Aligments for a candidate for BPHYT_RS34245 in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__Phaeo:GFF385 PGA1_c03960 ribose import
           ATP-binding protein RbsA
          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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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