GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS03640 in Azospirillum brasilense Sp245

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate AZOBR_RS31245 AZOBR_RS31245 ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__azobra:AZOBR_RS31245
          Length = 518

 Score =  352 bits (902), Expect = e-101
 Identities = 211/505 (41%), Positives = 306/505 (60%), Gaps = 22/505 (4%)

Query: 5   PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQ--GE 62
           P+L+M+GI K+F    AL D++L++R GEIHAL+GENGAGKSTLMKVLSGV+      GE
Sbjct: 4   PILEMKGITKTFPGVKALDDVNLSVREGEIHALIGENGAGKSTLMKVLSGVYPQGSFDGE 63

Query: 63  ILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRS 122
           I   G+P A R    S   GI +I+QELA+ P +S+  N+F+G+E  +R G+ID  A   
Sbjct: 64  IRFRGQPQAFRGIADSERLGIIIIHQELALVPLLSITENLFLGNEQASR-GVIDWDAATL 122

Query: 123 RTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQL 182
           R   +LR +G       L   + + +QQ VEIA+AL    +++I+DEPTA+L+E +++ L
Sbjct: 123 RARELLRLVGLHDPPETLITDIGVGKQQLVEIAKALSKEVKLLILDEPTASLNESDSDAL 182

Query: 183 FNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDE--IDSERIVQMMV 240
             ++ + +  G+A I ISH++ E+  +ADRVT+LRDG+ V  L   E  +  +RI++ MV
Sbjct: 183 LELLLQFKARGIASILISHKLNEIAKVADRVTILRDGTTVETLDCREAVVSQDRIIRGMV 242

Query: 241 GRSLSEFYQHQRIAPADAAQLPTVMQVRALAGGK--------IRPASFDVRAGEVLGFAG 292
           GR+LS+ Y  +   P D      + +V+  +           +R  +  VR GEV+G AG
Sbjct: 243 GRALSDRYPRRTTVPGDV-----LFEVKGWSADHPAHPGRRVVRDVNLTVRRGEVVGIAG 297

Query: 293 LVGAGRTELARLLFGADPRSG--GDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFL 350
           L+GAGRTE A  LFG        G   L+GR + +     AM  G+AY  EDRK  GL L
Sbjct: 298 LMGAGRTEFAMSLFGRSYGRNIRGQAFLDGREIDVSTISRAMANGLAYATEDRKHLGLVL 357

Query: 351 QMAVAANATM-NVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQK 409
              +  N T+ N+     R  +   R +  VA    +RL ++ A        LSGGNQQK
Sbjct: 358 DNDIRHNVTLANLRGVAKRWVIDHEREVQ-VAEEFRRRLRIRCADVFQETVNLSGGNQQK 416

Query: 410 VLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICD 469
           V+L++WL   P+VLILDEPTRG+D+ AK EIY ++++L ++G  VV+ISSE+PE++G+ D
Sbjct: 417 VVLSKWLFADPQVLILDEPTRGIDVGAKYEIYTIINQLVAEGRGVVLISSEMPELLGVAD 476

Query: 470 RVLVMREGMITGELAGAAITQENIM 494
           R+ VM  G +  E+  A  +QE IM
Sbjct: 477 RIYVMNAGEMVAEMPAAEASQEKIM 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: 688
Number of extensions: 48
Number of successful extensions: 11
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: 518
Length adjustment: 35
Effective length of query: 486
Effective length of database: 483
Effective search space:   234738
Effective search space used:   234738
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.

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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