Alignments for a candidate for HSERO_RS03640 in Paucidesulfovibrio gracilis DSM 16080

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Paucidesulfovibrio gracilis DSM 16080

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>NCBI__GCF_900167125.1:WP_078716498.1
          Length = 514

 Score =  253 bits (647), Expect = 9e-72
 Identities = 151/475 (31%), Positives = 255/475 (53%), Gaps = 12/475 (2%)

Query: 5   PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 64
           PL+ ++G+ K FG  +A  D+ L I PG + AL+GENGAGKSTLM +L+G + PD G I 
Sbjct: 23  PLVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIA 82

Query: 65  LDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRT 124
           LDG+PV       +  AGI ++YQ   +  +++VA NV +G E       ++   MR+R 
Sbjct: 83  LDGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQE---GSFFLNPKEMRNRV 139

Query: 125 DAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFN 184
             +  + G     +     LS+ E+Q+VEI + L   SR++I DEPTA L+ RET  LF 
Sbjct: 140 QELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFE 199

Query: 185 VVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSER-IVQMMVGRS 243
            + ++ ++G +I++ISH++ EV A+AD + +LR G   GE    E+ S+  +   MVG+ 
Sbjct: 200 ALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRMVGKE 259

Query: 244 LSEFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELAR 303
           +      + +   DA     V+QVR L G  +   +FD+  GEV+   G+ G G+  L  
Sbjct: 260 VLLEVDREAMPHGDA-----VLQVRNLTGIGLEDITFDLHQGEVVAVVGVAGNGQKALVE 314

Query: 304 LLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVA 363
            + G        + + G+       + + +  +AY+PEDR G      + +  N  +   
Sbjct: 315 AICGLRKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVDNLLLTTR 374

Query: 364 SRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVL 423
               R   +  +         I++ +++         +LSGGN QK +LAR L   P+++
Sbjct: 375 QGFARGPWLDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRLI 434

Query: 424 ILDEPTRGVDIYAKSEIYQLVHRLASQGVA-VVVISSELPEVIGICDRVLVMREG 477
           + ++PT+G+DI A  +++   H LA++ +A +++++ +L E + + DRV V+  G
Sbjct: 435 VAEQPTQGLDIAATEQVWN--HLLAAREMAGILLVTGDLNEALQLADRVAVIYRG 487



 Score = 87.4 bits (215), Expect = 1e-21
 Identities = 69/259 (26%), Positives = 117/259 (45%), Gaps = 16/259 (6%)

Query: 238 MMVGRSLSEFYQHQRIAPADAAQLPTVMQVRALAGGKIR--PASFDVRAGEVLGFAGLVG 295
           M V   L +  + +R  P     L ++  +    G  +     S ++  G V    G  G
Sbjct: 1   MDVSNLLKQLDRSKRDVPPQGIPLVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENG 60

Query: 296 AGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVA 355
           AG++ L  +L G      G I L+G+PV     R A+ AGI  V +      L   M VA
Sbjct: 61  AGKSTLMSMLAGRYQPDAGTIALDGKPVRFSSARDAIEAGIGMVYQHFM---LVESMTVA 117

Query: 356 ANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVA---HPETPVGKLSGGNQQKVLL 412
            N  +           +  + +    R  +Q L+V+      P   V  LS G +Q+V +
Sbjct: 118 ENVLLGQEGSF----FLNPKEM----RNRVQELSVRYGLDIDPAARVSDLSMGEKQRVEI 169

Query: 413 ARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVL 472
            + L    +VLI DEPT  +       +++ + ++A QG ++V IS +L EV+ + D + 
Sbjct: 170 LKLLYRDSRVLIFDEPTAVLTPRETFHLFEALWKIAEQGKSIVFISHKLEEVLAVADEIA 229

Query: 473 VMREGMITGELAGAAITQE 491
           ++R+G I GE + + +T +
Sbjct: 230 ILRQGRIEGEFSESEVTSK 248



 Score = 62.0 bits (149), Expect = 5e-14
 Identities = 63/234 (26%), Positives = 107/234 (45%), Gaps = 19/234 (8%)

Query: 20  LALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASR 79
           + L D+   +  GE+ A++G  G G+  L++ + G+  P    + + G+    RD  A  
Sbjct: 284 IGLEDITFDLHQGEVVAVVGVAGNGQKALVEAICGLRKPPVDTMFIMGK--RWRDFYAKP 341

Query: 80  AAGINLIYQE-----LAVAPNISVAANVFMGSELRTRLGL-----IDHAAMRSRTDAVLR 129
           +   +L Y       LA   N+++  N+     L TR G      +D       T  +++
Sbjct: 342 SWKNSLAYIPEDRLGLATCRNLNLVDNLL----LTTRQGFARGPWLDKKKAARDTTELIK 397

Query: 130 QLGAGFGA-SDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRR 188
           +     G  + LA +LS    Q+  +AR L    R+++ ++PT  L    TEQ++N +  
Sbjct: 398 KFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRLIVAEQPTQGLDIAATEQVWNHLLA 457

Query: 189 LRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGEL-VRDEIDSERIVQMMVG 241
            R E   I+ ++  + E   LADRV V+  G F+    V D+    RI  MM G
Sbjct: 458 AR-EMAGILLVTGDLNEALQLADRVAVIYRGRFMDVFSVSDKQKVNRIGLMMAG 510


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: 550
Number of extensions: 20
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: 514
Length adjustment: 35
Effective length of query: 486
Effective length of database: 479
Effective search space:   232794
Effective search space used:   232794
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:

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