GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Magnetospirillum magneticum AMB-1

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_011384263.1 AMB_RS09395 ABC transporter ATP-binding protein

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



>NCBI__GCF_000009985.1:WP_011384263.1
          Length = 273

 Score =  134 bits (337), Expect = 3e-36
 Identities = 72/194 (37%), Positives = 111/194 (57%), Gaps = 3/194 (1%)

Query: 16  GLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAILVDDADISGMSPK 75
           G    +++  L+I+ GEF+ L+GPSGCGKST +N +AG    + G + VD  +++G  P+
Sbjct: 27  GAHAAVEDFSLEIEPGEFVCLLGPSGCGKSTALNAVAGFLRPARGRVAVDGVEVTGPGPE 86

Query: 76  DRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLLQIEHLLSRKPGQ 135
                MVFQ ++L+P  +V +N+AFG +++    AE  +       L+ +     R P  
Sbjct: 87  R---GMVFQQHSLFPWKTVLENVAFGPRMQGKTRAEARDLAREYLDLVGLGGSAQRYPAA 143

Query: 136 LSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTHD 195
           LSGG  QRV + RAL   P + L DEP   LDA+ R  M+  +  +  ++  T ++VTHD
Sbjct: 144 LSGGMAQRVGIARALVNHPSVLLMDEPFGALDAQTRSIMQESLLRLWGQIGNTVLFVTHD 203

Query: 196 QIEAMTLGDKVAVM 209
             EA+ L D+V VM
Sbjct: 204 IDEALFLADRVVVM 217


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: 252
Number of extensions: 10
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: 273
Length adjustment: 28
Effective length of query: 358
Effective length of database: 245
Effective search space:    87710
Effective search space used:    87710
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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