GapMind for catabolism of small carbon sources

 

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

Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate Pf1N1B4_4286 Inositol transport system ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



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

 Score =  447 bits (1150), Expect = e-130
 Identities = 238/492 (48%), Positives = 335/492 (68%), Gaps = 3/492 (0%)

Query: 4   ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63
           +LE+ ++ K FPGV AL  V +   PG V A++GENGAGKSTLMKIIAG+YQPD GE+  
Sbjct: 32  LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 91

Query: 64  EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGI-FIDYKKMYREAE 122
            G+ V +  P  A+ AGI  + QEL++M ++S+AENI++G E+  G+  ID+++M+R   
Sbjct: 92  RGKPVVFETPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMIDHREMHRCTA 151

Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182
           K + E   I +DPEE +G  SIA +QMVEIA+AV   + +LI+DEPTS++T KE   LF 
Sbjct: 152 KLL-ERLRINLDPEELVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFS 210

Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242
           ++  LK +G  II+I+H++ E+F I D+V+V RDG YIG    +++  + ++ MMVGR+L
Sbjct: 211 IIADLKRQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGREL 270

Query: 243 EKFYIKEAHEPGEVVLEVKNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETIFGF 301
            + +       G+++L V++L  +  F++VSF L  GEILG AGL+G+GRT + E IFG 
Sbjct: 271 SQLFPVREKPIGDLLLSVRDLKLDGIFKDVSFDLHAGEILGIAGLMGSGRTNVAEAIFGI 330

Query: 302 RPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKK 361
            P  GGEI ++G+ V I+ P  AIE+G  L+ EDRK  GL   +S++ N+ +  L     
Sbjct: 331 TPSDGGEIRLDGEVVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYVG 390

Query: 362 GPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEP 421
             FI  K  + L +   K   ++    ++ +  LSGGNQQK +LA+WL   P+ILILDEP
Sbjct: 391 NGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEP 450

Query: 422 TRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEA 481
           TRGIDVGAKAEIYR++S LA EG+ VIMISSELPEVL MSDR+ VM  G L G +D  EA
Sbjct: 451 TRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEA 510

Query: 482 SQEKVMKLAAGL 493
           +QE+VM+LA+G+
Sbjct: 511 TQERVMQLASGM 522



 Score = 88.6 bits (218), Expect = 5e-22
 Identities = 63/225 (28%), Positives = 110/225 (48%), Gaps = 5/225 (2%)

Query: 270 NVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGI 329
           +V   +R G +L   G  GAG++ LM+ I G      GE+ + GK V    PL A++ GI
Sbjct: 50  DVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPVVFETPLAALQAGI 109

Query: 330 GLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPD 389
            ++ ++   L L+  MSI  N+ +   +++     I  +         ++   I    P+
Sbjct: 110 AMIHQE---LNLMPHMSIAENIWI-GREQLNGLHMIDHREMHRCTAKLLERLRIN-LDPE 164

Query: 390 RKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIM 449
             V  LS   +Q V +AK ++    ILI+DEPT  I     A ++ I++ L ++G G+I 
Sbjct: 165 ELVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSIIADLKRQGKGIIY 224

Query: 450 ISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494
           I+ ++ EV  ++D +AV   G   G+  A     + ++ +  G E
Sbjct: 225 ITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRE 269


Lambda     K      H
   0.318    0.138    0.385 

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: 649
Number of extensions: 29
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: 494
Length of database: 526
Length adjustment: 34
Effective length of query: 460
Effective length of database: 492
Effective search space:   226320
Effective search space used:   226320
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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 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