GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Paucidesulfovibrio gracilis DSM 16080

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= BRENDA::Q97UY8
         (353 letters)



>NCBI__GCF_900167125.1:WP_078717009.1
          Length = 370

 Score =  203 bits (517), Expect = 5e-57
 Identities = 124/333 (37%), Positives = 204/333 (61%), Gaps = 23/333 (6%)

Query: 4   IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63
           I +++V+K F  G+ V L +V ++I +GE   ILGPSG GKTT +R++AG + PS+GE+ 
Sbjct: 8   IRLEHVAKEFD-GETV-LHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGEII 65

Query: 64  FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEE 123
            D R +       VPP+ R++  VFQ++AL+P+++ F+N+AF L    + K EI +RV +
Sbjct: 66  LDGRSMRD-----VPPDGRRVNTVFQSYALFPHMSVFDNVAFGLRMSGIPKVEIGERVAK 120

Query: 124 VAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALV 183
             +++ +       P  LSGGQQQRVA+ARA+V  P +LLLDEP S LD ++R   R  +
Sbjct: 121 ALRMVGLAGQAGRRPTSLSGGQQQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTEL 180

Query: 184 KEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGE 243
           K+++  +G+T + V+HD  + F+++DRV V+ +G + QVG P ++Y+ PV++ VA  +GE
Sbjct: 181 KQLRREMGITFIFVTHDQEEAFSMSDRVVVMNEGCVAQVGTPVEVYEQPVNMFVARFVGE 240

Query: 244 INELEGKV-TNEGVVIGSL--RFPVSVSS-------DRAIIGIRPEDVKLSKDVIKDDS- 292
            N  EG    ++G ++ +L       +SS       DR  + +RPED+ + ++  +DD  
Sbjct: 241 TNVFEGVAGQSDGGILQALVEGRTCELSSHRGFQPGDRIRVLLRPEDLLVEREEPEDDDK 300

Query: 293 -WILVGKGKVKVIGYQGGLFRITITPLDSEEEI 324
            W+    G++    Y+G  + + +  LDS  EI
Sbjct: 301 LWL---PGRIMETVYKGSTWDM-VVQLDSGHEI 329


Lambda     K      H
   0.319    0.139    0.390 

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: 331
Number of extensions: 21
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 353
Length of database: 370
Length adjustment: 29
Effective length of query: 324
Effective length of database: 341
Effective search space:   110484
Effective search space used:   110484
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 (21.7 bits)
S2: 49 (23.5 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