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_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein

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



>NCBI__GCF_900129305.1:WP_073037934.1
          Length = 365

 Score =  286 bits (732), Expect = 6e-82
 Identities = 162/382 (42%), Positives = 224/382 (58%), Gaps = 19/382 (4%)

Query: 4   LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63
           +E+R+V K YG      ++ +  S++EG+ L+++GPSGCGK+TL+  IAGLE +T G I 
Sbjct: 3   IEIRDVRKDYGR--VQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIH 60

Query: 64  IGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLL 123
           I   DV+ + P  R+I+MVFQSYAL+P ++VRENI FGLK+RK+P  +I+  + RV  LL
Sbjct: 61  IAGTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVDLL 120

Query: 124 QIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183
            +   L+ KPG+LSGG QQRVA+GRA+     + L DEPLSNLDAKLR  MR E+  + +
Sbjct: 121 GLSGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQR 180

Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPMNF 243
           RL  T +YVTHDQ+EAMT+ D++ +M+DG I Q  +P+  Y  PAN FVA FIG+PPMN 
Sbjct: 181 RLGITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNI 240

Query: 244 VPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDSASS 303
           VPL               G A  E        G++    + G+RPE + LA       S 
Sbjct: 241 VPL-----------CPTQGGAALEPGGRLLFPGMDPDRYLFGIRPENLRLA------ESG 283

Query: 304 IRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFDANTGE 363
             A V   E  G DT V  +++  +V  R       + G  + L +DP  V LFDA T E
Sbjct: 284 QPAMVTGREYLGSDTFVSCEIHGQEVIVRTRGRRNIREGTVVHLTWDPGDVNLFDARTQE 343

Query: 364 RLGTASSLPAQGHADNVAQFKG 385
           R+ +      +G  +      G
Sbjct: 344 RVDSVVPARKEGRENPAGSIGG 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: 385
Number of extensions: 12
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: 386
Length of database: 365
Length adjustment: 30
Effective length of query: 356
Effective length of database: 335
Effective search space:   119260
Effective search space used:   119260
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