Alignments for a candidate for HSERO_RS03640 in Oscillibacter ruminantium GH1

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Oscillibacter ruminantium GH1

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_040660822.1 ON16_RS07570 ATP-binding cassette domain-containing protein

Query= uniprot:D8IZC7
         (521 letters)



>NCBI__GCF_000307265.1:WP_040660822.1
          Length = 499

 Score =  372 bits (956), Expect = e-107
 Identities = 197/500 (39%), Positives = 303/500 (60%), Gaps = 8/500 (1%)

Query: 1   MTQTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQ 60
           M Q  LLQM  I K F    AL  + LT++PG +HALMGENGAGKSTLMK L G++  D+
Sbjct: 1   MGQEVLLQMTDISKEFPGVKALDHVSLTVKPGTVHALMGENGAGKSTLMKCLFGIYGKDE 60

Query: 61  GEILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAM 120
           G+I L+G+ V+ +    +  +G+ +++QEL  A   SV  N+++G        +++   M
Sbjct: 61  GKIFLEGKEVSFKSSKEAMESGVAMVHQELNQALKRSVMDNIWLGRYPTIGGVMVNEKKM 120

Query: 121 RSRTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETE 180
            + T A+   LG       +   + ++++Q VEIA+A+ + S++V+ DEPT++L+E+E E
Sbjct: 121 YADTKAIFDDLGIDVDPHRIMSTIPVSQRQMVEIAKAVSYNSKVVVFDEPTSSLTEQEVE 180

Query: 181 QLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 240
            LF ++  LRD G+ IIYISH+MAE+  ++D VT++RDG +V      E+D+  I+++MV
Sbjct: 181 HLFRIINMLRDRGVGIIYISHKMAEILQISDEVTIMRDGCWVATKSAGELDTATIIKLMV 240

Query: 241 GRSLSEFYQHQRIAPADAAQLPTVMQVRALAG--GKIRPASFDVRAGEVLGFAGLVGAGR 298
           GR L   +  +   P +       ++V  L     ++   SF  R GE+LG AGL  +GR
Sbjct: 241 GRELGNQFPIKTNTPGEV-----YLEVEHLTAQYSQLEDVSFSARRGEILGLAGLDASGR 295

Query: 299 TELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANA 358
           TE    +FG   R  G I L GR V     R ++R G A + E+R+  G+F  +++  N 
Sbjct: 296 TETLENIFGIATRKSGTIRLGGREVKNRNSRESIRNGFALLTEERRATGIFGILSIRENT 355

Query: 359 TMNVASRHTRLGLV-RSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLE 417
            ++   +H R G +   +++    + +I  +  K     T +  LSGGNQQKV+L RWL 
Sbjct: 356 VISSLKKHLRAGFILNDKTMRQDTQWSIDAMRTKTPSQHTKIRSLSGGNQQKVILGRWLL 415

Query: 418 IAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREG 477
             P+VL+LDEPTRG+D+ AK EIYQL+  LA++G  V+++SSE+PE++G+CDR+LVM  G
Sbjct: 416 TNPEVLLLDEPTRGIDVGAKFEIYQLIIDLANKGKTVLMVSSEMPELLGVCDRILVMSGG 475

Query: 478 MITGELAGAAITQENIMRLA 497
            + GE+   + TQE IM LA
Sbjct: 476 RLAGEVDAKSTTQEEIMTLA 495



 Score = 86.3 bits (212), Expect = 2e-21
 Identities = 58/238 (24%), Positives = 110/238 (46%), Gaps = 11/238 (4%)

Query: 279 SFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAY 338
           S  V+ G V    G  GAG++ L + LFG   +  G I LEG+ V     + AM +G+A 
Sbjct: 26  SLTVKPGTVHALMGENGAGKSTLMKCLFGIYGKDEGKIFLEGKEVSFKSSKEAMESGVAM 85

Query: 339 VPEDRKGQGLFLQMAVAANATMNV-ASRHTRLG--LVRSRSLGGVARAAIQRLNVKVAHP 395
           V ++       L  A+  +   N+   R+  +G  +V  + +    +A    L + V  P
Sbjct: 86  VHQE-------LNQALKRSVMDNIWLGRYPTIGGVMVNEKKMYADTKAIFDDLGIDV-DP 137

Query: 396 ETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVV 455
              +  +    +Q V +A+ +    KV++ DEPT  +       ++++++ L  +GV ++
Sbjct: 138 HRIMSTIPVSQRQMVEIAKAVSYNSKVVVFDEPTSSLTEQEVEHLFRIINMLRDRGVGII 197

Query: 456 VISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTAPASHSSP 513
            IS ++ E++ I D V +MR+G      +   +    I++L     +    P   ++P
Sbjct: 198 YISHKMAEILQISDEVTIMRDGCWVATKSAGELDTATIIKLMVGRELGNQFPIKTNTP 255


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: 588
Number of extensions: 28
Number of successful extensions: 7
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: 499
Length adjustment: 34
Effective length of query: 487
Effective length of database: 465
Effective search space:   226455
Effective search space used:   226455
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