Alignments for a candidate for galE in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Azospirillum brasilense Sp245

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate AZOBR_RS33555 AZOBR_RS33555 UDP-glucose 4-epimerase

Query= curated2:Q59083
         (348 letters)



>FitnessBrowser__azobra:AZOBR_RS33555
          Length = 332

 Score =  570 bits (1469), Expect = e-167
 Identities = 283/331 (85%), Positives = 300/331 (90%)

Query: 1   MTDQTAASPRVLVTGGAGYIGSHVLHALTDAGIPAVTIDDLSAGRREAIPAAVPLVEGDI 60
           M D+TA   RVLVTGGAGYIGSHVLHAL DAGIPAVTID+LS GRR A+PA+VPLVEGD+
Sbjct: 1   MLDETATPHRVLVTGGAGYIGSHVLHALADAGIPAVTIDNLSTGRRAAVPASVPLVEGDV 60

Query: 61  GSAELLDRVMRDHRVDAVMHFAGSIVVPESVVKPLDYYRNNTANSLTLLGACLRAGIDKV 120
           GSAELL+RV+RDH VDAVMHFAGSIVVPESV KPL YYRNNT NSLTL+ AC+R G+  +
Sbjct: 61  GSAELLERVIRDHAVDAVMHFAGSIVVPESVEKPLAYYRNNTVNSLTLMDACVRLGVGNI 120

Query: 121 VFSSTAAVYGAPESVPIREDAPTVPINPYGASKLMTEQMLRDAGAAHGLRSVILRYFNVA 180
           VFSSTAAVYGAP+ VPI E  PT PINPYG SKLMTEQMLRDAGAAHGLRSVILRYFNVA
Sbjct: 121 VFSSTAAVYGAPDRVPIDEATPTAPINPYGTSKLMTEQMLRDAGAAHGLRSVILRYFNVA 180

Query: 181 GADPAGRTGQATPVATHLIKVACQALLGRRPPLAIFGTDYDTPDGTCIRDYIHVSDLADA 240
           GAD AGRTGQATP ATHLIKVACQALLGRRP L+IFGTDYDTPDGTCIRDYIHVSDLADA
Sbjct: 181 GADAAGRTGQATPTATHLIKVACQALLGRRPALSIFGTDYDTPDGTCIRDYIHVSDLADA 240

Query: 241 HVLALLHLRRGGGSLLMNCGYGRGASVREVVRTLEEVSGEQVPATFADRRPGDPPQLVAG 300
           HVLALLHLRRGG SL +NCGYGRGASV EVVRTLEEVSGE+VPAT A RRPGDPPQLVA 
Sbjct: 241 HVLALLHLRRGGESLTLNCGYGRGASVHEVVRTLEEVSGEKVPATLAPRRPGDPPQLVAK 300

Query: 301 ADRIREQLGWVPKHDRLDGIVRSALSWERSL 331
           ADRIRE+LGWVPKHDRLDGIVR AL+WERSL
Sbjct: 301 ADRIRERLGWVPKHDRLDGIVRDALAWERSL 331


Lambda     K      H
   0.319    0.136    0.401 

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: 517
Number of extensions: 17
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: 348
Length of database: 332
Length adjustment: 28
Effective length of query: 320
Effective length of database: 304
Effective search space:    97280
Effective search space used:    97280
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 AZOBR_RS33555 AZOBR_RS33555 (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.9096.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.2e-136  438.1   0.0   9.2e-136  438.0   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS33555  AZOBR_RS33555 UDP-glucose 4-epim


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS33555  AZOBR_RS33555 UDP-glucose 4-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.0   0.0  9.2e-136  9.2e-136       1     327 [.      10     330 ..      10     332 .] 0.99

  Alignments for each domain:
  == domain 1  score: 438.0 bits;  conditional E-value: 9.2e-136
                                 TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleee 69 
                                               ++LvtGgaGyiGshv+++l ++g   v++Dnls+g + a++a        lvegd+  +e le+v++++
  lcl|FitnessBrowser__azobra:AZOBR_RS33555  10 RVLVTGGAGYIGSHVLHALADAGIPAVTIDNLSTGRRAAVPASV-----PLVEGDVGSAELLERVIRDH 73 
                                               69**************************************9987.....8******************* PP

                                 TIGR01179  70 kidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesp 138
                                               ++dav+Hfa++i v+Esv++Pl YY+nn+vn+l+L++a+++ gv +++Fss+aavYg +++vpi E++p
  lcl|FitnessBrowser__azobra:AZOBR_RS33555  74 AVDAVMHFAGSIVVPESVEKPLAYYRNNTVNSLTLMDACVRLGVGNIVFSSTAAVYGAPDRVPIDEATP 142
                                               ********************************************************************* PP

                                 TIGR01179 139 lnpinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkr 207
                                               ++pinpYG+sklm+E++l+d+  a ++l+ viLRYFnvaGAd  g+ G+a+++athlik+++++ +g+r
  lcl|FitnessBrowser__azobra:AZOBR_RS33555 143 TAPINPYGTSKLMTEQMLRDAGAA-HGLRSVILRYFNVAGADAAGRTGQATPTATHLIKVACQALLGRR 210
                                               *********************998.******************************************** PP

                                 TIGR01179 208 ekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsg 276
                                               ++l+ifGtdy+t+DGtc+RDyiHv+Dla+aH+ al  l +gges ++n+G+g+g sv+ev++++++vsg
  lcl|FitnessBrowser__azobra:AZOBR_RS33555 211 PALSIFGTDYDTPDGTCIRDYIHVSDLADAHVLALLHLRRGGESLTLNCGYGRGASVHEVVRTLEEVSG 279
                                               ********************************************************************* PP

                                 TIGR01179 277 kdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekk 327
                                               ++++++la+rR+GDp++lva+a++i+++lgw pk+d L+ i+++a++We++
  lcl|FitnessBrowser__azobra:AZOBR_RS33555 280 EKVPATLAPRRPGDPPQLVAKADRIRERLGWVPKHDRLDGIVRDALAWERS 330
                                               ************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (332 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: 9.66
//
[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