GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Rhizobium freirei PRF 81

Align Ribose ABC transporter ATPase; SubName: Full=Sugar ABC transporter ATP-binding protein; SubName: Full=Sugar ABC transporter ATPase (characterized, see rationale)
to candidate WP_037149946.1 RHSP_RS05960 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A1N7TZ92
         (517 letters)



>NCBI__GCF_000359745.1:WP_037149946.1
          Length = 511

 Score =  401 bits (1031), Expect = e-116
 Identities = 223/505 (44%), Positives = 321/505 (63%), Gaps = 5/505 (0%)

Query: 1   MSSSAPNAVLSVSGIGKTYAQPV-LSDITLTLNRGEVLALTGENGAGKSTLSKIIGGLVT 59
           +S +  + +L + GIGK +   V L ++++ + RG+   L GENGAGKSTL  ++GG+  
Sbjct: 6   VSGTDDDFILKLDGIGKRFPGVVALRNVSMQIGRGKGHILLGENGAGKSTLINLLGGVFR 65

Query: 60  PTTGHMQFNGQDFRPGSRTQAEELGVRMVMQELNLLPTLTVAENLFLDNLPSHCGWISRK 119
           P  GH+ F+GQ + P S  +A + G+R++ QEL+ L  LTVAENL  ++LP   G ++ K
Sbjct: 66  PDDGHILFDGQRYDPSSPLEAFKAGIRVIHQELHPLSNLTVAENLLFEHLPRRYGLVNYK 125

Query: 120 QLRKAAIEAMAQVGLDAIDPDTLVGSLGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAR 179
           ++   A E +A+VGLD + P TL   L +   Q++EIA+ L  +  +L+LDEPTA LT++
Sbjct: 126 EMNSRAAELLAEVGLD-VAPTTLASRLSVAQLQLLEIAKALCYESKLLVLDEPTATLTSK 184

Query: 180 EVEMLFEQITRLQARGVAIIYISHRLEELARVAQRIAVLRDGKLVCVEPMANYNSEQLVT 239
           EV+ LFE + RL+ARGV  +YISHRLEE+  V   + VLRDG+ V   P+A     Q+V 
Sbjct: 185 EVDRLFEILRRLKARGVTTLYISHRLEEIFEVGDDVTVLRDGQHVITRPLAGLAIPQIVE 244

Query: 240 LMVGRELGEHIDL-GPRTIGGPALTVKGLTRSDKVRDVSFEVRAGEIYGISGLIGAGRTE 298
           LMVGR L +H    G   + G AL V GL  +    ++SF V  GEI GI+GL+G+GRTE
Sbjct: 245 LMVGRTLSDHGAFRGDSVVSGEALGVSGLKVTRNSPELSFSVAKGEIVGIAGLVGSGRTE 304

Query: 299 LLRLIFGADLADSGTVALGSPAQVVSIRSPVDAVGHGIALITEDRKGEGLLLTQSISANI 358
            +R IFGAD   +G + +      V I SP DAV  G+ L TEDRK +GL+L  S + N 
Sbjct: 305 AVRAIFGADTKAAGEIRIDGKR--VEIDSPKDAVAAGLCLATEDRKMQGLMLDMSCAENT 362

Query: 359 ALGNMPEISGGGVVNSRDETALAKRQIDAMRIRSSSPAQLVSELSGGNQQKVVIGRWLER 418
            + ++ ++S  G+++   E   A+R +  +RI++ S  Q+V   SGGNQQKVVI +WL R
Sbjct: 363 TITDLGKVSRNGLISRNAEDDHAQRLVRELRIKTPSIHQIVRTFSGGNQQKVVIAKWLFR 422

Query: 419 DCSVMLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGR 478
              V++FDEPTRGIDVGAK +IY LL +   +GK ++VVSSDL EL+ IC RI VLS G+
Sbjct: 423 GPKVLIFDEPTRGIDVGAKAEIYDLLWKFAAEGKGVLVVSSDLPELIGICHRIIVLSDGK 482

Query: 479 LIETFERDSWTQDELLAAAFAGYQK 503
           +     RD + +  +L+ A+  Y +
Sbjct: 483 IAGEIARDQFEESRILSLAYKEYSR 507


Lambda     K      H
   0.319    0.136    0.382 

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: 706
Number of extensions: 34
Number of successful extensions: 8
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: 517
Length of database: 511
Length adjustment: 35
Effective length of query: 482
Effective length of database: 476
Effective search space:   229432
Effective search space used:   229432
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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