Alignments for a candidate for araG in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for araG in Shewanella sp. ANA-3

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate 7024900 Shewana3_2074 ABC transporter related (RefSeq)

Query= CharProtDB::CH_014279
         (504 letters)



>FitnessBrowser__ANA3:7024900
          Length = 499

 Score =  341 bits (875), Expect = 3e-98
 Identities = 183/480 (38%), Positives = 303/480 (63%), Gaps = 8/480 (1%)

Query: 8   LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67
           L  + I K +PGVKAL D+S   +AG+VHAL+GENGAGKSTL+K+++G  +   G ++  
Sbjct: 5   LELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFL 64

Query: 68  GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQ 127
           G+   F+    A  AG++ +YQE++LVP +TVA+N++LG  P + G+++   +  +A   
Sbjct: 65  GEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARAV 124

Query: 128 LKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIR 187
           L    +DID   PL   SI   Q++ IA+ +A +AK++  DEPT+SL A+E+  LF ++ 
Sbjct: 125 LTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILN 184

Query: 188 ELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIGD 247
           +L+ +G  I++++H +++++ +SD ITV ++G+++  +    ++    L++AM+GR + +
Sbjct: 185 QLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYL-TAELPQPKLIEAMLGRSLQE 243

Query: 248 -IYGWQPRSYGEER-----LRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKG 301
            +   Q +     R     L L+ V   G    ++L V  G+ VGL GL+G+GRSE+   
Sbjct: 244 QLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNA 303

Query: 302 MFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARR 361
           +FG   + +G +++  Q +++ +P  AI+AG+ LCPEDRK +GII   S+R+NI I A +
Sbjct: 304 VFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENI-ILALQ 362

Query: 362 KHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVI 421
             +     ++N  ++  A   I  L I TP A++ I  LSGGNQQK IL RWL+ E  ++
Sbjct: 363 ARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILL 422

Query: 422 LLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGEL 481
           +LDEPTRGID+GA  EI  +I  L  +G+++L ASS+L E++  ++++VV+R+     EL
Sbjct: 423 VLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVREL 482



 Score = 77.4 bits (189), Expect = 1e-18
 Identities = 64/237 (27%), Positives = 109/237 (45%), Gaps = 17/237 (7%)

Query: 269 PGVRT--PISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQITAGQVYIDQQPIDIRKPS 326
           PGV+    +SL + +GE+  L G  GAG+S L+K M G      G +    +P     P 
Sbjct: 15  PGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFNTPM 74

Query: 327 HAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHVLGGCVINNGWEENNADHHIRSL 386
            A  AG+    ++     ++P  +V  N+ +    +  LG       + +  A      L
Sbjct: 75  DAQKAGISTVYQE---VNLVPNLTVAQNLFLGYEPRR-LGLIHFKKMYADARAVLTQFKL 130

Query: 387 NIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALA 446
           +I        + + S   QQ   + R ++   KV++LDEPT  +D      ++ ++  L 
Sbjct: 131 DIDVSAP---LSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLK 187

Query: 447 AQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHEQADERQALSLAMPKVSQAV 503
           A+GVA++F +  L +V  ++DRI V+R G+  GE L           L  PK+ +A+
Sbjct: 188 AKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYL--------TAELPQPKLIEAM 236


Lambda     K      H
   0.319    0.136    0.391 

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: 596
Number of extensions: 26
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: 504
Length of database: 499
Length adjustment: 34
Effective length of query: 470
Effective length of database: 465
Effective search space:   218550
Effective search space used:   218550
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 (21.7 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 (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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources