GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16930 in Rhodobacter johrii JA192

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein

Query= uniprot:B2SYR5
         (512 letters)



>NCBI__GCF_003046325.1:WP_069332735.1
          Length = 499

 Score =  362 bits (928), Expect = e-104
 Identities = 202/491 (41%), Positives = 301/491 (61%), Gaps = 7/491 (1%)

Query: 5   LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64
           L    + ++F  V+ L  V FD+  G+VH L+GENGAGKST +KIL G   P +G V++D
Sbjct: 6   LAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVLLD 65

Query: 65  GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRER 124
           G  V F S+  + AAG+ +IHQE      LTV EN+ LG+      +++ R  +   R  
Sbjct: 66  GRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKRGPFLDHRAMQAESRRL 125

Query: 125 LEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVR 184
           LE +  A+DP A++  LS+  RQMVEI KAL   ARV+ +DEPT+ L+HRET+ L + V 
Sbjct: 126 LERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLLEQVD 185

Query: 185 DLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREISD 244
            LRA   A++Y SH++DE+  + D  T+ RDGR++ + P  +G++ D +   MVGRE+S 
Sbjct: 186 RLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPA-KGLSEDRMAETMVGRELSG 244

Query: 245 IYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADH 304
           ++   + P  E      G+      + ASF +RRGE++GF GLVG+GR+ELM  + G   
Sbjct: 245 LFPPKSSPAPEPVLEVAGLTVPGFVRDASFTLRRGEVLGFAGLVGSGRTELMEGIVGL-R 303

Query: 305 KKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVG 364
              GE+ ++G P+   S   A   G+V   EDRKE+G++    + EN+ +     + RV 
Sbjct: 304 PATGEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLTLLALDRFGRV- 362

Query: 365 MFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSR-WLAEPDLKVVILDE 423
             +D+  E     + I    I+   R      LSGGNQQK +L++  LAEP  +VVI+DE
Sbjct: 363 -LIDKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLAKTMLAEP--RVVIIDE 419

Query: 424 PTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKD 483
           PTRGIDVG K +IY  I +LA  G +++++SSELPEV+G+++R+VVM  GRI+GE+  + 
Sbjct: 420 PTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGRIAGEVEGEA 479

Query: 484 ATEQSVLSLAL 494
            TE++++ LA+
Sbjct: 480 ITEENIVRLAM 490


Lambda     K      H
   0.320    0.136    0.385 

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: 665
Number of extensions: 34
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: 512
Length of database: 499
Length adjustment: 34
Effective length of query: 478
Effective length of database: 465
Effective search space:   222270
Effective search space used:   222270
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 24 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