnessBrowser__psRCH2:GFF69 232 YIHVVDLAKGHLKALERLQLIHGVSTWNLGTGKGHSVREMITAFEEVTGRSLPHVIKPRRSGDIAQCWSDPSKAERE 308
                                       ***************************************************************************** PP

                         TIGR01179 305 lgwkpkyddLeeiiksawdWekklkeg 331
                                       lgw+++ d L  ++++aw+W++++++g
  lcl|FitnessBrowser__psRCH2:GFF69 309 LGWRAEKD-LTSMLADAWRWQSRNPRG 334
                                       ******99.**************9986 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.73
//
[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