GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PS417_11890 in Shewanella sp. ANA-3

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

Query= reanno::WCS417:GFF2332
         (517 letters)



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

 Score =  363 bits (933), Expect = e-105
 Identities = 194/492 (39%), Positives = 313/492 (63%), Gaps = 7/492 (1%)

Query: 23  LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82
           +LE+  ISK +PGV AL DV LR+  G V AL+GENGAGKSTL+K++ G    D G+I  
Sbjct: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63

Query: 83  RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142
            G+P  F TP+ AQKAGI+ ++QE+NL+P++++A+N+++G E    L +++ ++M+    
Sbjct: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEP-RRLGLIHFKKMYADAR 122

Query: 143 ELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSI 202
            +L + ++++D    + + SIA +Q++ IA+ V+  + +L++DEPT+++  KEV  LF I
Sbjct: 123 AVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGI 182

Query: 203 IADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELS 262
           +  LK++G  IV+ITH +++V+ I+D + V R+G +IG      +    LI  M+GR L 
Sbjct: 183 LNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQ 242

Query: 263 -QLFPLRE-----TPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAE 316
            QL   +E     T    +LL++ D+++ G  + ++  +  G+ +G+AGL+GSGR+ V  
Sbjct: 243 EQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCN 302

Query: 317 TIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVL 376
            +FG+    SG I L G+ + +S P  AI  G AL  EDRK+ G+   LS+ EN+ +A+ 
Sbjct: 303 AVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQ 362

Query: 377 PHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLL 436
                  ++     + + +    KL++ TP  ++ I+ LSGGNQQK +LARWL   P LL
Sbjct: 363 ARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILL 422

Query: 437 ILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTL 496
           +LDEPTRGID+GA AEI +LI  L  EGM++++ SSEL E++  S++V+V+ +   +  L
Sbjct: 423 VLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVREL 482

Query: 497 DRSEATQEKVMQ 508
             +E T + VMQ
Sbjct: 483 SGAELTSQHVMQ 494



 Score = 79.0 bits (193), Expect = 4e-19
 Identities = 58/228 (25%), Positives = 109/228 (47%), Gaps = 14/228 (6%)

Query: 289 KDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKG 348
           +DVS  L AGE+  + G  G+G++ + + + G      G I   G+    + P  A + G
Sbjct: 21  EDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFNTPMDAQKAG 80

Query: 349 FALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKAL----RALCEDMCKKLRVK 404
            + + ++     L P L+V +N+ +   P   G   I  K +    RA+       + V 
Sbjct: 81  ISTVYQE---VNLVPNLTVAQNLFLGYEPRRLG--LIHFKKMYADARAVLTQFKLDIDVS 135

Query: 405 TPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEG 464
            P  +  I       QQ   +AR +  + ++L+LDEPT  +D      ++ ++  L ++G
Sbjct: 136 APLSDYSIAV-----QQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLKAKG 190

Query: 465 MAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG 512
           +A++ I+  L +V  +SDR+ V+  G+ +G    +E  Q K+++   G
Sbjct: 191 VAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLG 238


Lambda     K      H
   0.320    0.136    0.381 

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: 533
Number of extensions: 25
Number of successful extensions: 7
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: 517
Length of database: 499
Length adjustment: 34
Effective length of query: 483
Effective length of database: 465
Effective search space:   224595
Effective search space used:   224595
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: 52 (24.6 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