GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AGP1 in Escherichia coli BW25113

Align general amino acid permease AGP1 (characterized)
to candidate 14398 b0260 putative amino acid/amine transport protein (VIMSS)

Query= CharProtDB::CH_091105
         (633 letters)



>FitnessBrowser__Keio:14398
          Length = 467

 Score =  229 bits (583), Expect = 3e-64
 Identities = 139/446 (31%), Positives = 221/446 (49%), Gaps = 22/446 (4%)

Query: 109 TGHKSDSLKKTIQPRHVLMIALGTGIGTGLLVGNGTALVHAGPAGLLIGYAIMGSILYCI 168
           T  ++  LK+T++ RH++M++LG  IGTGL    G  +   G AG L+ Y I   +++ +
Sbjct: 3   TTQQNAPLKRTMKTRHLIMLSLGGVIGTGLFFNTGYIISTTGAAGTLLAYLIGALVVWLV 62

Query: 169 IQACGEMALVYSNLTGGYNAYPSFLVDDGFGFAVAWVYCLQWLCVCPLELVTASMTIKYW 228
           +Q  GE+++     TG ++ Y +  +    G+ VAW+Y L W          A   ++YW
Sbjct: 63  MQCLGELSVAMPE-TGAFHVYAARYLGPATGYTVAWLYWLTWTVALGSSFTAAGFCMQYW 121

Query: 229 TTSVNPDVFVIIFYVLVITINIFGARGYAEAEFFFNCCKILMMTGFFILGIIIDVGGAGN 288
              V   V+ ++F  ++  +N+   R +AE EF+F+  K++ +  F ILG      GA  
Sbjct: 122 FPQVPVWVWCVVFCAIIFGLNVISTRFFAEGEFWFSLVKVVTIIAFIILG------GAAI 175

Query: 289 DGFIGGKYWHDPGAFNGKHAIDRFKG----VAATLVTAAFAFGGSEFIAITTAEQSNPRK 344
            GFI  +        +   A   F      +  T+V   FAF G+E I I   E  NPRK
Sbjct: 176 FGFIPMQDGSPAPGLSNITAEGWFPHGGLPILMTMVAVNFAFSGTELIGIAAGETENPRK 235

Query: 345 AIPGAAKQMIYRILFLFLATIILLGFLVPYNSDQLLGSTGGGTKASPYVIAVASHGVRVV 404
            IP A +  I R++  F+ T+ +L  L+P            G + SP+V+     G+   
Sbjct: 236 VIPVAIRTTIARLIIFFIGTVFVLAALIPMQQV--------GVEKSPFVLVFEKVGIPYA 287

Query: 405 PHFINAVILLSVLSMANSSFYSSARLFLTLSEQGYAPKVFSYIDRAGRPLIAMGVSALFA 464
               N VIL ++LS ANS  Y+S R+  +LS +   P  F+ + + G PL A+ VS L  
Sbjct: 288 ADIFNFVILTAILSAANSGLYASGRMLWSLSNERTLPACFARVTKNGVPLTALSVSMLGG 347

Query: 465 VIAFCAASPKEEQVFTWLLAISGLSQLFTWTAICLSHLRFRRAMKVQGRSLGELGFKSQT 524
           V+A  ++    + VF  L AISG + +  W +IC SH  FRR    QG++L EL +++  
Sbjct: 348 VLALFSSVVAPDTVFVALSAISGFAVVAVWLSICASHFVFRRRHLQQGKALSELHYRAP- 406

Query: 525 GVWGSAYACIMMILILIAQFWVAIAP 550
             W      +  +L L+A   +A  P
Sbjct: 407 --WYPLVPVLGFVLCLVACVGLAFDP 430


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: 710
Number of extensions: 36
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: 467
Length adjustment: 35
Effective length of query: 598
Effective length of database: 432
Effective search space:   258336
Effective search space used:   258336
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 (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:

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. 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:

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:

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