GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Rhizobium freirei PRF 81

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_004127637.1 RHSP_RS29440 ABC transporter ATP-binding protein

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



>NCBI__GCF_000359745.1:WP_004127637.1
          Length = 354

 Score =  364 bits (935), Expect = e-105
 Identities = 196/370 (52%), Positives = 254/370 (68%), Gaps = 24/370 (6%)

Query: 1   MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60
           M+ LE++N+ K+YGA   +TLK I++S++ GEFL+L+G SGCGKSTL+N IAGL   T G
Sbjct: 1   MSALEIQNIRKSYGA--LETLKGIDISLESGEFLVLLGSSGCGKSTLLNIIAGLAEATSG 58

Query: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120
            I IGD+ V G+ PKDRDIAMVFQSYALYP +SV  NI FGL++RK+P A+ D  V   A
Sbjct: 59  DIRIGDRSVLGVHPKDRDIAMVFQSYALYPNLSVHRNIGFGLEMRKVPAAERDKAVREAA 118

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

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240
           +HQ LKTT VYVTHDQIEAMTL  ++AVM+DG I+Q G P EIYN+PA  +VA+F+G+PP
Sbjct: 179 LHQMLKTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLGRPDEIYNHPATLYVATFVGAPP 238

Query: 241 MNFVPLRLQRKDGRLVALLDSGQARCE-----LALNTTEAGL-EDRDVILGLRPEQIMLA 294
           MN            L A  D G  R +     L + T +A + + +++++G+RPE + L 
Sbjct: 239 MNL-----------LNATADQGSLRIDGTSITLPMPTAKAEIKQGQELVVGIRPETLYL- 286

Query: 295 AGEGDSASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKV 354
               D    + A  +V E TGP+ +V       ++   L P      G+TL L FD S +
Sbjct: 287 ----DEQGQLEAVCEVAELTGPELIVTAHTGSQRLMACLPPRTTIAEGQTLKLGFDASAL 342

Query: 355 LLFDANTGER 364
            LFD  TG R
Sbjct: 343 HLFDRATGRR 352


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: 384
Number of extensions: 8
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: 354
Length adjustment: 30
Effective length of query: 356
Effective length of database: 324
Effective search space:   115344
Effective search space used:   115344
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: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. 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