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 m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate WP_040659172.1 ON16_RS02720 ATP-binding cassette domain-containing protein

Query= reanno::pseudo3_N2E3:AO353_21385
         (521 letters)



>NCBI__GCF_000307265.1:WP_040659172.1
          Length = 516

 Score =  349 bits (896), Expect = e-100
 Identities = 201/498 (40%), Positives = 306/498 (61%), Gaps = 14/498 (2%)

Query: 27  LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDA--GEL 84
           LLE+ ++ K FPGV AL +V L V  G + AL+GENGAGKSTLM +++GIY      G++
Sbjct: 5   LLEMRSIIKEFPGVRALDNVNLEVEQGEIHALVGENGAGKSTLMNVLSGIYPYGTYQGDI 64

Query: 85  RLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRC 144
              G+   F     +   G+ +IHQEL L+P+++I EN+++G EQ      ID  + +  
Sbjct: 65  VYDGEVCKFGKINDSESKGVVIIHQELALVPYLTIGENMFLGNEQGRASR-IDWDKTYDL 123

Query: 145 TAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLF 204
            A+ L+ + +   P   + ++ + ++Q+VEIAKA++ +  +LI+DEPT+++ + +   L 
Sbjct: 124 AAKYLKTVGLEESPRTLIKDIGVGKQQLVEIAKALTKNVRLLILDEPTASLNETDSQKLL 183

Query: 205 SIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIG--LQRADSMDGDSLISMMVG 262
            ++   KAQG   I I+HK++EV  +AD++ + RDGA I   ++  D    + +I  MVG
Sbjct: 184 DLLLQFKAQGMTCIIISHKLSEVSYVADKITIIRDGATIETLVKGVDDFHEERIIKGMVG 243

Query: 263 RELSQLFPVREKPIGDLLMSVRDLRLDG-------VFKGVSFDLHAGEILGIAGLMGSGR 315
           REL   FP RE  IGD++M V+D   +        V   VS ++  GEI+G++GLMG+GR
Sbjct: 244 RELVDRFPKRESHIGDVVMEVQDWCAEHPTYAGRMVCNHVSMNVRRGEIVGVSGLMGAGR 303

Query: 316 TNVAEAIFGITPSDG--GEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLE 373
           T +A +IFG +      G + L+GQ VR+     AI    A +TEDRK +GL    ++ E
Sbjct: 304 TELAMSIFGRSYGANIKGSLLLNGQEVRLHSVTDAINHKLAYVTEDRKGNGLILSETIRE 363

Query: 374 NMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWL 433
           N  MA +   + +  + +        +  + LR K   +EQ +  LSGGNQQK LL++W+
Sbjct: 364 NTTMARMERISRHQVLDKDLEIKYANEYKEILRTKCAGIEQNVGNLSGGNQQKVLLSKWM 423

Query: 434 MTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHE 493
              P +LILDEPTRGIDVGAK EIY +++ L S+G AV+MISSE+PE+LGM DR+ VM+E
Sbjct: 424 FAEPDVLILDEPTRGIDVGAKYEIYCIMNDLVSQGKAVLMISSEMPELLGMCDRIYVMNE 483

Query: 494 GDLMGTLDRSEATQERVM 511
           G ++G L   +A+QE +M
Sbjct: 484 GSVVGELTHEQASQESIM 501



 Score = 80.9 bits (198), Expect = 1e-19
 Identities = 61/232 (26%), Positives = 116/232 (50%), Gaps = 7/232 (3%)

Query: 37  FPGVVALSDVQLRVRPGSVLALMGENGAGKSTL-MKIIAGIYQPDA-GELRLRGKPVTFD 94
           + G +  + V + VR G ++ + G  GAG++ L M I    Y  +  G L L G+ V   
Sbjct: 274 YAGRMVCNHVSMNVRRGEIVGVSGLMGAGRTELAMSIFGRSYGANIKGSLLLNGQEVRLH 333

Query: 95  TPLAALQAGIAMIHQELN---LMPHMSIAENIWIGREQLNGFHMIDHREMH-RCTAQLLE 150
           +   A+   +A + ++     L+   +I EN  + R +    H +  +++  +   +  E
Sbjct: 334 SVTDAINHKLAYVTEDRKGNGLILSETIRENTTMARMERISRHQVLDKDLEIKYANEYKE 393

Query: 151 RLRINLDPEEQ-VGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSIIAD 209
            LR      EQ VGNLS   +Q V ++K +  + D+LI+DEPT  I       ++ I+ D
Sbjct: 394 ILRTKCAGIEQNVGNLSGGNQQKVLLSKWMFAEPDVLILDEPTRGIDVGAKYEIYCIMND 453

Query: 210 LKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMV 261
           L +QGK ++ I+ +M E+  + D + V  +G+ +G    +    +S+++ ++
Sbjct: 454 LVSQGKAVLMISSEMPELLGMCDRIYVMNEGSVVGELTHEQASQESIMACIL 505


Lambda     K      H
   0.321    0.137    0.391 

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: 616
Number of extensions: 33
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 521
Length of database: 516
Length adjustment: 35
Effective length of query: 486
Effective length of database: 481
Effective search space:   233766
Effective search space used:   233766
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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Protein sequences (fasta format)
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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