GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34240 in Alkalihalobacterium alkalinitrilicum DSM 22532

Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate WP_078430749.1 BK574_RS01735 ABC transporter permease

Query= uniprot:B2T9V8
         (351 letters)



>NCBI__GCF_002019605.1:WP_078430749.1
          Length = 321

 Score =  142 bits (357), Expect = 2e-38
 Identities = 90/305 (29%), Positives = 158/305 (51%), Gaps = 9/305 (2%)

Query: 43  LLPALALLIVIGAFISPSFLTKANLISVLGASAALALVVLAESLIVLTGKFDLSLESTVG 102
           ++  L ++I+       SF +  N I++    + L ++ L  +L++   +FDLS    +G
Sbjct: 22  IIAGLGIIIIFSILSPSSFASFDNFINITRQISFLVIIALGATLVMAVKEFDLS----IG 77

Query: 103 IAPAVGAMLVMPAASAGFGMQWPAAAGLLAIVVVGAVIGFINGFLVVRLRLNAFIVTLAM 162
              ++G +L    A++G     P    LL  ++VG V+GF NG +V + ++ +F+ TLAM
Sbjct: 78  AMASLGGVLSALLAASGT----PIIFCLLVPIIVGFVVGFFNGAIVTKFKVLSFVTTLAM 133

Query: 163 LIVLRGMLVGATKGGTLFD-MPTSFFALATTIVLGLPLSVWLAAAAFAIAAFMLRYHRLG 221
             V+ G+    T G T+F+ +P  F  L  + +  LP    +      I  +++    LG
Sbjct: 134 GTVIGGVTFWLTGGATVFENIPEGFKFLGQSKLAFLPTLSVIMFVLVIIFWYIMSQTSLG 193

Query: 222 RALYAIGGNPEAARAAGIRVERITWGVFVLGSILASVGGLIVTGYVGAINANQGNGMIFT 281
           R LYAIGGN +A+  +GI + R     F L  +LA+  G ++   +G+ +   G+G    
Sbjct: 194 RRLYAIGGNEKASEVSGINIARYKNIAFALCGMLAAFTGALLASRLGSAHPTGGDGFFLN 253

Query: 282 VFAAAVIGGISLDGGKGTMFGALTGVLLLGVVQNLLTLAQVPSFWIQAIYGAIILGSLMV 341
            +AA  +G   +  G   + G L G  ++G++ N LT+ +VPSF    I GAII+ +L+ 
Sbjct: 254 AYAAVFLGMTIVKNGVPNILGTLFGAAIIGIMANGLTILEVPSFIQNIITGAIIIIALIS 313

Query: 342 ARLAS 346
            ++ S
Sbjct: 314 QKIGS 318


Lambda     K      H
   0.326    0.140    0.397 

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: 282
Number of extensions: 17
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: 351
Length of database: 321
Length adjustment: 28
Effective length of query: 323
Effective length of database: 293
Effective search space:    94639
Effective search space used:    94639
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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