GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Methanosarcina acetivorans C2A

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_011020381.1 MA_RS01715 ATP-binding cassette domain-containing protein

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



>NCBI__GCF_000007345.1:WP_011020381.1
          Length = 353

 Score =  182 bits (463), Expect = 1e-50
 Identities = 110/344 (31%), Positives = 188/344 (54%), Gaps = 13/344 (3%)

Query: 1   MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60
           M+ LE+R++    G      LK I+L+ + G+++ L+GPSG GKS L+  I G      G
Sbjct: 1   MSFLEVRDIYLDVGSF---ELKGIDLRAEKGDYVALIGPSGSGKSLLLETIIGFYGPRQG 57

Query: 61  AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120
           ++ ++  DI+  SP  R I++V+Q   L+P M + +NIA+ L+ +     +I+ EV +++
Sbjct: 58  SVFLEGRDITFFSPDKRQISIVYQDNMLFPHMDIFENIAYALRKKLKDKKQIELEVTQIA 117

Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
            +L I  LL RKP  LSGG++QR ++ R+L  RPK+ L DEP S LDA+ R ++R  +K 
Sbjct: 118 GVLGIRELLHRKPDTLSGGEKQRASLARSLVARPKLLLLDEPFSALDARTREKLREMLKK 177

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240
                 TT ++VTHD  +   L ++V V++ G + Q G P+ ++  P+  FVA F+G+  
Sbjct: 178 AIADYSTTVLHVTHDFEDVWALANRVVVIRKGEVMQVGDPESVFRRPSPDFVAEFLGT-- 235

Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANG--EA 298
            N +   ++  +G+L  +   G     + +   D       V + IRPE+IILA G  E+
Sbjct: 236 -NVLKGTVKALEGKLTVIDAEG-----MEIYSADPAEPGENVTVSIRPEEIILAGGTVES 289

Query: 299 NGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVG 342
           +   T++  V          +V V + ++++   + P     +G
Sbjct: 290 SARNTLKGRVSGIFKKEHLVVVEVKMGNSEIKAVVTPTSCEMLG 333


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: 317
Number of extensions: 11
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: 353
Length adjustment: 30
Effective length of query: 356
Effective length of database: 323
Effective search space:   114988
Effective search space used:   114988
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: 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