GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c07320 in Paucidesulfovibrio gracilis DSM 16080

Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF717
         (261 letters)



>NCBI__GCF_900167125.1:WP_078716498.1
          Length = 514

 Score =  159 bits (402), Expect = 1e-43
 Identities = 86/250 (34%), Positives = 147/250 (58%), Gaps = 8/250 (3%)

Query: 6   PLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDIL 65
           PL+ ++G+ K FG V+A   +S++++PG    LLG+NGAGKST +  ++G ++P  G I 
Sbjct: 23  PLVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIA 82

Query: 66  FEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYAN 125
            +G+P+ F+  RDAI AGI  V+QH  ++  M+V+ N  +G E     G   L   +  N
Sbjct: 83  LDGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQE-----GSFFLNPKEMRN 137

Query: 126 RITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTA 185
           R+  E   + G+++  P   V  LS GE+Q V I + ++  ++VLI DEPT+ L  R+T 
Sbjct: 138 RV-QELSVRYGLDI-DPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETF 195

Query: 186 NVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAE-ELQDMM 244
           ++   + K+ +QG ++VFI+H +   LAV D   +L +G+  G     +++++ +L   M
Sbjct: 196 HLFEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRM 255

Query: 245 AGGQELATLE 254
            G + L  ++
Sbjct: 256 VGKEVLLEVD 265



 Score = 55.8 bits (133), Expect = 2e-12
 Identities = 57/240 (23%), Positives = 103/240 (42%), Gaps = 21/240 (8%)

Query: 21  IALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLH--FADP-- 76
           I L  ++ D+  GE   ++G  G G+   ++ + G+ KP    +   G+     +A P  
Sbjct: 284 IGLEDITFDLHQGEVVAVVGVAGNGQKALVEAICGLRKPPVDTMFIMGKRWRDFYAKPSW 343

Query: 77  RDAIA------AGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITME 130
           ++++A       G+AT      +  L+  +R  F         GP    D   A R T E
Sbjct: 344 KNSLAYIPEDRLGLATCRNLNLVDNLLLTTRQGFAR-------GPW--LDKKKAARDTTE 394

Query: 131 EMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLAT 190
            ++K  I           LSGG  Q   +AR ++   ++++ ++PT  L +  T  V   
Sbjct: 395 LIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRLIVAEQPTQGLDIAATEQVWNH 454

Query: 191 IDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGD-ISAEELQDMMAGGQE 249
           +   R+    ++ +T ++  AL + DR  V+ RG+ +      D      +  MMAG +E
Sbjct: 455 LLAAREM-AGILLVTGDLNEALQLADRVAVIYRGRFMDVFSVSDKQKVNRIGLMMAGVEE 513


Lambda     K      H
   0.321    0.137    0.395 

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: 299
Number of extensions: 13
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 261
Length of database: 514
Length adjustment: 29
Effective length of query: 232
Effective length of database: 485
Effective search space:   112520
Effective search space used:   112520
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 (21.9 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