GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Paucidesulfovibrio gracilis DSM 16080

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

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897
         (386 letters)



>NCBI__GCF_900167125.1:WP_200806763.1
          Length = 406

 Score =  214 bits (546), Expect = 3e-60
 Identities = 114/270 (42%), Positives = 174/270 (64%), Gaps = 11/270 (4%)

Query: 4   LELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAIL 63
           + L+ + K +G  +   ++  +L I+ GE + L+GPSGCGK+T++  IAGLET + G I 
Sbjct: 45  VRLQGLMKRFGKTV--AVQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGDIY 102

Query: 64  VDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLL 123
           +    I+      R++ M+FQ+YAL+P  ++ +N+AFGLK R +   E+ E+VA+  +++
Sbjct: 103 IKGRRINDTPIHKRNLGMIFQNYALFPHKTIFENVAFGLKYRNVSREEMREKVAQALEMV 162

Query: 124 QIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183
           ++  +  R   QLSGGQQQR+A+ RA+   P + L DEPLS LD KLR EMR E+  + Q
Sbjct: 163 RLPGVEKRYASQLSGGQQQRIALARAIVIEPDVLLMDEPLSALDEKLREEMRMEIDNIQQ 222

Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNF 243
           +L  TT++VTHDQ EA+++ +K+ VMKDG  QQ GTP+D+Y+ P N FVA F+G    NF
Sbjct: 223 QLNLTTLFVTHDQREALSMSNKIVVMKDGRKQQEGTPEDVYDYPDNYFVADFLGH--ANF 280

Query: 244 IPLRLQRKDGRLLALLDSGQARCELPLGMQ 273
                   D R+L +LD+ Q R  +  G++
Sbjct: 281 F-------DARVLEVLDNDQVRVRIAEGLE 303


Lambda     K      H
   0.319    0.138    0.393 

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: 379
Number of extensions: 13
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: 406
Length adjustment: 31
Effective length of query: 355
Effective length of database: 375
Effective search space:   133125
Effective search space used:   133125
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 (21.7 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