GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PGA1_c07320 in Shewanella sp. ANA-3

Align Inositol transport system ATP-binding protein (characterized)
to candidate 7024900 Shewana3_2074 ABC transporter related (RefSeq)

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



>lcl|FitnessBrowser__ANA3:7024900 Shewana3_2074 ABC transporter
           related (RefSeq)
          Length = 499

 Score =  171 bits (432), Expect = 4e-47
 Identities = 94/240 (39%), Positives = 146/240 (60%), Gaps = 5/240 (2%)

Query: 7   LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILF 66
           ++ ++ I KH+  V AL  VS+ +F GE H LLG+NGAGKST +K M+G      GDILF
Sbjct: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63

Query: 67  EGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANR 126
            G+P HF  P DA  AGI+TV+Q + ++P ++V++N F+G EP R++G L  F   YA+ 
Sbjct: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEP-RRLG-LIHFKKMYADA 121

Query: 127 ITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTAN 186
             +    K+ I++  P   +   S   +Q +AIAR V   AKVL+LDEPT++L  ++   
Sbjct: 122 RAVLTQFKLDIDVSAP---LSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQV 178

Query: 187 VLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAG 246
           +   +++++ +GVA+VFITH +     + DR TVL  G+ +G     ++   +L + M G
Sbjct: 179 LFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLG 238



 Score = 68.9 bits (167), Expect = 2e-16
 Identities = 52/229 (22%), Positives = 106/229 (46%), Gaps = 5/229 (2%)

Query: 22  ALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLHFADPRDAIA 81
           ++  +++ V  G+   L G  G+G+S     + G+     G I   GQ L+ + P DAI+
Sbjct: 273 SIQSMNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAIS 332

Query: 82  AGIATVHQHL---AMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEMRKMGIN 138
           AGIA   +      +I  +S+  N  +  +   +IG  +   +     I    + K+ I 
Sbjct: 333 AGIALCPEDRKIDGIIGPLSIRENIILALQA--RIGWWRYLSNTRQQEIAQFFIDKLQIA 390

Query: 139 LRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQG 198
               D+ +  LSGG +Q V +AR +     +L+LDEPT  + +   A ++  I  +  +G
Sbjct: 391 TPDADKPIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEG 450

Query: 199 VAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAGG 247
           ++++  +  +   +A  ++  VL     +      +++++ +   +A G
Sbjct: 451 MSLLVASSELDELVAFSNKVVVLRDRYAVRELSGAELTSQHVMQAIAEG 499


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: 328
Number of extensions: 14
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: 499
Length adjustment: 29
Effective length of query: 232
Effective length of database: 470
Effective search space:   109040
Effective search space used:   109040
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 Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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