GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PS417_12065 in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_4286 Inositol transport system ATP-binding protein

Query= uniprot:A0A1N7TX47
         (495 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4286 Inositol transport
           system ATP-binding protein
          Length = 526

 Score =  396 bits (1018), Expect = e-115
 Identities = 220/492 (44%), Positives = 310/492 (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: 30  PYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGEL 89

Query: 64  LLNGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRR 123
            L G PV F  P  AL AGIAMI QEL  +P+M++AENIW+GRE      ++D++ ++R 
Sbjct: 90  RLRGKPVVFETPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMIDHREMHRC 149

Query: 124 TRELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLF 183
           T +LL+ L  ++D    +  LS+A+ Q+VEIAKA S+D  ++IMDEPTSAI + E   LF
Sbjct: 150 TAKLLERLRINLDPEELVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLF 209

Query: 184 KAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQE 243
             I  L  QG GI+Y++H+++E+  IAD+ ++FRDGA++   R   +D D L+  +VG+E
Sbjct: 210 SIIADLKRQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRE 269

Query: 244 LTRIDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIY 303
           L+++   V  +   +  L V +L   G F D+S  L  GEILGI GLMGSGR+     I+
Sbjct: 270 LSQL-FPVREKPIGDLLLSVRDLKLDGIFKDVSFDLHAGEILGIAGLMGSGRTNVAEAIF 328

Query: 304 GLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRL 363
           G+T +D G + L G+ + I  P   I  G +L+TEDRK SGL    S+L N+ ++     
Sbjct: 329 GITPSDGGEIRLDGEVVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHY 388

Query: 364 SSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCD 423
                I  +    L EDM K+L++KT SLE  + ++SGGNQQK +LA+ L T P  L+ D
Sbjct: 389 VGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILD 448

Query: 424 EPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDT 483
           EPTRGID GAK EIY L+      G A I++SSE PE+L +SDR+ V   G L+     +
Sbjct: 449 EPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRS 508

Query: 484 ALSQEALLRLAS 495
             +QE +++LAS
Sbjct: 509 EATQERVMQLAS 520


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: 592
Number of extensions: 23
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: 526
Length adjustment: 34
Effective length of query: 461
Effective length of database: 492
Effective search space:   226812
Effective search space used:   226812
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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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