GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS03640 in Pseudomonas stutzeri RCH2

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate GFF1357 Psest_1392 ABC-type uncharacterized transport systems, ATPase components

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__psRCH2:GFF1357
          Length = 518

 Score =  281 bits (720), Expect = 3e-80
 Identities = 182/501 (36%), Positives = 271/501 (54%), Gaps = 27/501 (5%)

Query: 2   TQTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQG 61
           +QT  LQ+ GI K +   LA   + L+I+PGEIHAL+GENGAGKSTLMK++ GV  PD G
Sbjct: 4   SQTARLQLCGITKQYPGCLANDRIDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDAG 63

Query: 62  EILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMR 121
           EI   G  V +RDP  +R  GI +++Q  ++   +SVA N+ +   L  + G       +
Sbjct: 64  EIHWQGERVTMRDPAQARERGIGMVFQHFSLFETLSVAENIALA--LGAKAGTPKQLEPK 121

Query: 122 SRTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQ 181
            R   V ++ G       L   LSI E+Q+VEI R L+   R++I+DEPT+ L+ +E ++
Sbjct: 122 IR--EVSQRYGMPLEPQRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADE 179

Query: 182 LFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVG 241
           LF  +RRL  EG +I++ISH++ EV AL    TVLR G   GE +  E     + ++MVG
Sbjct: 180 LFVTLRRLAAEGCSILFISHKLNEVRALCQSATVLRAGRVSGECIPAECSDLELARLMVG 239

Query: 242 RS---LSEFYQHQRIAPADAAQLPTVMQVRALA-------GGKIRPASFDVRAGEVLGFA 291
            +    +E+ + +  AP         ++V  L+       G  ++    +VRAGE++G A
Sbjct: 240 DAEGLEAEYPKSEGRAP--------FLRVERLSWHNADPFGVSLKEVDLEVRAGEIVGIA 291

Query: 292 GLVGAGRTELARLLFGADPRSGGD---ILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGL 348
           G+ G G+ EL  LL G           I   G  V   +P A  R G+A+VP +R G G 
Sbjct: 292 GVAGNGQDELLALLSGEQRLQAAQAMRIRFLGDDVAHLRPGARRRHGMAFVPAERLGHGA 351

Query: 349 FLQMAVAANATMNVASR--HTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGN 406
              M++A N  +    +      GL+R   +   A   IQR  VK    +TP   LSGGN
Sbjct: 352 VPSMSLADNGLLTAYQQTGMVEQGLIRRGRVRAFAEQVIQRFAVKTPDAQTPAASLSGGN 411

Query: 407 QQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIG 466
            QK +L R +   PK+LI   PT GVD+ A + I++ +  L   G A++VIS +L E+  
Sbjct: 412 LQKFILGREILQQPKLLIAAHPTWGVDVGAAAAIHRALIELRDAGAAILVISEDLEELFQ 471

Query: 467 ICDRVLVMREGMITGELAGAA 487
           I DR+  + +G ++ + A A+
Sbjct: 472 ISDRIAALSDGRLSPQRATAS 492



 Score = 84.3 bits (207), Expect = 1e-20
 Identities = 61/215 (28%), Positives = 105/215 (48%), Gaps = 9/215 (4%)

Query: 282 VRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPE 341
           ++ GE+    G  GAG++ L ++++G      G+I  +G  V +  P  A   GI  V +
Sbjct: 31  IQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGEIHWQGERVTMRDPAQARERGIGMVFQ 90

Query: 342 DRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGK 401
                 LF  ++VA N  + + ++         + L    R   QR  + +  P+  V  
Sbjct: 91  HFS---LFETLSVAENIALALGAKAGT-----PKQLEPKIREVSQRYGMPL-EPQRLVHS 141

Query: 402 LSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSEL 461
           LS G +Q+V + R L    ++LILDEPT  +      E++  + RLA++G +++ IS +L
Sbjct: 142 LSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVTLRRLAAEGCSILFISHKL 201

Query: 462 PEVIGICDRVLVMREGMITGELAGAAITQENIMRL 496
            EV  +C    V+R G ++GE   A  +   + RL
Sbjct: 202 NEVRALCQSATVLRAGRVSGECIPAECSDLELARL 236


Lambda     K      H
   0.320    0.135    0.378 

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: 661
Number of extensions: 39
Number of successful extensions: 10
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: 521
Length of database: 518
Length adjustment: 35
Effective length of query: 486
Effective length of database: 483
Effective search space:   234738
Effective search space used:   234738
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