GapMind for catabolism of small carbon sources

 

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

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate 7024900 Shewana3_2074 ABC transporter related (RefSeq)

Query= uniprot:A0A0C4Y5F6
         (540 letters)



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

 Score =  335 bits (858), Expect = 3e-96
 Identities = 199/508 (39%), Positives = 301/508 (59%), Gaps = 17/508 (3%)

Query: 13  LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72
           +L L+ I K +PGV+AL  V L  +AGEVHAL+GENGAGKSTL+K+++GA + D G    
Sbjct: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63

Query: 73  IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACA 132
           + G+    + P  A+  G++ +YQE++L PNL+VA+N++LG   +R GL+    M     
Sbjct: 64  L-GEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADAR 122

Query: 133 PTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFAL 192
             L +   D   +A ++  SIA +QL+ IAR V   A++LV+DEPT  L   E   LF +
Sbjct: 123 AVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGI 182

Query: 193 IRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDLS 252
           + QL+ +G+AI++I+H + ++ +++DR+TVLR+G F+G    A L Q  L++ M+GR L 
Sbjct: 183 LNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQ 242

Query: 253 ----GFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELAR 308
                   K         V+LS+ DV+    ++  +  +  G+ +GLAGL+G+GR+E+  
Sbjct: 243 EQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCN 302

Query: 309 LVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHE 368
            VFG D    G + +A          L    P  AI AGIA   EDRK+ G+    S+ E
Sbjct: 303 AVFGLDLVDSGSIHLAGQ-------KLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRE 355

Query: 369 NINLIVAARDALGLGR-LNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSR 427
           NI L + AR  +G  R L+ T  +      ID L I    A   +  LSGGNQQKV+L+R
Sbjct: 356 NIILALQAR--IGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILAR 413

Query: 428 LLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVM 487
            L I+P +L+LDEPTRG+DIGA +EI +LI  L   G+++L+ SSEL E+V   ++V+V+
Sbjct: 414 WLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVL 473

Query: 488 REGTLAGEVRPAGSAAETQERIIALATG 515
           R+     E+  +G+   +Q  + A+A G
Sbjct: 474 RDRYAVREL--SGAELTSQHVMQAIAEG 499


Lambda     K      H
   0.320    0.136    0.382 

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: 551
Number of extensions: 30
Number of successful extensions: 9
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: 540
Length of database: 499
Length adjustment: 35
Effective length of query: 505
Effective length of database: 464
Effective search space:   234320
Effective search space used:   234320
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