Alignments for a candidate for xylG in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylG in Pseudomonas stutzeri RCH2

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 GFF1357 Psest_1392 ABC-type uncharacterized transport systems, ATPase components

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__psRCH2:GFF1357
          Length = 518

 Score =  265 bits (676), Expect = 4e-75
 Identities = 173/484 (35%), Positives = 261/484 (53%), Gaps = 22/484 (4%)

Query: 5   LEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYE 64
           L++  I K++PG  A   + +   PGE+HA++GENGAGKSTLMKII GV QPD GEI ++
Sbjct: 9   LQLCGITKQYPGCLANDRIDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGEIHWQ 68

Query: 65  GRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKF 124
           G  V    P++A   GI  VFQ  S+ + LSVAENI +    K G     +   RE    
Sbjct: 69  GERVTMRDPAQARERGIGMVFQHFSLFETLSVAENIALALGAKAGTPKQLEPKIRE---- 124

Query: 125 MKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVV 184
           + + +G+ ++P+  +   SI  +Q VEI R + +  ++LILDEPTS LT +E ++LF  +
Sbjct: 125 VSQRYGMPLEPQRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVTL 184

Query: 185 KSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVG--RKL 242
           + L  +G +I+FISH+L E+  +C   +VLR G   G       +  ++  +MVG    L
Sbjct: 185 RRLAAEGCSILFISHKLNEVRALCQSATVLRAGRVSGECIPAECSDLELARLMVGDAEGL 244

Query: 243 EKFYIKEAHEPGEVVLEVKNLS-------GERFENVSFSLRRGEILGFAGLVGAGRTELM 295
           E  Y K   E     L V+ LS       G   + V   +R GEI+G AG+ G G+ EL+
Sbjct: 245 EAEYPKS--EGRAPFLRVERLSWHNADPFGVSLKEVDLEVRAGEIVGIAGVAGNGQDELL 302

Query: 296 ETIFG---FRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVS 352
             + G    +  +   I   G  V    P      G+  VP +R   G +  MS+  N  
Sbjct: 303 ALLSGEQRLQAAQAMRIRFLGDDVAHLRPGARRRHGMAFVPAERLGHGAVPSMSLADNGL 362

Query: 353 LPSLDR---IKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWL 409
           L +  +   +++G  I   R +  A+  I+ F ++          LSGGN QK +L + +
Sbjct: 363 LTAYQQTGMVEQG-LIRRGRVRAFAEQVIQRFAVKTPDAQTPAASLSGGNLQKFILGREI 421

Query: 410 ALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSF 469
             +PK+LI   PT G+DVGA A I+R + +L   G  +++IS +L E+ Q+SDRIA +S 
Sbjct: 422 LQQPKLLIAAHPTWGVDVGAAAAIHRALIELRDAGAAILVISEDLEELFQISDRIAALSD 481

Query: 470 GKLA 473
           G+L+
Sbjct: 482 GRLS 485



 Score = 90.5 bits (223), Expect = 1e-22
 Identities = 65/224 (29%), Positives = 109/224 (48%), Gaps = 9/224 (4%)

Query: 269 ENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQG 328
           + +  S++ GEI    G  GAG++ LM+ I+G      GEI+ +G+RV +  P  A E+G
Sbjct: 25  DRIDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGEIHWQGERVTMRDPAQARERG 84

Query: 329 IGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYP 388
           IG+V +      L   +S+  N++L        G      ++ E     +      P  P
Sbjct: 85  IGMVFQH---FSLFETLSVAENIALAL------GAKAGTPKQLEPKIREVSQRYGMPLEP 135

Query: 389 DRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVI 448
            R V  LS G +Q+V + + L    ++LILDEPT  +      E++  + +LA EG  ++
Sbjct: 136 QRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVTLRRLAAEGCSIL 195

Query: 449 MISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAG 492
            IS +L EV  +     V+  G+++G     E S  ++ +L  G
Sbjct: 196 FISHKLNEVRALCQSATVLRAGRVSGECIPAECSDLELARLMVG 239


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: 604
Number of extensions: 24
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: 518
Length adjustment: 34
Effective length of query: 460
Effective length of database: 484
Effective search space:   222640
Effective search space used:   222640
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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 (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 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