GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00885 in Methylocystis bryophila S285

Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate WP_085773505.1 B1812_RS04375 branched-chain amino acid ABC transporter permease

Query= uniprot:D8IUY4
         (309 letters)



>NCBI__GCF_002117405.1:WP_085773505.1
          Length = 299

 Score =  159 bits (402), Expect = 8e-44
 Identities = 94/306 (30%), Positives = 164/306 (53%), Gaps = 16/306 (5%)

Query: 4   FIQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQVAPG 63
           F++ +I GL+ G MY+L+A+G+ ++Y    ++NFA G  ++  A+  +SLL    +    
Sbjct: 10  FVEVLIGGLLSGVMYSLVAMGFVLIYKTSGVLNFAQGSQILFAALTFVSLL----ERGYN 65

Query: 64  LPGIVQLVIAIVGAIPVCIVVSLLIERIAYRPLRNAPRLAPLITAIGVSILLQTLAMMIW 123
           LP    + IA +      +V+ LLIERI  RPL N P +   +  +G+S +++  A + W
Sbjct: 66  LPTTFAITIAAM------VVLGLLIERIVLRPLVNRPPITLFMATLGLSYVIEGAAQLAW 119

Query: 124 GRSPLPFPQVMPSDPVHIAGALISPTQIMLLALAVLAMVGLVLIVEKTKMGRAMRATAEN 183
           G         +   P+ ++G  +S   ++  A+A L +V   L    T++G A RA AE+
Sbjct: 120 GAQVHGLDLGIDDRPLDVSGIFVSRFDLLAAAIAGLMVVMFSLFFRFTRIGLAFRAVAED 179

Query: 184 PRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGLKAFSAAVLGG 243
           P  A  +G+  +++  + +     +A +AG++W A     QF++  V  LKA    VLGG
Sbjct: 180 PIAAMSVGLRLSRIWAMVWTASGLVALVAGLIWGARLG-VQFSLSLVV-LKALPVLVLGG 237

Query: 244 IGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVLTLRPSGIMGE 303
             +I G ++ G+L+G  E L   YIG+    + G   +  FA++  +  L ++PSG+ G+
Sbjct: 238 FDSIAGVIVAGLLIGATEKLSEVYIGE----YFGGGIESWFAYVAALAFLLVQPSGLFGQ 293

Query: 304 RVADRA 309
           R  +RA
Sbjct: 294 RPVERA 299


Lambda     K      H
   0.328    0.144    0.416 

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: 231
Number of extensions: 10
Number of successful extensions: 5
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: 309
Length of database: 299
Length adjustment: 27
Effective length of query: 282
Effective length of database: 272
Effective search space:    76704
Effective search space used:    76704
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 (21.7 bits)
S2: 48 (23.1 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