Alignments for a candidate for PS417_11890 in Oscillibacter ruminantium GH1

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Oscillibacter ruminantium GH1

Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_040660822.1 ON16_RS07570 ATP-binding cassette domain-containing protein

Query= reanno::WCS417:GFF2332
         (517 letters)



>NCBI__GCF_000307265.1:WP_040660822.1
          Length = 499

 Score =  453 bits (1166), Expect = e-132
 Identities = 240/491 (48%), Positives = 330/491 (67%), Gaps = 2/491 (0%)

Query: 23  LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82
           LL++ +ISK FPGV AL  V L V+PGTV ALMGENGAGKSTLMK + GIY  D G+I L
Sbjct: 6   LLQMTDISKEFPGVKALDHVSLTVKPGTVHALMGENGAGKSTLMKCLFGIYGKDEGKIFL 65

Query: 83  RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142
            GK + F++   A ++G+AM+HQELN     S+ +NIW+GR       MVN ++M+  T 
Sbjct: 66  EGKEVSFKSSKEAMESGVAMVHQELNQALKRSVMDNIWLGRYPTIGGVMVNEKKMYADTK 125

Query: 143 ELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSI 202
            +   L I++DP   +  + +++RQMVEIAKAVSY+S +++ DEPTS++TE+EV HLF I
Sbjct: 126 AIFDDLGIDVDPHRIMSTIPVSQRQMVEIAKAVSYNSKVVVFDEPTSSLTEQEVEHLFRI 185

Query: 203 IADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELS 262
           I  L+ +G GI+YI+HKM E+  I+DEV + RDG ++  + A  +++ ++I +MVGREL 
Sbjct: 186 INMLRDRGVGIIYISHKMAEILQISDEVTIMRDGCWVATKSAGELDTATIIKLMVGRELG 245

Query: 263 QLFPLRETPIGDLLLTVRDLTLD-GVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGI 321
             FP++    G++ L V  LT      +DVSF    GEILG+AGL  SGRT   E IFGI
Sbjct: 246 NQFPIKTNTPGEVYLEVEHLTAQYSQLEDVSFSARRGEILGLAGLDASGRTETLENIFGI 305

Query: 322 TPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTG 381
               SG I L G+ V+  +   +I  GFALLTE+R+ +G+F  LS+ EN  ++ L  +  
Sbjct: 306 ATRKSGTIRLGGREVKNRNSRESIRNGFALLTEERRATGIFGILSIRENTVISSLKKHLR 365

Query: 382 NGFI-QQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDE 440
            GFI   K +R   +     +R KTPS    I +LSGGNQQK +L RWL+TNP +L+LDE
Sbjct: 366 AGFILNDKTMRQDTQWSIDAMRTKTPSQHTKIRSLSGGNQQKVILGRWLLTNPEVLLLDE 425

Query: 441 PTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSE 500
           PTRGIDVGAK EIY+LI  LA++G  V+M+SSE+PE+LG+ DR++VM  G L G +D   
Sbjct: 426 PTRGIDVGAKFEIYQLIIDLANKGKTVLMVSSEMPELLGVCDRILVMSGGRLAGEVDAKS 485

Query: 501 ATQEKVMQLAS 511
            TQE++M LA+
Sbjct: 486 TTQEEIMTLAA 496



 Score = 79.3 bits (194), Expect = 3e-19
 Identities = 58/243 (23%), Positives = 118/243 (48%), Gaps = 9/243 (3%)

Query: 274 DLLLTVRDLTLD--GV--FKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQI 329
           ++LL + D++ +  GV     VS  +  G +  + G  G+G++ + + +FGI     G+I
Sbjct: 4   EVLLQMTDISKEFPGVKALDHVSLTVKPGTVHALMGENGAGKSTLMKCLFGIYGKDEGKI 63

Query: 330 TLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKA 389
            L+GK V       A+E G A++ ++   +      SV++N+ +   P   G   + +K 
Sbjct: 64  FLEGKEVSFKSSKEAMESGVAMVHQELNQALK---RSVMDNIWLGRYPTI-GGVMVNEKK 119

Query: 390 LRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGA 449
           + A  + +   L +      + + T+    +Q   +A+ +  N ++++ DEPT  +    
Sbjct: 120 MYADTKAIFDDLGIDVDP-HRIMSTIPVSQRQMVEIAKAVSYNSKVVVFDEPTSSLTEQE 178

Query: 450 KAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQL 509
              ++R+I  L   G+ +I IS ++ E+L +SD V +M +G  + T    E     +++L
Sbjct: 179 VEHLFRIINMLRDRGVGIIYISHKMAEILQISDEVTIMRDGCWVATKSAGELDTATIIKL 238

Query: 510 ASG 512
             G
Sbjct: 239 MVG 241


Lambda     K      H
   0.320    0.136    0.381 

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: 540
Number of extensions: 29
Number of successful extensions: 6
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: 517
Length of database: 499
Length adjustment: 34
Effective length of query: 483
Effective length of database: 465
Effective search space:   224595
Effective search space used:   224595
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