GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__SB2B:6939439
          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 (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