Alignments for a candidate for HSERO_RS03640 in Duganella sacchari Sac-22

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Duganella sacchari Sac-22

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_072785131.1 BUA36_RS13070 ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>NCBI__GCF_900143065.1:WP_072785131.1
          Length = 509

 Score =  280 bits (715), Expect = 1e-79
 Identities = 180/497 (36%), Positives = 272/497 (54%), Gaps = 28/497 (5%)

Query: 5   PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 64
           P ++ RGI K FGA  A +D+  +I  G IH L+GENGAGKSTLM +L G +  D GEIL
Sbjct: 3   PAVEFRGISKHFGAVKANTDVSFSIAKGSIHGLVGENGAGKSTLMSILYGYYRADGGEIL 62

Query: 65  LDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRT 124
           LDG+   + +   + A GI +++Q   +  N++V  NV +GSE   +L      A R++ 
Sbjct: 63  LDGQARRIHNSQEAIALGIGMVHQHFMLVENMTVLDNVMLGSEGGFKLN-----AKRAKV 117

Query: 125 DAVLRQLGAGF--GASDLA--GRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETE 180
           +A LR++   +      LA    LS+  QQ+VEI + +   + I+I+DEPTA L+ +ETE
Sbjct: 118 EAELREICKRYRLDVDPLATIHDLSVGAQQRVEILKQIYRSANILILDEPTAVLTAQETE 177

Query: 181 QLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 240
            LF ++R  +++G  II I+H++ E+  + D VTV+R G  +G +       E +  MMV
Sbjct: 178 SLFEILRLFKEQGKTIILITHKLQEILDITDTVTVMRGGRVIGAVPTAGTTKEDLANMMV 237

Query: 241 GRSLSEFYQHQRIAP------ADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLV 294
           GR +      +   P       D  QL     V+ LA        F +RAGE++  AG+ 
Sbjct: 238 GRPIENNLPRKPYNPGAPVLEVDQLQLLDDQGVKLLA-----DIGFTLRAGEIVAIAGVS 292

Query: 295 GAGRTELARLLFGAD-PRSGGDILLE------GRPVHIDQPRAAMRAGIAYVPEDRKGQG 347
           G G++EL  +L G   P SG    L       GR      PR     GIA+VPEDR   G
Sbjct: 293 GNGQSELMEILSGMRLPTSGKLNFLNKALPFAGRSDADGLPRTFRELGIAHVPEDRLRDG 352

Query: 348 LFLQMAVAANATMNVASR-HTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGN 406
           +    +V  N       +   R GL+  +++       ++  +V+  + +  +G LSGGN
Sbjct: 353 VIKAFSVMHNTIFGYQDKLKNRWGLLDFKAIAARCAELMKNFDVRPNNHDLRIGLLSGGN 412

Query: 407 QQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIG 466
           QQKV++AR +   PK++++ +PTRGVDI     I+  + +L  +GVA++++S EL EV  
Sbjct: 413 QQKVVIAREVLAQPKLMLVGQPTRGVDIGTIESIHTQLLKLRDEGVAILLVSVELEEVRA 472

Query: 467 ICDRVLVMREGMITGEL 483
           + DR+LVM  G ITGEL
Sbjct: 473 LADRILVMCGGRITGEL 489



 Score =  115 bits (287), Expect = 5e-30
 Identities = 83/254 (32%), Positives = 133/254 (52%), Gaps = 24/254 (9%)

Query: 3   QTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGE 62
           Q  LL  +G++        L+D+  T+R GEI A+ G +G G+S LM++LSG+  P  G+
Sbjct: 261 QLQLLDDQGVK-------LLADIGFTLRAGEIVAIAGVSGNGQSELMEILSGMRLPTSGK 313

Query: 63  ILLDGRPVALRDPGASRAAGINLIYQELAVA------------PNISVAANVFMG--SEL 108
           +    +  AL   G S A G+   ++EL +A               SV  N   G   +L
Sbjct: 314 LNFLNK--ALPFAGRSDADGLPRTFRELGIAHVPEDRLRDGVIKAFSVMHNTIFGYQDKL 371

Query: 109 RTRLGLIDHAAMRSRTDAVLRQLGAGFGASDLA-GRLSIAEQQQVEIARALVHRSRIVIM 167
           + R GL+D  A+ +R   +++         DL  G LS   QQ+V IAR ++ + +++++
Sbjct: 372 KNRWGLLDFKAIAARCAELMKNFDVRPNNHDLRIGLLSGGNQQKVVIAREVLAQPKLMLV 431

Query: 168 DEPTAALSERETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVR 227
            +PT  +     E +   + +LRDEG+AI+ +S  + EV ALADR+ V+  G   GEL  
Sbjct: 432 GQPTRGVDIGTIESIHTQLLKLRDEGVAILLVSVELEEVRALADRILVMCGGRITGELKI 491

Query: 228 DEIDSERIVQMMVG 241
           +E D+ RI  +M G
Sbjct: 492 EEFDTTRIGLLMGG 505



 Score = 89.0 bits (219), Expect = 4e-22
 Identities = 63/235 (26%), Positives = 111/235 (47%), Gaps = 6/235 (2%)

Query: 279 SFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAY 338
           SF +  G + G  G  GAG++ L  +L+G     GG+ILL+G+   I   + A+  GI  
Sbjct: 24  SFSIAKGSIHGLVGENGAGKSTLMSILYGYYRADGGEILLDGQARRIHNSQEAIALGIGM 83

Query: 339 VPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETP 398
           V +      L   M V  N  +  +    +L   R++ +    R   +R  + V  P   
Sbjct: 84  VHQHFM---LVENMTVLDNVMLG-SEGGFKLNAKRAK-VEAELREICKRYRLDV-DPLAT 137

Query: 399 VGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVIS 458
           +  LS G QQ+V + + +  +  +LILDEPT  +       +++++     QG  +++I+
Sbjct: 138 IHDLSVGAQQRVEILKQIYRSANILILDEPTAVLTAQETESLFEILRLFKEQGKTIILIT 197

Query: 459 SELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTAPASHSSP 513
            +L E++ I D V VMR G + G +  A  T+E++  +     +    P    +P
Sbjct: 198 HKLQEILDITDTVTVMRGGRVIGAVPTAGTTKEDLANMMVGRPIENNLPRKPYNP 252


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: 670
Number of extensions: 33
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
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 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 2024 update 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