GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gguA in Desulfovibrio vulgaris Hildenborough

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>MicrobesOnline__882:206505
          Length = 524

 Score =  229 bits (583), Expect = 2e-64
 Identities = 154/505 (30%), Positives = 252/505 (49%), Gaps = 25/505 (4%)

Query: 5   ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64
           ++ +  I K+F  V+A  ++ L +  G I AL+GENGAGKSTLM +LSG     T  G I
Sbjct: 34  VVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDT--GII 91

Query: 65  HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRT 124
           H +G    FR+  D+   GI +++Q   LV  +++AEN+ LG   A      W    + +
Sbjct: 92  HVDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQSGA------WLSPVHMS 145

Query: 125 R---ELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEA 181
           R   EL  + GL   P   + D+ +G++Q VEI K L +  ++LILDEPTA L   ++E 
Sbjct: 146 RVVAELAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQ 205

Query: 182 LLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRN- 240
           L   L      G   + I+HK+ EV  +AD+I +LR G  V   + H+ E+  +  + N 
Sbjct: 206 LFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVD--EFHESEVPGEAELANR 263

Query: 241 MVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMG 300
           MVGR++        +  G+ +L V               L  ++  VRKGEV  IAG+ G
Sbjct: 264 MVGREVILEVAAEPLEPGDRVLHVDGLAG--------DGLKGLSFEVRKGEVFAIAGVAG 315

Query: 301 AGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDN 360
            G+ E    V G        G+V + G P      +     GLAY+ EDR+ L   L+ +
Sbjct: 316 NGQRELVECVTG--LRRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPEDRQGLATCLSLD 373

Query: 361 ILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLS 420
           ++ N  L      ++   +D       A D      ++         +LSGGN QK+V+ 
Sbjct: 374 LVDNFLLTARGCFTRGPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVG 433

Query: 421 KWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYV 480
           +  +  P +++ + PT+G+D+ A  E++  + ++ +   GVL++S ++ E+L   DR+ V
Sbjct: 434 REFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSHA-GVLLVSGDLNEVLALADRVAV 492

Query: 481 MNEGRIVAELPKGEASQESIMRAIM 505
           M  G  +  L + + ++   +  +M
Sbjct: 493 MYRGCFIGLLDRSDTNKVDAIGLMM 517


Lambda     K      H
   0.316    0.135    0.374 

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: 590
Number of extensions: 28
Number of successful extensions: 11
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: 512
Length of database: 524
Length adjustment: 35
Effective length of query: 477
Effective length of database: 489
Effective search space:   233253
Effective search space used:   233253
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: 52 (24.6 bits)

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:

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