GapMind for catabolism of small carbon sources

 

Aligments for a candidate for galE in Azospirillum brasilense Sp245

Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate AZOBR_RS22395 AZOBR_RS22395 UDP-glucose 4-epimerase

Query= SwissProt::Q7WTB1
         (330 letters)



>FitnessBrowser__azobra:AZOBR_RS22395
          Length = 339

 Score =  310 bits (794), Expect = 3e-89
 Identities = 152/325 (46%), Positives = 210/325 (64%), Gaps = 2/325 (0%)

Query: 3   VLVIGGAGYIGSHAVRELVKEGNDVLVLDALYTGHRKAVDPKAKFYQGDIEDTFLVSKIL 62
           VLV GGAGY+GSH V EL+  G  V+VLD L  GHR AV   A F + D+ D   ++++ 
Sbjct: 7   VLVTGGAGYVGSHCVAELLDRGFRVVVLDNLRQGHRAAVPSDAAFVEADLADMDALTRVF 66

Query: 63  RDEKIDAVMHFAAYSLVPESVKKPLKYYDNNVTGMISLLQAMNDANVKYLVFSSSAATYG 122
            + + DAV HFAA SLV ES++ P  Y   N    ++L++A   A V+ +VFSS+A  +G
Sbjct: 67  AEWRFDAVFHFAALSLVGESMRDPHLYLHGNTVNSLNLIRAATTAGVRKMVFSSTANLFG 126

Query: 123 IPKKLPITEDTPLNPINPYGETKMMMEKIMAWADKADGIKYTALRYFNVAGASSDGSIGE 182
            P++ PI E+T ++P +PYGE+K  +E+ + WAD+  G++   LRYFN AGA  +G IGE
Sbjct: 127 TPERQPIDEETTIDPGSPYGESKFFIERALHWADRCHGLRSACLRYFNAAGAHPNGIIGE 186

Query: 183 DHAPETHLIPNILKSAISGDGKFTIFGDDYDTKDGTNVRDYVQVEDLIDAHILALKHMMK 242
           DH PETHLIP +L +A        IFGDDY T DGT VRDYV V DL DAH+  L  +  
Sbjct: 187 DHDPETHLIPLVLDAASGRRSHIEIFGDDYPTPDGTCVRDYVHVCDLADAHLRVLPAL-- 244

Query: 243 TNKSDVFNLGTAHGYSNLEILESAKKVTGIDIPYTMGPRRGGDPDSLVADSTKARTVLGW 302
             +S  FNLG   GYS  E++++ ++VTG+ +P  +GPRR GDP  L+A S + R  LGW
Sbjct: 245 ETRSVRFNLGNGTGYSVREVIDATERVTGLTVPVKVGPRRAGDPAMLIASSERIRGELGW 304

Query: 303 KPKHENVDDVIATAWKWHKSHPKGY 327
            P+  ++D +I +AW+W + HP GY
Sbjct: 305 SPRFPDLDSIIGSAWEWRRRHPGGY 329


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: 342
Number of extensions: 10
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: 330
Length of database: 339
Length adjustment: 28
Effective length of query: 302
Effective length of database: 311
Effective search space:    93922
Effective search space used:    93922
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 AZOBR_RS22395 AZOBR_RS22395 (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.32032.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.5e-126  405.2   0.0   9.7e-126  405.0   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS22395  AZOBR_RS22395 UDP-glucose 4-epim


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS22395  AZOBR_RS22395 UDP-glucose 4-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.0   0.0  9.7e-126  9.7e-126       2     331 ..       7     328 ..       6     329 .. 0.98

  Alignments for each domain:
  == domain 1  score: 405.0 bits;  conditional E-value: 9.7e-126
                                 TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeek 70 
                                               +LvtGgaGy+Gsh v +ll++g++vvvlDnl +g++ a++        ++ve+dlad  +l++v++e +
  lcl|FitnessBrowser__azobra:AZOBR_RS22395   7 VLVTGGAGYVGSHCVAELLDRGFRVVVLDNLRQGHRAAVPSDA-----AFVEADLADMDALTRVFAEWR 70 
                                               8***************************************998.....7******************** PP

                                 TIGR01179  71 idaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespl 139
                                               +dav Hfaal  vgEs+++P  Y + n+vn+l+L++a ++agv+k++Fss+a ++g++e+ pi Ee+++
  lcl|FitnessBrowser__azobra:AZOBR_RS22395  71 FDAVFHFAALSLVGESMRDPHLYLHGNTVNSLNLIRAATTAGVRKMVFSSTANLFGTPERQPIDEETTI 139
                                               ********************************************************************* PP

                                 TIGR01179 140 npinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkre 208
                                                p +pYG+sk  +Er l+ + +  ++l+ + LRYFn+aGA+++g iGe++ ++thli+lv+++a+g+r+
  lcl|FitnessBrowser__azobra:AZOBR_RS22395 140 DPGSPYGESKFFIERALHWADRC-HGLRSACLRYFNAAGAHPNGIIGEDHDPETHLIPLVLDAASGRRS 207
                                               ********************999.********************************************* PP

                                 TIGR01179 209 kleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgk 277
                                               ++eifG+dypt+DGtcvRDy+Hv+Dla+aHl+ l ale  + s  +nlG+g+g+sv+evi+a+++v+g 
  lcl|FitnessBrowser__azobra:AZOBR_RS22395 208 HIEIFGDDYPTPDGTCVRDYVHVCDLADAHLRVLPALE--TRSVRFNLGNGTGYSVREVIDATERVTGL 274
                                               *************************************9..58999************************ PP

                                 TIGR01179 278 dikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklkeg 331
                                               +++v++ +rRaGDpa+l+a++++i+ elgw+p++ dL+ ii saw+W+++++ g
  lcl|FitnessBrowser__azobra:AZOBR_RS22395 275 TVPVKVGPRRAGDPAMLIASSERIRGELGWSPRFPDLDSIIGSAWEWRRRHPGG 328
                                               *************************************************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (339 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: 6.58
//
[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:

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:

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:

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