GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglE' in Nocardiopsis gilva YIM 90087

Align Putative bacterial solute-binding protein 1 family (characterized, see rationale)
to candidate WP_017617377.1 CDO52_RS08520 carbohydrate ABC transporter substrate-binding protein

Query= uniprot:A8LLL6
         (452 letters)



>NCBI__GCF_002263495.1:WP_017617377.1
          Length = 452

 Score =  266 bits (679), Expect = 1e-75
 Identities = 157/435 (36%), Positives = 218/435 (50%), Gaps = 19/435 (4%)

Query: 18  MAGAGGHLAFTPGEGEFNWDSYQAFAEATDLSGQDLSIFGPWLAGEADAFSNLVAFFNEA 77
           ++G GG  A   G G       + FAE  D+ G  + I+      E +        F+E 
Sbjct: 30  LSGTGGTSAERGGAG------CEPFAEWADVEGGTVDIYASIRDEEGERMQRAWKNFSEC 83

Query: 78  TGANATYVGSDSLEQQIVIDAEAGSAPDLTVFPQPGLATTMAARGFLTPLPDGTDDWLRE 137
           TG N  Y GS   E Q+ +  + G+APD+  FPQPGL +     G   PLP+      +E
Sbjct: 84  TGINIRYEGSGEFEAQVQVKIDGGNAPDIAFFPQPGLLSRFVESGDALPLPESVAKRAQE 143

Query: 138 NYAAGQSWIDLGTYADGSGNDQLYGFFFNVNVKSLVWYIPENFEDFDYEVPETMEEFKAL 197
            Y   + W+    Y +  G  +LYG     NVKS VWY P  F +  YE P T ++   L
Sbjct: 144 GYP--EDWLQ---YVEHDG--KLYGTPLGANVKSFVWYSPGFFTENGYETPTTWDDLIKL 196

Query: 198 MDQMVEDGQTPLCVGLGSGGATGWPATDWVEDLMLRTQPPEVYDAWVSNEMPFDDPRVVA 257
            D M +DG  P C G+ SG ATGWP TDW+E++MLR   P+VYD W+ +E+PFDDP+V  
Sbjct: 197 SDAMADDGVKPWCAGIESGEATGWPVTDWLENVMLREHGPDVYDQWIDHEIPFDDPKVAT 256

Query: 258 AIEEYGSFTRNDDYVVGNANDTASVDFRES-PLGLFASPPACMMHRQASFIPAYFPEGTE 316
           A++  G   RN DYV G      S+    S   G+      C M+   SF  A +PEGTE
Sbjct: 257 ALDRVGDILRNPDYVNGGHGGVKSIATTSSQDGGIPILEDKCGMYLMGSFYAAQWPEGTE 316

Query: 317 LGEDADFFYF--PAFEEKDLGRPVLGAGTLFAITNENPAASAFIEFLKTPFAHEIMMAQD 374
           + ED D F F  P  +E ++G PVLG G   A  ++ P   A  E+L T         + 
Sbjct: 317 IAEDGDVFAFNLPTIDE-EIGTPVLGGGEFTAAFSDRPEVVAVQEYLATVDYANRRAQEG 375

Query: 375 GFLTPFKGANPAAYASDTLRGQGEILTNA-TTFRFDGSDLMPGGVGAGTFWTGMVDYSSG 433
            + +  K  +  A  +   R   E+L +  T FR+DG D MP  VG+GTFW  M ++ +G
Sbjct: 376 AWFSAHKELDLNALDNPNDRFAAELLRDPDTVFRWDGGDYMPAAVGSGTFWRAMTNWING 435

Query: 434 AKSAADVASEIQASW 448
           +    DV   ++ SW
Sbjct: 436 S-DTEDVLGYVEQSW 449


Lambda     K      H
   0.317    0.134    0.413 

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: 743
Number of extensions: 52
Number of successful extensions: 5
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: 452
Length of database: 452
Length adjustment: 33
Effective length of query: 419
Effective length of database: 419
Effective search space:   175561
Effective search space used:   175561
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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