GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Desulfoscipio geothermicus DSM 3669

Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate WP_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein

Query= TCDB::P31134
         (377 letters)



>NCBI__GCF_900115975.1:WP_092484009.1
          Length = 344

 Score =  195 bits (496), Expect = 1e-54
 Identities = 111/301 (36%), Positives = 178/301 (59%), Gaps = 11/301 (3%)

Query: 31  GQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIMLDGVDLSQVPPYL 90
           G+  + D++L + +GE F +LG +G GK+ +L  +AG  +P  G I     +L+ + P  
Sbjct: 12  GEFQLLDINLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRFKERNLATLAPEQ 71

Query: 91  RPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLVHMQEFAKRKPHQL 150
           R +  ++Q YALFPH+TV++NI FG +  KLPK  I S+++E++ ++ +     R P  L
Sbjct: 72  RKVGFVYQDYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVAMLGIGHLLNRHPSTL 131

Query: 151 SGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILERVGVTCVMVTHDQ 210
           SGG++QR ALAR+L   P++LLLDEP+ ALD + ++  Q E+  I + +  T + VTHD 
Sbjct: 132 SGGEQQRTALARALIISPEILLLDEPLSALDPRSKENFQEELKKIHQTLKTTTLHVTHDF 191

Query: 211 EEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVNVFEGVLKERQEDGLVL 270
            EAM +A +I +M++G+ +Q+G P+EI+  P   + A F+G  N+FEG    +  D  V 
Sbjct: 192 NEAMYLADKIGVMHQGQIIQVGTPQEIFYKPQNDFVASFVGIENIFEG----QVNDDKVS 247

Query: 271 DSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCEEPPANGCNFAV-GEVIHIAYLGDL 329
            +P       VD   +      V VA+ PE I L +EP     ++   G+V++I+  G L
Sbjct: 248 LAP------DVDIFVNTGKQGKVKVAVPPEDIALSKEPFDLCYHYQFNGKVLNISNQGAL 301

Query: 330 S 330
           S
Sbjct: 302 S 302


Lambda     K      H
   0.321    0.137    0.400 

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: 303
Number of extensions: 16
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: 377
Length of database: 344
Length adjustment: 29
Effective length of query: 348
Effective length of database: 315
Effective search space:   109620
Effective search space used:   109620
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: 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