Alignments for a candidate for galE in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Shewanella oneidensis MR-1

Align UDP-glucose 4-epimerase (EC 5.1.3.7; EC 5.1.3.2) (characterized)
to candidate 200829 SO1664 UDP-glucose 4-epimerase (NCBI ptt file)

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



>FitnessBrowser__MR1:200829
          Length = 337

 Score =  484 bits (1246), Expect = e-141
 Identities = 233/336 (69%), Positives = 271/336 (80%)

Query: 1   MAILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLL 60
           M ILVTGGAGYIG+HT VELLN+G E++VLDNLSNSS EAL+RV+ ITGK +TFY+ D+L
Sbjct: 1   MTILVTGGAGYIGTHTVVELLNAGSEVIVLDNLSNSSIEALDRVERITGKSVTFYQGDIL 60

Query: 61  DREAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIV 120
           ++  +  VF+++ I+AVIHFAGLKAVGESVA PLKYY NN+TGT ILC+ M ++ VK +V
Sbjct: 61  NKALLQKVFSDHSIDAVIHFAGLKAVGESVAKPLKYYENNVTGTLILCQVMAEFKVKNLV 120

Query: 121 FSSSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRDLHTADNEWSVALLRYFNPF 180
           FSSSATVYG P + PITEDFP GATNPYGQ+KLM+E IL DLH +D  W++A LRYFNP 
Sbjct: 121 FSSSATVYGDPASLPITEDFPTGATNPYGQSKLMVEHILADLHHSDPSWNIARLRYFNPV 180

Query: 181 GAHPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLAE 240
           GAH SG IGEDPN IPNNLMP++AQVAVGK E LSVFGNDYPT DGTGVRDYIHVVDLA 
Sbjct: 181 GAHASGLIGEDPNDIPNNLMPFIAQVAVGKREALSVFGNDYPTHDGTGVRDYIHVVDLAI 240

Query: 241 GHVKALEKVLNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCFA 300
           GH+KALEK+    G   YNLGTG GYSVL+MVKAFEK  GK + Y  A RRPGDIA C+A
Sbjct: 241 GHLKALEKLATKPGLVTYNLGTGQGYSVLDMVKAFEKACGKSIAYLIAPRRPGDIAACYA 300

Query: 301 DPAKAKRELGWEAKRGLEEMCADSWRWQSSNVNGYK 336
           DP  AK +L W+A   LE+M   SW WQS+N NGYK
Sbjct: 301 DPDHAKTDLDWQATHSLEDMANSSWHWQSTNPNGYK 336


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: 468
Number of extensions: 8
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: 339
Length of database: 337
Length adjustment: 28
Effective length of query: 311
Effective length of database: 309
Effective search space:    96099
Effective search space used:    96099
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 200829 SO1664 (UDP-glucose 4-epimerase (NCBI ptt file))
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.1621.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-147  475.6   0.0   3.6e-147  475.5   0.0    1.0  1  lcl|FitnessBrowser__MR1:200829  SO1664 UDP-glucose 4-epimerase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:200829  SO1664 UDP-glucose 4-epimerase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  475.5   0.0  3.6e-147  3.6e-147       2     331 ..       3     334 ..       2     335 .. 0.99

  Alignments for each domain:
  == domain 1  score: 475.5 bits;  conditional E-value: 3.6e-147
                       TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavleeekidaviHfa 78 
                                     iLvtGgaGyiG h+v++ll++g ev+vlDnls++s eal ++e+it  +v++++gd+ +k+ l++v+++++idaviHfa
  lcl|FitnessBrowser__MR1:200829   3 ILVTGGAGYIGTHTVVELLNAGSEVIVLDNLSNSSIEALDRVERITgkSVTFYQGDILNKALLQKVFSDHSIDAVIHFA 81 
                                     9********************************************9999****************************** PP

                       TIGR01179  79 aliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYGrsklmvErilk 157
                                     +l+avgEsv++PlkYYennv++tl L+++m++++vk+l+Fsssa+vYg++ ++pi+E++p++++npYG+sklmvE+il 
  lcl|FitnessBrowser__MR1:200829  82 GLKAVGESVAKPLKYYENNVTGTLILCQVMAEFKVKNLVFSSSATVYGDPASLPITEDFPTGATNPYGQSKLMVEHILA 160
                                     ******************************************************************************* PP

                       TIGR01179 158 dlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkrekleifGtdyptkDGtcvRDyiHveDla 235
                                     dl+++d++++++ LRYFn++GA+ +g iGe++++++ +l++ +a+vavgkre+l++fG+dypt+DGt+vRDyiHv Dla
  lcl|FitnessBrowser__MR1:200829 161 DLHHSDPSWNIARLRYFNPVGAHASGLIGEDPNDIPnNLMPFIAQVAVGKREALSVFGNDYPTHDGTGVRDYIHVVDLA 239
                                     ************************************9****************************************** PP

                       TIGR01179 236 eaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpaslvadaskikrelgwkpkyddL 314
                                      +Hl+ale+l+++ +  +ynlG+gqg+sv+++++a++k++gk+i++ +a+rR+GD+a+++ad++++k+ l+w++++  L
  lcl|FitnessBrowser__MR1:200829 240 IGHLKALEKLATKPGLVTYNLGTGQGYSVLDMVKAFEKACGKSIAYLIAPRRPGDIAACYADPDHAKTDLDWQATHS-L 317
                                     ***************************************************************************99.* PP

                       TIGR01179 315 eeiiksawdWekklkeg 331
                                     e++ +s+w+W++++++g
  lcl|FitnessBrowser__MR1:200829 318 EDMANSSWHWQSTNPNG 334
                                     *************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (337 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: 00:00:00.01
# Mc/sec: 6.36
//
[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