GapMind for catabolism of small carbon sources

 

Aligments for a candidate for BPHYT_RS34245 in Pseudomonas fluorescens GW456-L13

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate PfGW456L13_3911 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= uniprot:B2T9V9
         (510 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3911 Ribose ABC
           transport system, ATP-binding protein RbsA (TC
           3.A.1.2.1)
          Length = 517

 Score =  266 bits (680), Expect = 1e-75
 Identities = 169/480 (35%), Positives = 259/480 (53%), Gaps = 15/480 (3%)

Query: 30  LNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAPSIADRDAWRE 89
           L  + + +M GE  AL G NGAGKSTL  I+ GL  P TG++++ G      +   A   
Sbjct: 24  LAGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQYQGQDYRPGSRAQAEAL 83

Query: 90  RVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARALLDHWKID-VREDARA 148
            +  V Q   ++  LSVAENLF++  P +GG I  + +R+ A   + H  +D +  D   
Sbjct: 84  GIRMVMQELNLLPTLSVAENLFLDNLPSKGGWISRKQLRKAAIEAMAHVGLDAIDPDTLV 143

Query: 149 GDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQREGVTFLFISH 208
           G+L +  +Q+VEIAR L      +ILDEPTA L   E++ LF +I+ LQ  GV+ ++ISH
Sbjct: 144 GELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQSRGVSIIYISH 203

Query: 209 HLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGGLAVADAAARGALPADT 268
            L+E+  + Q + VLRD   +   P++    EQL+  M G   G  +   A +   P  T
Sbjct: 204 RLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTLMVGRELGEHIDMGARKIGAPVLT 263

Query: 269 AVALELKELTGADYEGVSFTVKRGEVVGLTGATSSGRTSVAEAIAGLRAAKRGTISVDGA 328
              L   +        VSF V+ GE+ G++G   +GRT +   I G   A  GTI++   
Sbjct: 264 VNGLSRSDKV----RDVSFEVRAGEIFGISGLIGAGRTELLRLIFGADIADSGTIALGAP 319

Query: 329 -----ILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIARVLGKFGIAAPAK 383
                +  P D   ++ HGI  + +DR  EGL+LTQS+  N ++     +   G     K
Sbjct: 320 AQVINVRSPVD---AVGHGIALITEDRKGEGLLLTQSIGANIALGNMPGISGAGFVDNDK 376

Query: 384 KNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLVLIDPTAGVDVKS 443
           + A  Q+ IDA+ I + GP  +VS LSGGNQQKVV+ R L  + +VL+  +PT G+DV +
Sbjct: 377 ERALAQRQIDAMRIRSSGPAQLVSELSGGNQQKVVIGRWLERDCSVLLFDEPTRGIDVGA 436

Query: 444 KEALLSVVDRVREEGKAVLVVSGELDDLR-TCDRVLVMFRGRVAAEFPA-GWQDHDLIAS 501
           K  + +++  +  +GKA++VVS +L +L   CDR+ V+  G +   F    W   +L+A+
Sbjct: 437 KFDIYNLLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGSLIDTFDRDSWTQDELLAA 496


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: 619
Number of extensions: 39
Number of successful extensions: 9
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: 517
Length adjustment: 35
Effective length of query: 475
Effective length of database: 482
Effective search space:   228950
Effective search space used:   228950
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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