GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS03640 in Burkholderia phytofirmans PsJN

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate BPHYT_RS28215 BPHYT_RS28215 D-ribose transporter ATP binding protein

Query= uniprot:D8IZC7
         (521 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS28215 BPHYT_RS28215 D-ribose
           transporter ATP binding protein
          Length = 509

 Score =  455 bits (1170), Expect = e-132
 Identities = 243/509 (47%), Positives = 338/509 (66%), Gaps = 9/509 (1%)

Query: 5   PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 64
           P L++R   KSFG   ALSD  L + PGE+HAL+GENGAGKST++K+L+GVH PD GE++
Sbjct: 9   PRLELRHASKSFGRVRALSDGDLALWPGEVHALLGENGAGKSTVVKILAGVHQPDTGELV 68

Query: 65  LDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRT 124
           +DG       P  +R AG+ +IYQE  +  ++S+A N+FMG +   R+G I + AMR   
Sbjct: 69  VDGEARRFATPAEARDAGLAVIYQEPTLFFDLSIAENIFMGRQPVDRIGRIQYDAMRREV 128

Query: 125 DAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFN 184
           D +L  LG    A  L   LSIA+QQ +EIA+AL   + ++IMDEPTAALS  E E+LF 
Sbjct: 129 DGLLASLGVDLRADQLVRGLSIADQQVIEIAKALSLNANVLIMDEPTAALSLPEVERLFT 188

Query: 185 VVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSL 244
           +VR+LR+  +AI++I+HR+ EV+AL  RVT++RDG+ V + +  ++++E IV  MVGR L
Sbjct: 189 IVRKLRERDVAILFITHRLDEVFALTQRVTIMRDGAKVFDGLTTDLNTEAIVAKMVGRDL 248

Query: 245 SEFYQHQRIAPADAAQLPTVMQVRALAG-GKIRPASFDVRAGEVLGFAGLVGAGRTELAR 303
             FY      P +       + VR L   G  +  SFDVRAGE++  AGLVGAGR+E+AR
Sbjct: 249 ETFYPKAERPPGEVR-----LSVRGLTRVGVFKDISFDVRAGEIVALAGLVGAGRSEVAR 303

Query: 304 LLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVA 363
            +FG DP   G+I + G+ +   +P AA+RAG+A VPEDR+ QGL L++++A NA+M V 
Sbjct: 304 AIFGIDPLDSGEIWIAGKRLTAGRPAAAVRAGLALVPEDRRQQGLALELSIARNASMTVL 363

Query: 364 SRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVL 423
            R  + GL+ +RS   +A     RL +K   P  PVG LSGGNQQKV+L +WL   PKVL
Sbjct: 364 GRLVKHGLISARSETQLANQWGTRLRLKAGDPNAPVGTLSGGNQQKVVLGKWLATGPKVL 423

Query: 424 ILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGEL 483
           I+DEPTRG+D+ AK+E+Y  +  L   G+AV++ISSELPEV+G+ DRVLVM EG I+ ++
Sbjct: 424 IIDEPTRGIDVGAKAEVYSALAELVRDGMAVLMISSELPEVLGMADRVLVMHEGRISADI 483

Query: 484 AGAAITQENIMRLATDTNVPRTAPASHSS 512
           A A   +E IM  A    +P   P  H++
Sbjct: 484 ARADADEERIMGAALGQPMP---PLGHAA 509


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: 793
Number of extensions: 44
Number of successful extensions: 6
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: 509
Length adjustment: 35
Effective length of query: 486
Effective length of database: 474
Effective search space:   230364
Effective search space used:   230364
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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