GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_12065 in Pseudomonas fluorescens FW300-N2E3

Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate AO353_21385 AO353_21385 D-ribose transporter ATP-binding protein

Query= uniprot:A0A1N7TX47
         (495 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_21385
          Length = 521

 Score =  402 bits (1032), Expect = e-116
 Identities = 220/492 (44%), Positives = 313/492 (63%), Gaps = 1/492 (0%)

Query: 4   PLLLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSI 63
           P LL+  +V+K + GV AL D +L +R GSV AL G NGAGKST + I+ GI Q DAG +
Sbjct: 25  PYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGEL 84

Query: 64  LLNGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRR 123
            L G PV F+ P  AL AGIAMI QEL  +P+M++AENIW+GRE      ++D++ ++R 
Sbjct: 85  RLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRC 144

Query: 124 TRELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLF 183
           T +LL+ L  ++D    +  LS+A+ Q+VEIAKA S+D  ++IMDEPTSAI + E   LF
Sbjct: 145 TAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLF 204

Query: 184 KAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQE 243
             I  L AQG GI+Y++H+++E+  IAD+ ++FRDGA++   R   +D D L+  +VG+E
Sbjct: 205 SIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRE 264

Query: 244 LTRIDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIY 303
           L+++   V  +   +  + V +L   G F  +S  L  GEILGI GLMGSGR+     I+
Sbjct: 265 LSQL-FPVREKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIF 323

Query: 304 GLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRL 363
           G+T +D G + L G+P+ I  P   I  G +L+TEDRK SGL    S+L N+ ++     
Sbjct: 324 GITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHY 383

Query: 364 SSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCD 423
           +    I  +    L EDM K+L++KT SLE  + ++SGGNQQK +LA+ L T P  L+ D
Sbjct: 384 AGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILD 443

Query: 424 EPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDT 483
           EPTRGID GAK EIY L+      G A I++SSE PE+L +SDR+ V   G L+     +
Sbjct: 444 EPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRS 503

Query: 484 ALSQEALLRLAS 495
             +QE +++LAS
Sbjct: 504 EATQERVMQLAS 515


Lambda     K      H
   0.319    0.135    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: 594
Number of extensions: 26
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 495
Length of database: 521
Length adjustment: 34
Effective length of query: 461
Effective length of database: 487
Effective search space:   224507
Effective search space used:   224507
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 17 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:

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:

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:

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:

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