GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Desulfacinum infernum DSM 9756

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= uniprot:D8IPI1
         (406 letters)



>NCBI__GCF_900129305.1:WP_073038605.1
          Length = 368

 Score =  319 bits (818), Expect = 7e-92
 Identities = 162/349 (46%), Positives = 235/349 (67%), Gaps = 3/349 (0%)

Query: 19  VLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARERNV 78
           V+    L + D EFVVL+GPSGCGKST LRMIAGLE+++ G + IGG VVN +P ++R++
Sbjct: 18  VVRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVTSGEISIGGRVVNHVPPKDRDI 77

Query: 79  AMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRAMSGG 138
           AMVFQ+YALYPHM+VY N+AFGL     P  EIDRRV++ A +L +  LL+R+P  +SGG
Sbjct: 78  AMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEIDRRVKQAAEILGISDLLQRRPAQLSGG 137

Query: 139 QQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQLEA 198
           Q+QR A+ RAI++ P  FLFDEPLSNLDAKLR Q+R ++ +LH+RL++T VYVTHDQ+EA
Sbjct: 138 QRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMRAELAKLHERLQSTIVYVTHDQIEA 197

Query: 199 MTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDGQLFIET 258
           MTLADR+++M+DG+I+Q G P E+Y  P N F AGFIG+P+MNFL   +  + G L+++ 
Sbjct: 198 MTLADRIVVMKDGKIMQVGPPLEVYERPANRFVAGFIGSPSMNFLDVRLVEEAGDLWVDG 257

Query: 259 AHQRWALTGERFSRLRHAM--AVKLAVRPDHVR-IAGEREPAASLTCPVSVELVEILGAD 315
              R  +   R    R  +   V   +RP+ V+   G+  P         V++ E +G++
Sbjct: 258 ESFRLKVPRHRAPAFRGHVNRPVIFGIRPEDVKERPGDALPEGVEPLRAEVDVREPIGSE 317

Query: 316 ALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFDVESGENLS 364
            ++T   G    TA +  +   +    + LA++ +++H+FD ES + L+
Sbjct: 318 VIITATVGSHAFTARISPNVAVRVHDPIDLAVNMNKMHLFDPESEQALN 366


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: 403
Number of extensions: 16
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: 368
Length adjustment: 30
Effective length of query: 376
Effective length of database: 338
Effective search space:   127088
Effective search space used:   127088
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 Apr 09 2024. 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