GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gguA in Pseudomonas stutzeri RCH2

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate GFF1357 Psest_1392 ABC-type uncharacterized transport systems, ATPase components

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__psRCH2:GFF1357
          Length = 518

 Score =  224 bits (572), Expect = 4e-63
 Identities = 159/494 (32%), Positives = 254/494 (51%), Gaps = 31/494 (6%)

Query: 6   LEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEIH 65
           L++  ITK +PG  A + ++L ++ GEIHAL+GENGAGKSTLMK++ GV       GEIH
Sbjct: 9   LQLCGITKQYPGCLANDRIDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDA--GEIH 66

Query: 66  YEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRTR 125
           ++G     R    + + GI ++ Q  +L   LS+AENI L     +    + +Q   + R
Sbjct: 67  WQGERVTMRDPAQARERGIGMVFQHFSLFETLSVAENIALALGAKAG---TPKQLEPKIR 123

Query: 126 ELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLNL 185
           E+ ++ G+   P+ L+  + +G++Q VEI + L + ++LLILDEPT+ L   +++ L   
Sbjct: 124 EVSQRYGMPLEPQRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVT 183

Query: 186 LMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVG-- 243
           L     +G + + I+HKLNEVR +    TVLR G    + +C   E S+  + R MVG  
Sbjct: 184 LRRLAAEGCSILFISHKLNEVRALCQSATVLRAGRV--SGECIPAECSDLELARLMVGDA 241

Query: 244 RDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGR 303
             LE  YP  +       +E  +W   H        L ++++ VR GE+VGIAG+ G G+
Sbjct: 242 EGLEAEYPKSEGRAPFLRVERLSW---HNADPFGVSLKEVDLEVRAGEIVGIAGVAGNGQ 298

Query: 304 TEFAMSVFG-------KSYGHRITGDVLIDGKPVDVSTVRKAIDA--GLAYVTEDRKHLG 354
            E    + G       ++   R  GD        DV+ +R       G+A+V  +R   G
Sbjct: 299 DELLALLSGEQRLQAAQAMRIRFLGD--------DVAHLRPGARRRHGMAFVPAERLGHG 350

Query: 355 LVLNDNILHN--TTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGG 412
            V + ++  N   T     G+ +  +I   +    A     R  +++        +LSGG
Sbjct: 351 AVPSMSLADNGLLTAYQQTGMVEQGLIRRGRVRAFAEQVIQRFAVKTPDAQTPAASLSGG 410

Query: 413 NQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELL 472
           N QK +L + +   P +LI   PT G+DVGA   I+  + +L   G  +L+IS ++ EL 
Sbjct: 411 NLQKFILGREILQQPKLLIAAHPTWGVDVGAAAAIHRALIELRDAGAAILVISEDLEELF 470

Query: 473 GNCDRIYVMNEGRI 486
              DRI  +++GR+
Sbjct: 471 QISDRIAALSDGRL 484



 Score = 63.5 bits (153), Expect = 2e-14
 Identities = 54/227 (23%), Positives = 105/227 (46%), Gaps = 11/227 (4%)

Query: 283 INVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAG 342
           I+++++ GE+  + G  GAG++     ++G +      G++   G+ V +    +A + G
Sbjct: 27  IDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPD--AGEIHWQGERVTMRDPAQARERG 84

Query: 343 LAYVTEDRKHLGLVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGI 402
           +  V +   H  L    ++  N  LA  A       ++  K  +V+  +   L  +    
Sbjct: 85  IGMVFQ---HFSLFETLSVAENIALALGAKAGTPKQLEP-KIREVSQRYGMPLEPQ---- 136

Query: 403 FQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVL 462
            +   +LS G +Q+V + + L  +  +LILDEPT  +      E++  + +LAA+G  +L
Sbjct: 137 -RLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVTLRRLAAEGCSIL 195

Query: 463 MISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIMRSGE 509
            IS ++ E+   C    V+  GR+  E    E S   + R ++   E
Sbjct: 196 FISHKLNEVRALCQSATVLRAGRVSGECIPAECSDLELARLMVGDAE 242


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: 548
Number of extensions: 25
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 512
Length of database: 518
Length adjustment: 35
Effective length of query: 477
Effective length of database: 483
Effective search space:   230391
Effective search space used:   230391
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