GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Sinorhizobium fredii NGR234

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

Query= reanno::Smeli:SMc04256
         (361 letters)



>NCBI__GCF_000018545.1:WP_015887278.1
          Length = 360

 Score =  327 bits (839), Expect = 2e-94
 Identities = 179/359 (49%), Positives = 241/359 (67%), Gaps = 8/359 (2%)

Query: 1   MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60
           M+++ +R++   +G V  L  +++ ++ GEFLVLLGSSGCGKSTLLN IAGL + S G I
Sbjct: 1   MSALEIRNIRKRYGDVETLKSIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60

Query: 61  FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120
            I +R++    PKDR I MVFQSYALYP M+V +N+ FGL++ K+P AE EK V+  + +
Sbjct: 61  LIGERSILGAHPKDRDIAMVFQSYALYPNMSVARNIGFGLEMRKVPAAEREKAVRDTARL 120

Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180
           LQI+ LL RKPS+LSGGQRQRVAIGRALVR+  VFLFDEPLSNLDAKLR E+R E+KRLH
Sbjct: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVREPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180

Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240
           Q LK T++YVTHDQIEA+TLA RIAVM+ G I+QL  P  IY+ P  L+VAGF+GSP MN
Sbjct: 181 QMLKTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLGTPAEIYDRPATLYVAGFVGSPPMN 240

Query: 241 FFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKV--DEARDGEP 298
                ++ +   S +R  G    +    A      G++V +G+RPE +++  D+A  G  
Sbjct: 241 I----LDAEGTGSGLRILGSENTLPLGGAFPNGTTGRRVKVGIRPEALRLAGDDATGGRL 296

Query: 299 THQAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAES 357
           T  A+V++ E  G + ++      Q ++  +  +    PGST   SFD     +FD ES
Sbjct: 297 T--AIVEVMELTGPELVITARIGEQRITACLPPRTSLEPGSTQAFSFDEAALHLFDPES 353


Lambda     K      H
   0.320    0.137    0.392 

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: 402
Number of extensions: 18
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: 361
Length of database: 360
Length adjustment: 29
Effective length of query: 332
Effective length of database: 331
Effective search space:   109892
Effective search space used:   109892
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 (21.8 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