GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglF' in Dyella japonica UNC79MFTsu3.2

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate N515DRAFT_3134 N515DRAFT_3134 multiple sugar transport system permease protein

Query= uniprot:A8LLL5
         (334 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3134
          Length = 292

 Score =  129 bits (324), Expect = 9e-35
 Identities = 93/285 (32%), Positives = 150/285 (52%), Gaps = 24/285 (8%)

Query: 54  WIFLFPALFVLLLYLGYPVVETLRLSLLER-----VPGGGYQWVGLDNYAQMASEPKFWE 108
           W+FL PAL VL L+   PV+  L LSL +            ++V L NY ++   P FW 
Sbjct: 8   WLFLAPALLVLGLFFLLPVIAALALSLTDYDLYALADIRDLRFVALGNYWELLHRPLFWS 67

Query: 109 AMRNNMFWLIVVPALSTAFGLLAAQLTDR--IKWGNVAKSIIFMPMAISFVGASVIWKLV 166
           A+ + +++++V   LS    L AA L +    +   + ++ +F P+  + V  +VIW+ +
Sbjct: 68  ALGHTLYFVLVGVPLSIVASLGAALLLNSPLARCKPLFRTALFAPVVTTVVAVAVIWRYL 127

Query: 167 YDGRPIEQEQIGILNAIIVGLGGDPVTFLTIPFWNNFFLMIVLVWVQTGFAMVILSAALR 226
           ++ +       G+ N  + GLG  PV +L  P W    +++  VW   G+ M+I  AAL+
Sbjct: 128 FNTK------YGLANYALGGLGIHPVDWLGDPRWAMPTIILFAVWKNFGYNMIIFLAALQ 181

Query: 227 GIPEETIEAAIIDGASPLQIFFKIKVPQIMPTVVVVWTTITLVVLKVFDIVFAMTNG--- 283
            IP +  EAA IDGASPL+ F  I +P + PT+++V         ++F   F MT G   
Sbjct: 182 AIPADLYEAARIDGASPLRQFRHITLPMLGPTLLMVGILTVSGYFQLFAEPFVMTEGGPL 241

Query: 284 QWETQVLANYMFDKLFRANDWGVGSASAM-----VIMLLVTPILI 323
           Q  T VL   M+++ F+   W +GSASA+     +IM  VT +++
Sbjct: 242 QSTTSVL-YLMYEEGFKW--WNLGSASAVAFLLFLIMFAVTAVML 283


Lambda     K      H
   0.329    0.143    0.455 

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: 262
Number of extensions: 15
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: 334
Length of database: 292
Length adjustment: 27
Effective length of query: 307
Effective length of database: 265
Effective search space:    81355
Effective search space used:    81355
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 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