GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS17020 in Shewanella amazonensis SB2B

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate 6939439 Sama_3531 molybdenum ABC transporter, ATP-binding protein (RefSeq)

Query= uniprot:D8IPI1
         (406 letters)



>lcl|FitnessBrowser__SB2B:6939439 Sama_3531 molybdenum ABC
           transporter, ATP-binding protein (RefSeq)
          Length = 370

 Score =  145 bits (367), Expect = 1e-39
 Identities = 111/348 (31%), Positives = 177/348 (50%), Gaps = 28/348 (8%)

Query: 30  GEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVND------LPARERNVAMVFQ 83
           GEF+ ++GPSG GK+T+LRMIAGL     G++R G  +  D         + R++  V Q
Sbjct: 28  GEFLAVVGPSGGGKTTLLRMIAGLAKPENGSIRCGKRIWFDSDEGIHCSPQNRHIGFVPQ 87

Query: 84  NYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAAL--LNLEALLERKPRAMSGGQQQ 141
           ++ L+P +S   NI   L  L  P+ E  RR R +AAL  +NL  L +R P  +SGGQ+Q
Sbjct: 88  HFGLFPKLSALGNIMAALDHL--PSQE--RRPRALAALEKVNLHGLTDRLPSQLSGGQKQ 143

Query: 142 RAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQLEAMTL 201
           R A+ARA+ + P V L DEP S +D + R +L  ++ RL   L    + VTHD  EA+ L
Sbjct: 144 RVALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKAELNIPVIMVTHDLNEALLL 203

Query: 202 ADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQD---GQLFIET 258
           AD ++L+  G ++Q G+P +++  PRN   A  +G    N  +  V  QD   G  +++ 
Sbjct: 204 ADSMLLISQGHMLQHGTPQDVFSRPRNEAVARQMG--LRNIFNAHVVAQDCAKGVTWLKF 261

Query: 259 AHQRWALTGERFSRLRHAMAVKLAVRPDHVR---IAGEREPAASLTCPVSVELVEILGAD 315
             +   +  +   R+     V+  +    +R   IA  R   +    P+ ++ +  LG  
Sbjct: 262 GDR--LIASDSLPRVNIGDKVRWVIPNQGIRFNSIASGRLCRSFNILPIHIDNMLTLGES 319

Query: 316 ALLTTRCGD--QTLTALVP---ADRLP-QPGATLTLALDQHELHVFDV 357
             L     D  + L   +P   A +L    GA   +AL   ++H+ ++
Sbjct: 320 VRLEASVQDSGERLNVEIPLHLAHKLALTQGAATEVALKSDQVHILEM 367


Lambda     K      H
   0.321    0.137    0.403 

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: 320
Number of extensions: 10
Number of successful extensions: 2
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: 406
Length of database: 370
Length adjustment: 30
Effective length of query: 376
Effective length of database: 340
Effective search space:   127840
Effective search space used:   127840
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: 50 (23.9 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, the preprint 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