Alignments for a candidate for rbsA in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Pseudomonas stutzeri RCH2

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate GFF1357 Psest_1392 ABC-type uncharacterized transport systems, ATPase components

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__psRCH2:GFF1357
          Length = 518

 Score =  257 bits (657), Expect = 6e-73
 Identities = 163/486 (33%), Positives = 263/486 (54%), Gaps = 21/486 (4%)

Query: 3   ALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLL 62
           A LQL GI K +PG  A     L++ PG + AL+GENGAGKST+MK++ G+   DAG + 
Sbjct: 7   ARLQLCGITKQYPGCLANDRIDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGEIH 66

Query: 63  WLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEA 122
           W G+  T   P  ++E GIG++ Q  +L   L++AENI L      + G    K +  + 
Sbjct: 67  WQGERVTMRDPAQARERGIGMVFQHFSLFETLSVAENIALA--LGAKAGTP--KQLEPKI 122

Query: 123 DKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFR 182
            ++  +  +  +  +LV  LSIG++Q VEI + L  + +++I+DEPT  LT  E + LF 
Sbjct: 123 REVSQRYGMPLEPQRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFV 182

Query: 183 VIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVG--R 240
            +R L ++G  I++ISH++ E+  +C   TV R G+   E   A  ++  L  +MVG   
Sbjct: 183 TLRRLAAEGCSILFISHKLNEVRALCQSATVLRAGRVSGECIPAECSDLELARLMVGDAE 242

Query: 241 KLEDQYPHLD-KAPGDIRLKVDNLC-------GPGVNDVSFTLRKGEILGVSGLMGAGRT 292
            LE +YP  + +AP    L+V+ L        G  + +V   +R GEI+G++G+ G G+ 
Sbjct: 243 GLEAEYPKSEGRAP---FLRVERLSWHNADPFGVSLKEVDLEVRAGEIVGIAGVAGNGQD 299

Query: 293 ELMKVLYGALPRTSGY---VTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKE 349
           EL+ +L G     +     +   G +V    P     +G+ ++  +R   G V  MS+ +
Sbjct: 300 ELLALLSGEQRLQAAQAMRIRFLGDDVAHLRPGARRRHGMAFVPAERLGHGAVPSMSLAD 359

Query: 350 NMSLTALRYFSRA-GGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIAR 408
           N  LTA +       G ++    +      I+ F VKTP  +     LSGGN QK  + R
Sbjct: 360 NGLLTAYQQTGMVEQGLIRRGRVRAFAEQVIQRFAVKTPDAQTPAASLSGGNLQKFILGR 419

Query: 409 GLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVM 468
            ++ +PK+LI   PT GVDVGA   I++ + + +  G +I+++S ++ E+  +SDRI  +
Sbjct: 420 EILQQPKLLIAAHPTWGVDVGAAAAIHRALIELRDAGAAILVISEDLEELFQISDRIAAL 479

Query: 469 HEGHLS 474
            +G LS
Sbjct: 480 SDGRLS 485



 Score = 82.0 bits (201), Expect = 5e-20
 Identities = 70/247 (28%), Positives = 114/247 (46%), Gaps = 18/247 (7%)

Query: 263 LCG-----PG--VND-VSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGH 314
           LCG     PG   ND +  +++ GEI  + G  GAG++ LMK++YG     +G +   G 
Sbjct: 11  LCGITKQYPGCLANDRIDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGEIHWQGE 70

Query: 315 EVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQA 374
            V  R P      GI  + +      L   +SV EN+   AL   ++AG   +   + + 
Sbjct: 71  RVTMRDPAQARERGIGMVFQ---HFSLFETLSVAENI---ALALGAKAGTPKQLEPKIRE 124

Query: 375 VSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEI 434
           VS    +        ++ +  LS G +Q+V I R LM   ++LILDEPT  +      E+
Sbjct: 125 VSQRYGM----PLEPQRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADEL 180

Query: 435 YQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
           +  + +  A+G SI+ +S ++ EV  +     V+  G +SGE    + +   L    VG 
Sbjct: 181 FVTLRRLAAEGCSILFISHKLNEVRALCQSATVLRAGRVSGECIPAECSDLELARLMVGD 240

Query: 495 LNRVNQE 501
              +  E
Sbjct: 241 AEGLEAE 247



 Score = 58.2 bits (139), Expect = 7e-13
 Identities = 49/232 (21%), Positives = 104/232 (44%), Gaps = 10/232 (4%)

Query: 19  ALSGAALNVYPGRVMALVGENGAGKSTMMKVLTG---IYTRDAGTLLWLGKETTFTGPKS 75
           +L    L V  G ++ + G  G G+  ++ +L+G   +    A  + +LG +     P +
Sbjct: 274 SLKEVDLEVRAGEIVGIAGVAGNGQDELLALLSGEQRLQAAQAMRIRFLGDDVAHLRPGA 333

Query: 76  SQEAGIGIIHQEL---NLIPQLTIAENIFLG---REFVNRFGKIDWKTMYAEADKLLAKL 129
            +  G+  +  E      +P +++A+N  L    +  +   G I    + A A++++ + 
Sbjct: 334 RRRHGMAFVPAERLGHGAVPSMSLADNGLLTAYQQTGMVEQGLIRRGRVRAFAEQVIQRF 393

Query: 130 NLRFKSDKL-VGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVIRELK 188
            ++    +     LS G+ Q   + + +  + K++I   PT  +      ++ R + EL+
Sbjct: 394 AVKTPDAQTPAASLSGGNLQKFILGREILQQPKLLIAAHPTWGVDVGAAAAIHRALIELR 453

Query: 189 SQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGR 240
             G  I+ IS  ++E+F+I D +    DG+   +R  AS     +   M G+
Sbjct: 454 DAGAAILVISEDLEELFQISDRIAALSDGRLSPQRATASTCPVEVGRWMAGQ 505


Lambda     K      H
   0.318    0.137    0.380 

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: 564
Number of extensions: 27
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 501
Length of database: 518
Length adjustment: 34
Effective length of query: 467
Effective length of database: 484
Effective search space:   226028
Effective search space used:   226028
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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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 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