GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AGP1 in Klebsiella michiganensis M5al

Align general amino acid permease AGP1 (characterized)
to candidate BWI76_RS06025 BWI76_RS06025 amino acid transporter

Query= CharProtDB::CH_091105
         (633 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS06025 BWI76_RS06025 amino acid
           transporter
          Length = 468

 Score =  230 bits (587), Expect = 9e-65
 Identities = 139/450 (30%), Positives = 219/450 (48%), Gaps = 30/450 (6%)

Query: 109 TGHKSDSLKKTIQPRHVLMIALGTGIGTGLLVGNGTALVHAGPAGLLIGYAIMGSILYCI 168
           T  +   LK+T++ RH++M++LG  IGTGL    G  +   G AG L+ Y I   +++ +
Sbjct: 4   TQQQGGQLKRTMKTRHLIMLSLGGVIGTGLFFNTGYIISTTGAAGTLLAYLIGALVVWLV 63

Query: 169 IQACGEMALVYSNLTGGYNAYPSFLVDDGFGFAVAWVYCLQWLCVCPLELVTASMTIKYW 228
           +Q  GE+++     TG ++ Y +  +    G+ VAW+Y L W          A   ++YW
Sbjct: 64  MQCLGELSVAMPE-TGAFHVYAARYLGPATGYTVAWLYWLTWTVALGSSFTAAGFCMQYW 122

Query: 229 TTSVNPDVFVIIFYVLVITINIFGARGYAEAEFFFNCCKILMMTGFFILG------IIID 282
              V   V+ ++F  ++  +N+   R +AE EF+F+  K++ +  F ILG      II  
Sbjct: 123 FPQVPVWVWCVVFCAVIFALNVISTRFFAEGEFWFSLVKVITIIAFIILGGAAIFGIIPM 182

Query: 283 VGGAGNDGF--IGGKYWHDPGAFNGKHAIDRFKGVAATLVTAAFAFGGSEFIAITTAEQS 340
             G+   G   I  + W   G             +  T+V   FAF G+E I I   E  
Sbjct: 183 QDGSPAPGLRNITAEGWFPHGGLP----------ILMTMVAVNFAFSGTELIGIAAGETE 232

Query: 341 NPRKAIPGAAKQMIYRILFLFLATIILLGFLVPYNSDQLLGSTGGGTKASPYVIAVASHG 400
           NP K IP A +  I R++  F+ T+ +L  L+P            G + SP+V+     G
Sbjct: 233 NPHKVIPVAIRTTIARLIIFFIGTVFVLAALIPMQQ--------AGVEKSPFVLVFEKVG 284

Query: 401 VRVVPHFINAVILLSVLSMANSSFYSSARLFLTLSEQGYAPKVFSYIDRAGRPLIAMGVS 460
           +       N VIL ++LS ANS  Y+S R+  +LS +   P  F+ + R G PL A+ VS
Sbjct: 285 IPYAADIFNFVILTAILSAANSGLYASGRMLWSLSNENTLPACFTKLTRNGVPLTAISVS 344

Query: 461 ALFAVIAFCAASPKEEQVFTWLLAISGLSQLFTWTAICLSHLRFRRAMKVQGRSLGELGF 520
            L  V+A  ++    + VF  L AISG + +  W +IC SH  FRR    QG++L EL +
Sbjct: 345 MLGGVLALFSSVVAPDTVFVALSAISGFAVVAVWLSICASHFMFRRRHLQQGKALSELHY 404

Query: 521 KSQTGVWGSAYACIMMILILIAQFWVAIAP 550
           ++    W      +  +L L+A   +A  P
Sbjct: 405 RAP---WYPLVPALGFVLCLVACVGLAFDP 431


Lambda     K      H
   0.324    0.138    0.424 

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: 702
Number of extensions: 38
Number of successful extensions: 4
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: 633
Length of database: 468
Length adjustment: 35
Effective length of query: 598
Effective length of database: 433
Effective search space:   258934
Effective search space used:   258934
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 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