GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Desulfacinum infernum DSM 9756

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= reanno::WCS417:GFF4321
         (386 letters)



>NCBI__GCF_900129305.1:WP_073038605.1
          Length = 368

 Score =  330 bits (846), Expect = 4e-95
 Identities = 178/369 (48%), Positives = 246/369 (66%), Gaps = 8/369 (2%)

Query: 1   MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60
           MA ++L  VNK +       +++  L++ + EF++LVGPSGCGKST +  IAGLE +T G
Sbjct: 1   MAEIKLDQVNKRFKKNW--VVRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVTSG 58

Query: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120
            I IG + V+ + PKDRDIAMVFQSYALYP M+V +N+ FGL  R +P+ +ID  V + A
Sbjct: 59  EISIGGRVVNHVPPKDRDIAMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEIDRRVKQAA 118

Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
           ++L I  LL R+P QLSGGQ+QRVAMGRA+ R P+ +LFDEPLSNLDAKLRV+MR E+  
Sbjct: 119 EILGISDLLQRRPAQLSGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMRAELAK 178

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240
           +H+RL++T VYVTHDQIEAMTL D++ VMKDG I Q G P E+Y  PAN+FVA FIGSP 
Sbjct: 179 LHERLQSTIVYVTHDQIEAMTLADRIVVMKDGKIMQVGPPLEVYERPANRFVAGFIGSPS 238

Query: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEA--GLEDRDVILGLRPEQIMLAAGEG 298
           MNF+ +RL  + G L   +D    R ++  +   A  G  +R VI G+RPE +    G+ 
Sbjct: 239 MNFLDVRLVEEAGDL--WVDGESFRLKVPRHRAPAFRGHVNRPVIFGIRPEDVKERPGDA 296

Query: 299 --DSASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLL 356
             +    +RAEV V EP G + ++   +       R++P+VA +V + + L  + +K+ L
Sbjct: 297 LPEGVEPLRAEVDVREPIGSEVIITATVGSHAFTARISPNVAVRVHDPIDLAVNMNKMHL 356

Query: 357 FDANTGERL 365
           FD  + + L
Sbjct: 357 FDPESEQAL 365


Lambda     K      H
   0.318    0.135    0.382 

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: 377
Number of extensions: 13
Number of successful extensions: 3
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: 386
Length of database: 368
Length adjustment: 30
Effective length of query: 356
Effective length of database: 338
Effective search space:   120328
Effective search space used:   120328
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: 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