Alignments for a candidate for HSERO_RS03640 in Beijerinckia indica ATCC 9039

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Beijerinckia indica ATCC 9039

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_012385982.1 BIND_RS15565 sugar ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>NCBI__GCF_000019845.1:WP_012385982.1
          Length = 511

 Score =  354 bits (909), Expect = e-102
 Identities = 211/499 (42%), Positives = 303/499 (60%), Gaps = 10/499 (2%)

Query: 6   LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGV--HAPDQGEI 63
           +L+MRGI KSF    AL+D++LT++ GEIHAL+GENGAGKSTLMKVLSGV  H   +G I
Sbjct: 4   ILEMRGISKSFTGVKALNDVNLTVKAGEIHALVGENGAGKSTLMKVLSGVYPHGSYEGAI 63

Query: 64  LLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSR 123
             DG      D   + A GI +I+QELA+ P +S+A N+F+ +   +R G+ID   + +R
Sbjct: 64  FYDGEERHFHDINDTEALGIIIIHQELALIPLMSIAENIFIANP-PSRFGVIDRDTVYTR 122

Query: 124 TDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLF 183
              +L ++G       L   + + +QQ VEIA+AL  + R++I+DEPTA+L+E ++E L 
Sbjct: 123 AKELLAKVGLNEAPDTLITNIGVGKQQLVEIAKALSKKVRLLILDEPTASLNENDSEALL 182

Query: 184 NVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELV--RDEIDSERIVQMMVG 241
           +++   R +G+  I ISH++ EV  +AD++TVLRDG  V  +    + I+ +RI++ MV 
Sbjct: 183 DLLIEFRAQGITSILISHKLNEVSRVADQITVLRDGRTVDTMDCHAEAIEEDRIIRKMVD 242

Query: 242 RSLSEFYQHQRI---APADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGR 298
           R L   Y  +     A   + +  +V   +      I+  +F V+ GE++G AGL+GAGR
Sbjct: 243 RDLEHRYPKREPKIGAAIFSIENWSVYHPQHPDRQLIKNVNFHVKRGEIVGIAGLMGAGR 302

Query: 299 TELARLLFGAD--PRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAA 356
           TE A  +FG     +  G  +L GR V +     A+ AG+AYV EDRK  GL L   +  
Sbjct: 303 TEFAMSVFGRSWGQKITGRAVLNGREVDLSTVSRAINAGLAYVTEDRKELGLLLSDDIRK 362

Query: 357 NATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWL 416
           N T+          ++       VA     R+ ++ +     VGKLSGGNQQKV+L++WL
Sbjct: 363 NVTLANLEGVANQRVIDDMKEFKVASDYRSRMRIRSSGVYQEVGKLSGGNQQKVVLSKWL 422

Query: 417 EIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMRE 476
              P++LILDEPTRG+DI AK EIY +++ LA+ G  VVVISSE+PE++GI DR+ VM E
Sbjct: 423 FAGPEILILDEPTRGIDIGAKYEIYCIINDLANAGKGVVVISSEMPELLGISDRIYVMNE 482

Query: 477 GMITGELAGAAITQENIMR 495
           G   GE   A  TQE IMR
Sbjct: 483 GAFVGEFPTAEATQEKIMR 501



 Score = 73.9 bits (180), Expect = 1e-17
 Identities = 57/228 (25%), Positives = 109/228 (47%), Gaps = 11/228 (4%)

Query: 22  LSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQ--GEILLDGRPVALRDPGASR 79
           + +++  ++ GEI  + G  GAG++     + G     +  G  +L+GR V L     SR
Sbjct: 279 IKNVNFHVKRGEIVGIAGLMGAGRTEFAMSVFGRSWGQKITGRAVLNGREVDLST--VSR 336

Query: 80  AAGINLIY-----QELAVAPNISVAANVFMGS--ELRTRLGLIDHAAMRSRTDAVLRQLG 132
           A    L Y     +EL +  +  +  NV + +   +  +  + D    +  +D   R   
Sbjct: 337 AINAGLAYVTEDRKELGLLLSDDIRKNVTLANLEGVANQRVIDDMKEFKVASDYRSRMRI 396

Query: 133 AGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDE 192
              G     G+LS   QQ+V +++ L     I+I+DEPT  +      +++ ++  L + 
Sbjct: 397 RSSGVYQEVGKLSGGNQQKVVLSKWLFAGPEILILDEPTRGIDIGAKYEIYCIINDLANA 456

Query: 193 GLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 240
           G  ++ IS  M E+  ++DR+ V+ +G+FVGE    E   E+I++ ++
Sbjct: 457 GKGVVVISSEMPELLGISDRIYVMNEGAFVGEFPTAEATQEKIMRSIM 504


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: 655
Number of extensions: 32
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 521
Length of database: 511
Length adjustment: 35
Effective length of query: 486
Effective length of database: 476
Effective search space:   231336
Effective search space used:   231336
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.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources