GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34245 in Pseudomonas stutzeri RCH2

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate GFF1357 Psest_1392 ABC-type uncharacterized transport systems, ATPase components

Query= uniprot:B2T9V9
         (510 letters)



>FitnessBrowser__psRCH2:GFF1357
          Length = 518

 Score =  217 bits (553), Expect = 7e-61
 Identities = 151/483 (31%), Positives = 236/483 (48%), Gaps = 23/483 (4%)

Query: 20  VTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAP 79
           +TK++    A + + + + PGE HAL+G NGAGKSTL+ I+ G+ +PD GE+ + G    
Sbjct: 14  ITKQYPGCLANDRIDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGEIHWQGERVT 73

Query: 80  SIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARALLDHWK 139
                 A    +  V+QH ++   LSVAEN+ +      G     + +    R +   + 
Sbjct: 74  MRDPAQARERGIGMVFQHFSLFETLSVAENIALALGAKAGTP---KQLEPKIREVSQRYG 130

Query: 140 IDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQRE 199
           + +        LS+  RQ VEI R L    R +ILDEPT+ L   E   LF  +  L  E
Sbjct: 131 MPLEPQRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVTLRRLAAE 190

Query: 200 GVTFLFISHHLQEVYEICQAVTVLRDAR---HIVSAPVSALPREQLIEAMTGERGGLAVA 256
           G + LFISH L EV  +CQ+ TVLR  R     + A  S L   +L   M G+  GL   
Sbjct: 191 GCSILFISHKLNEVRALCQSATVLRAGRVSGECIPAECSDL---ELARLMVGDAEGLEAE 247

Query: 257 DAAARGALPADTAVALELKELT--GADYEGVSFTVKRGEVVGLTGATSSGRTSVAEAIAG 314
              + G  P      L        G   + V   V+ GE+VG+ G   +G+  +   ++G
Sbjct: 248 YPKSEGRAPFLRVERLSWHNADPFGVSLKEVDLEVRAGEIVGIAGVAGNGQDELLALLSG 307

Query: 315 ---LRAAKRGTISV---DGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMT 368
              L+AA+   I     D A L PG   A   HG+  VP +R   G V + S+A+N  +T
Sbjct: 308 EQRLQAAQAMRIRFLGDDVAHLRPG---ARRRHGMAFVPAERLGHGAVPSMSLADNGLLT 364

Query: 369 IARVLG--KFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATN 426
             +  G  + G+    +  AF +++I    +     +   + LSGGN QK ++ R +   
Sbjct: 365 AYQQTGMVEQGLIRRGRVRAFAEQVIQRFAVKTPDAQTPAASLSGGNLQKFILGREILQQ 424

Query: 427 PNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDDL-RTCDRVLVMFRGRV 485
           P +L+   PT GVDV +  A+   +  +R+ G A+LV+S +L++L +  DR+  +  GR+
Sbjct: 425 PKLLIAAHPTWGVDVGAAAAIHRALIELRDAGAAILVISEDLEELFQISDRIAALSDGRL 484

Query: 486 AAE 488
           + +
Sbjct: 485 SPQ 487


Lambda     K      H
   0.318    0.134    0.377 

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: 588
Number of extensions: 32
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 510
Length of database: 518
Length adjustment: 35
Effective length of query: 475
Effective length of database: 483
Effective search space:   229425
Effective search space used:   229425
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 (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