GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Bb in Phaeacidiphilus oryzae TH49

Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= uniprot:Q6MNM2
         (347 letters)



>NCBI__GCF_000744815.1:WP_037573817.1
          Length = 369

 Score =  273 bits (698), Expect = 5e-78
 Identities = 149/321 (46%), Positives = 200/321 (62%), Gaps = 18/321 (5%)

Query: 1   MAKIQFSNIKKSFGSAD--VLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSG 58
           MA + +    + +   D   +  +DL+IA GEFLVLVGPSGCGKST LR LAGLE  ++G
Sbjct: 1   MATVTYDKATRIYPGGDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNG 60

Query: 59  TISIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEIS 118
            I I  + +  + P++RDIAMVFQ+YALYPHMTVA+NMGF LK+  +  AEI  +V E +
Sbjct: 61  AIRIGERDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAA 120

Query: 119 ELLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKR 178
           ++L +   LDRKPK LSGGQRQRVA+GRA+ R+  V L DEPLSNLDA LR   R +I  
Sbjct: 121 KILDLTEFLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAG 180

Query: 179 LHHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPE 238
           L      T +YVTHDQ+EA T+GDR+AVLKDG+++Q+ TP  +Y RP N F+A FIGSP 
Sbjct: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPA 240

Query: 239 MNFLEGAV-------------LEKIPWPEARKADQ---ILGIRPDAFALNQGPLGTQEVA 282
           MN +E  +             + +    EA  A      +G+RP+   +  G  G  E  
Sbjct: 241 MNLVEVPITDGGVKFGESVVQVSRDAVGEAANAGDKTVTVGVRPEHLDIVGGTEGGGEDK 300

Query: 283 LGDFQIDISENLGGQQMLHGT 303
                +++ E LG    ++G+
Sbjct: 301 GLAVTVNVVEELGADGYVYGS 321


Lambda     K      H
   0.318    0.136    0.383 

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: 342
Number of extensions: 13
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: 347
Length of database: 369
Length adjustment: 29
Effective length of query: 318
Effective length of database: 340
Effective search space:   108120
Effective search space used:   108120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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