GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Paucidesulfovibrio gracilis DSM 16080

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_200806763.1 B5D49_RS03200 ABC transporter ATP-binding protein

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



>NCBI__GCF_900167125.1:WP_200806763.1
          Length = 406

 Score =  209 bits (531), Expect = 1e-58
 Identities = 120/291 (41%), Positives = 175/291 (60%), Gaps = 8/291 (2%)

Query: 3   SVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFI 62
           +V ++ L   FG    +   +L I+ GE + LLG SGCGK+T+L  IAGL   + G I+I
Sbjct: 44  AVRLQGLMKRFGKTVAVQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGDIYI 103

Query: 63  KDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQ 122
           K R +       R +GM+FQ+YAL+P  T+ +N++FGLK   +   E+ ++V +A E+++
Sbjct: 104 KGRRINDTPIHKRNLGMIFQNYALFPHKTIFENVAFGLKYRNVSREEMREKVAQALEMVR 163

Query: 123 IQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQS 182
           +  + KR  S+LSGGQ+QR+A+ RA+V + DV L DEPLS LD KLR E+R+EI  + Q 
Sbjct: 164 LPGVEKRYASQLSGGQQQRIALARAIVIEPDVLLMDEPLSALDEKLREEMRMEIDNIQQQ 223

Query: 183 LKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFF 242
           L  T ++VTHDQ EAL+++++I VMK G  QQ   P  +Y+ P+N FVA F+G    NFF
Sbjct: 224 LNLTTLFVTHDQREALSMSNKIVVMKDGRKQQEGTPEDVYDYPDNYFVADFLG--HANFF 281

Query: 243 RGEVEPKDGRSFVR---AGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKV 290
              V        VR   A G+ F         R + GQ V L +R + + V
Sbjct: 282 DARVLEVLDNDQVRVRIAEGLEFTADHV---GRWRQGQDVHLVMRAQKINV 329


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: 354
Number of extensions: 11
Number of successful extensions: 1
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: 406
Length adjustment: 30
Effective length of query: 331
Effective length of database: 376
Effective search space:   124456
Effective search space used:   124456
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: 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