GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Phaeacidiphilus oryzae TH49

Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein

Query= reanno::Smeli:SM_b21216
         (360 letters)



>NCBI__GCF_000744815.1:WP_037572389.1
          Length = 386

 Score =  226 bits (575), Expect = 1e-63
 Identities = 128/310 (41%), Positives = 183/310 (59%), Gaps = 10/310 (3%)

Query: 4   LEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIG 63
           L +  + K++G    + G+D+ +  G F  LLG+SGCGK+T L +I+GL  P+ G I +G
Sbjct: 19  LRLTGLTKKFGSFTAVDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIHLG 78

Query: 64  ERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLLQI 123
           ++ V    P  R +  VFQ+YAL+P+L +  N+ FGL  R +   +  K V D   L+++
Sbjct: 79  DQDVTDRKPYRRPVNTVFQNYALFPHLDIFENVAFGLRRRGIRSVK--KPVEDMLDLVEL 136

Query: 124 ENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQML 183
            +L  RKP+QLSGGQ+QR+A+ RAL+  PQV L DEPL  LD KLR +M+ ELKR+   +
Sbjct: 137 GHLARRKPTQLSGGQQQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQLEV 196

Query: 184 RTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMNILD 243
             T V+VTHDQ EAMT+A  IAVM  GRIEQL +P E+Y+ P T +VA F+G   +    
Sbjct: 197 GLTFVHVTHDQEEAMTMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLGQSNLIAGT 256

Query: 244 AE-MTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLA-----AGSEAQRLT 297
            E ++ + +++      L LPAA          V +G+RPE +R+A       S A  LT
Sbjct: 257 VESVSGDVVQVAAHGRSLALPAA--RCRTTSGPVILGVRPEKVRIAKTEAEVPSGANHLT 314

Query: 298 ASVEVVELTG 307
             V      G
Sbjct: 315 GKVTDASFIG 324


Lambda     K      H
   0.320    0.136    0.385 

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: 316
Number of extensions: 16
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: 360
Length of database: 386
Length adjustment: 30
Effective length of query: 330
Effective length of database: 356
Effective search space:   117480
Effective search space used:   117480
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