GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natH in Methanospirillum lacunae Ki8-1

Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate WP_109969962.1 DK846_RS15735 amino acid ABC transporter permease

Query= uniprot:Q31RN9
         (396 letters)



>NCBI__GCF_003173355.1:WP_109969962.1
          Length = 225

 Score = 95.5 bits (236), Expect = 1e-24
 Identities = 67/214 (31%), Positives = 117/214 (54%), Gaps = 16/214 (7%)

Query: 187 DW-----SGLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLPLVT 241
           DW     SG+ +T+    ++++  + LG+ +ALG+      IR +   Y+  FRGLP++ 
Sbjct: 9   DWFPYLLSGIFITVGLVAVALLIGIILGLPMALGQVYGKHLIRSVISIYVWFFRGLPVLV 68

Query: 242 ILF---FGQVMVPLMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAA 298
           +LF   FG +   L LD    +   +   V L +  +AY ++  RG +Q+I +GQ  AA 
Sbjct: 69  LLFLFYFG-IFPGLGLD----LPAFVVGAVVLGLRGAAYQSQIFRGAIQSIAEGQMTAAR 123

Query: 299 ALGLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILANPA 358
           +LG++  Q  R I+LPQA+RI++P     +  +L ++++   +G+ ELL  S  I++   
Sbjct: 124 SLGMSRAQAIRSIILPQAMRIALPGWSNEYPEILTESSICYAIGVAELLTRSSQIVSQ-T 182

Query: 359 YLGRYAEVYLFLGVLYWLCCYGLAQLSRRLEQRL 392
           Y+     +YL   V++ L  Y    L +RLE+R+
Sbjct: 183 YV--TMPIYLACAVMFILLSYAGTHLIQRLEKRI 214


Lambda     K      H
   0.329    0.142    0.471 

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: 205
Number of extensions: 12
Number of successful extensions: 3
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: 396
Length of database: 225
Length adjustment: 26
Effective length of query: 370
Effective length of database: 199
Effective search space:    73630
Effective search space used:    73630
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 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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