Alignments for a candidate for HSERO_RS03640 in Pseudomonas stutzeri RCH2

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:

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, 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

GapMind for catabolism of small carbon sources