GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS03640 in Bradyrhizobium sp. BTAi1

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_012042345.1 BBTA_RS09915 sugar ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>NCBI__GCF_000015165.1:WP_012042345.1
          Length = 516

 Score =  374 bits (961), Expect = e-108
 Identities = 208/491 (42%), Positives = 304/491 (61%), Gaps = 5/491 (1%)

Query: 6   LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65
           LL++RG+ KSFGA  AL D+  T+  GEIHAL+GENGAGKSTL+KV++GV A D G + L
Sbjct: 14  LLEIRGLTKSFGALKALQDVDFTLGEGEIHALLGENGAGKSTLIKVVTGVFARDAGTVRL 73

Query: 66  DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 125
            G  +A R    +  AGI  +YQE+ + PN+SVA N+++G +  TR G++  A MR R  
Sbjct: 74  AGDEIAPRSAKDAVEAGIATVYQEVNLLPNLSVAQNLYLGRQ-PTRFGVVRQAEMRRRAH 132

Query: 126 AVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 185
           A+L   G            S+A Q    IARA+   +R++I+DEPTA+L   E E LF V
Sbjct: 133 ALLLDYGLDIDVGAPLASYSVAVQHITAIARAVDLSARVLILDEPTASLDRHEVEILFRV 192

Query: 186 VRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERI--VQMMVGRS 243
           +R+L  +G+ I+++SH + +VY + DRVTVLR+G  +G   RD  D  R+  ++MM+GR 
Sbjct: 193 MRKLAADGIGIVFVSHFLDQVYEICDRVTVLRNGRLIG--TRDITDLPRLDLIRMMLGRE 250

Query: 244 LSEFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELAR 303
           L+E    +  +  D A+   V        G + P   ++R GEV+G AGL+G+GRTE AR
Sbjct: 251 LAETTHERAASQPDTAREVCVSFKGFGKQGYVAPFDLELRRGEVVGLAGLLGSGRTETAR 310

Query: 304 LLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVA 363
           L+FGA+    G+  + G+ V ++ PR A   G  Y PE+RK +G+   + V  N  + + 
Sbjct: 311 LVFGAERADSGEASVAGKAVRLNSPRDAAGLGFGYCPEERKTEGIVADLTVRENIVLALQ 370

Query: 364 SRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVL 423
           +R      +  R    +A   I+ L+++   PE P+G LSGGNQQK LLARWL  +PK+L
Sbjct: 371 ARRGLHRPLSRREQDEIAMRYIRMLDIRPPDPERPIGLLSGGNQQKALLARWLATSPKLL 430

Query: 424 ILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGEL 483
           +LDEPTRG+D+ A +EI +LV  L  QG+A++VISSEL E++   +RV+V+R+     EL
Sbjct: 431 VLDEPTRGIDVGAHAEIIRLVRDLCEQGLALLVISSELDEIVTYSNRVVVLRDRAHVEEL 490

Query: 484 AGAAITQENIM 494
            G A+   +I+
Sbjct: 491 KGDAVEVSSIL 501


Lambda     K      H
   0.320    0.135    0.378 

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: 723
Number of extensions: 38
Number of successful extensions: 7
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: 521
Length of database: 516
Length adjustment: 35
Effective length of query: 486
Effective length of database: 481
Effective search space:   233766
Effective search space used:   233766
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 Apr 09 2024. 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