GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Sinorhizobium fredii NGR234

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_015887278.1 NGR_RS05625 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

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



>NCBI__GCF_000018545.1:WP_015887278.1
          Length = 360

 Score =  355 bits (910), Expect = e-102
 Identities = 189/368 (51%), Positives = 252/368 (68%), Gaps = 8/368 (2%)

Query: 1   MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60
           M+ LE+RN+ K YG    +TLK+I+++++ GEFL+L+G SGCGKSTL+N IAGL   +GG
Sbjct: 1   MSALEIRNIRKRYGD--VETLKSIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGG 58

Query: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120
            I+IG++ + G  PKDRDIAMVFQSYALYP MSV  NI FGL++RK+P A+ +  V   A
Sbjct: 59  DILIGERSILGAHPKDRDIAMVFQSYALYPNMSVARNIGFGLEMRKVPAAEREKAVRDTA 118

Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
           +LLQIE+LL+RKP QLSGGQ+QRVA+GRAL R P+++LFDEPLSNLDAKLR+EMRTE+K 
Sbjct: 119 RLLQIENLLDRKPSQLSGGQRQRVAIGRALVREPQVFLFDEPLSNLDAKLRMEMRTELKR 178

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240
           +HQ LKTT VYVTHDQIEAMTL  ++AVM+DG I+Q GTP EIY+ PA  +VA F+GSPP
Sbjct: 179 LHQMLKTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLGTPAEIYDRPATLYVAGFVGSPP 238

Query: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDS 300
           MN +       +G    L   G             G   R V +G+RPE + L AG+  +
Sbjct: 239 MNILD-----AEGTGSGLRILGSENTLPLGGAFPNGTTGRRVKVGIRPEALRL-AGDDAT 292

Query: 301 ASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFDAN 360
              + A V+V E TGP+ ++  ++ + ++   L P  + + G T    FD + + LFD  
Sbjct: 293 GGRLTAIVEVMELTGPELVITARIGEQRITACLPPRTSLEPGSTQAFSFDEAALHLFDPE 352

Query: 361 TGERLGTA 368
           +G  L  A
Sbjct: 353 SGLSLRMA 360


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: 405
Number of extensions: 11
Number of successful extensions: 4
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: 360
Length adjustment: 30
Effective length of query: 356
Effective length of database: 330
Effective search space:   117480
Effective search space used:   117480
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