GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05250 in Azospirillum brasilense Sp245

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate AZOBR_RS06625 AZOBR_RS06625 heme ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__azobra:AZOBR_RS06625
          Length = 511

 Score =  297 bits (761), Expect = 5e-85
 Identities = 189/513 (36%), Positives = 285/513 (55%), Gaps = 23/513 (4%)

Query: 21  PVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDIL 80
           P +  R V K F    A  +    +  G +H ++GENGAGKST+M I+ G    D G IL
Sbjct: 6   PALETRGVNKWFGANHANRDVSLAVPKGTIHGVIGENGAGKSTIMSIVYGYLPADGGTIL 65

Query: 81  LDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREP--RKAMGLFIDEDELN 138
           +DG+PV +  PR A A GIG++HQ   L++  +  +N+ +G E     A G+     EL 
Sbjct: 66  VDGRPVAVRSPRDALAAGIGMVHQHFMLVDPFTVLENVLLGAEGGVTLAAGMARARTELT 125

Query: 139 RQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAE 198
           R A        L++D   PVGEL V  QQ VEI KAL   + +LI+DEPT  L   E   
Sbjct: 126 RLARDY----GLEVDLDRPVGELPVGAQQRVEILKALYRGADILILDEPTGVLTPQETDH 181

Query: 199 LFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG 258
           LFRI+R L+ QG  +V I+HK+ E+ ++ D V+VMR G+ +A V    TS + +  +MVG
Sbjct: 182 LFRILRALREQGKTVVIITHKLREIMELTDNVTVMRRGQVVANVATARTSREELAELMVG 241

Query: 259 R-ALDGEQRIPPDTSRNDVVLEVRGL----NRG-RAIRDVSFTLRKGEILGFAGLMGAGR 312
           R  L   +++P   +    VLEV GL      G   ++ +  T+R GEI+G AG+ G G+
Sbjct: 242 RKVLLRVEKVP--ATPGPAVLEVSGLCVRDGAGVERVKGIGLTVRAGEIVGIAGVSGNGQ 299

Query: 313 TEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAH-----GIGYLSEDRKHFGLAVGMD 367
           +E+  A+ G  P   G + +  G+ +  +P    A      G+G++ EDR+  GL  G +
Sbjct: 300 SELLEALAGMRPPAEGSVRLR-GEELTATPDRFTARGLRALGVGHVPEDRQRVGLVTGFE 358

Query: 368 VQANIALSSMG--RFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIV 425
            Q    L   G   F     MD+RA+ +     +    ++       A   SGGNQQKIV
Sbjct: 359 AQECAILGHQGDPAFNGRLLMDRRALFDRCASEMDAYDVRPRDPRLPAANFSGGNQQKIV 418

Query: 426 IAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRV 485
           +A+ + R+ D+L   +PTRG+D+GA   I++ L AL +QGKAI+++S EL E+  +S R+
Sbjct: 419 LAREMERNPDLLLVGQPTRGVDIGAIEFIHRRLVALRDQGKAILLVSVELDEIRALSDRI 478

Query: 486 LVMCEGRITGELARADATQEKI-MQLATQRESA 517
           LVM +GR+ GE+A  +A + ++ + +A   E+A
Sbjct: 479 LVMFDGRLVGEVAPGEADERRLGLMMAGVAEAA 511


Lambda     K      H
   0.320    0.135    0.372 

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: 711
Number of extensions: 39
Number of successful extensions: 9
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: 520
Length of database: 511
Length adjustment: 35
Effective length of query: 485
Effective length of database: 476
Effective search space:   230860
Effective search space used:   230860
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 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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