GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34245 in Phaeobacter inhibens BS107

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate GFF385 PGA1_c03960 ribose import ATP-binding protein RbsA

Query= uniprot:B2T9V9
         (510 letters)



>FitnessBrowser__Phaeo:GFF385
          Length = 509

 Score =  248 bits (634), Expect = 3e-70
 Identities = 170/513 (33%), Positives = 260/513 (50%), Gaps = 27/513 (5%)

Query: 11  SVPVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGE 70
           + P +E   ++K FG   A  D+SIRV PG  H ++G NGAGKSTL+SIL G  K D GE
Sbjct: 2   TAPAIELKGISKAFGPVQANKDISIRVAPGTIHGIIGENGAGKSTLMSILYGFYKADKGE 61

Query: 71  VRFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVI--DWQAMR 128
           V   G        + A    +  V+QH  ++ + +V EN+ +  +   GG++       R
Sbjct: 62  VWIHGKRTEIPDSQAAISAGIGMVFQHFKLVENFTVLENIILGAED--GGLLKPSLSKAR 119

Query: 129 RDARALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKR 188
           +  + L   ++++V  DAR  ++ V  +Q VEI +AL   A  +ILDEPT  L   E  +
Sbjct: 120 KSLKDLAAEYELNVDPDARIDEIGVGMQQRVEILKALYRQADILILDEPTGVLTPAEADQ 179

Query: 189 LFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTG 248
           LFR +  L+ EG T + I+H L+E+ E    V+V+R      +   +    E L E M G
Sbjct: 180 LFRILDRLRAEGKTIILITHKLREIMEYTDTVSVMRRGEMTATVKTAETSPEHLAELMVG 239

Query: 249 ERGGLAVADAAARGALPADTAVALELKELTGADYEGVS------FTVKRGEVVGLTGATS 302
            +  L V    A    P      LE++ L+  D  GV+       TV+ GE++G+ G   
Sbjct: 240 RKVLLRVDKVPATPGKP-----ILEIENLSVVDEAGVARVKNIDLTVRAGEILGIAGVAG 294

Query: 303 SGRTSVAEAIAGLRAAKRGTISVDGAILP----PGDVPASLAHGIGCVPKDRHHEGLVLT 358
           +G++ + E + G+R   +G+I ++GA LP      D  A  A  +  VP+DR  EGL++ 
Sbjct: 295 NGQSELMEVLGGMREG-QGSIRLNGAPLPLSGAGSDARARRAAHVAHVPEDRQREGLIMD 353

Query: 359 QSVAENASMTI--ARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQK 416
               EN +     A    +  +   A   A  +  +    +    P       SGGNQQK
Sbjct: 354 FHAWENVAFGYHHAPEYQRGLLMNNAALRADTEAKMAKFDVRPPDPWLAAKNFSGGNQQK 413

Query: 417 VVMARALATNPNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCD 475
           +V+AR +  NP +L++  PT GVD+ + E +   +  +R++GKA+L+VS EL++ L   D
Sbjct: 414 IVVAREIERNPELLLIGQPTRGVDIGAIEFIHKQIVELRDQGKAILLVSVELEEILSLAD 473

Query: 476 RVLVMFRGRVAAEFPAGWQDHD----LIASVEG 504
           RV VMF G +  E PA   D      L+A V G
Sbjct: 474 RVAVMFDGMIMGERPADQTDEKELGLLMAGVAG 506



 Score = 73.2 bits (178), Expect = 2e-17
 Identities = 69/254 (27%), Positives = 113/254 (44%), Gaps = 18/254 (7%)

Query: 15  VEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFS 74
           +E L V    G  A + ++ + V  GE   + G  G G+S L+ +L G+R+   G +R +
Sbjct: 260 IENLSVVDEAG-VARVKNIDLTVRAGEILGIAGVAGNGQSELMEVLGGMREGQ-GSIRLN 317

Query: 75  GAAAP-SIADRDAWRERVACVY------QHSTIIRDLSVAENLFINRQPL----RGGVID 123
           GA  P S A  DA   R A V       Q   +I D    EN+           RG +++
Sbjct: 318 GAPLPLSGAGSDARARRAAHVAHVPEDRQREGLIMDFHAWENVAFGYHHAPEYQRGLLMN 377

Query: 124 WQAMRRDARALLDHWKIDVRED---ARAGDLSVEARQLVEIARALSYGARFIILDEPTAQ 180
             A+R D  A +   K DVR       A + S   +Q + +AR +      +++ +PT  
Sbjct: 378 NAALRADTEAKMA--KFDVRPPDPWLAAKNFSGGNQQKIVVAREIERNPELLLIGQPTRG 435

Query: 181 LDGDEIKRLFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPRE 240
           +D   I+ + ++I EL+ +G   L +S  L+E+  +   V V+ D   +   P      +
Sbjct: 436 VDIGAIEFIHKQIVELRDQGKAILLVSVELEEILSLADRVAVMFDGMIMGERPADQTDEK 495

Query: 241 QLIEAMTGERGGLA 254
           +L   M G  G  A
Sbjct: 496 ELGLLMAGVAGEAA 509


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: 605
Number of extensions: 31
Number of successful extensions: 9
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: 510
Length of database: 509
Length adjustment: 34
Effective length of query: 476
Effective length of database: 475
Effective search space:   226100
Effective search space used:   226100
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