GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00885 in Escherichia coli BW25113

Align ABC transporter permease (characterized, see rationale)
to candidate 17518 b3457 leucine/isoleucine/valine transporter subunit (NCBI)

Query= uniprot:A0A165KC95
         (309 letters)



>FitnessBrowser__Keio:17518
          Length = 308

 Score =  244 bits (624), Expect = 1e-69
 Identities = 135/305 (44%), Positives = 197/305 (64%), Gaps = 19/305 (6%)

Query: 5   LQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIG--MMQGAMP 62
           LQQ+ NG+ LGS YALIA+GYTMVYGII +INFAHGEV MIG+  S+  I   MM G   
Sbjct: 9   LQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGI-- 66

Query: 63  GAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMII 122
              GW+++    + A V+A+   + IE+VAYRP+R+S RL  LI+AIGMSI LQ    + 
Sbjct: 67  -DTGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLT 125

Query: 123 WKPNYKPYPTMLPSSPFEIG-----GAFITPTQILILGVTAVALASLVYLVNHTNLGRAM 177
                   P++  +  + +G      A IT  Q +I  VT +A+ +L   + ++ +GRA 
Sbjct: 126 EGSRDVALPSLF-NGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRAC 184

Query: 178 RATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFT 237
           RA AE+ ++ASL+G+  D VI+ TF+IGA +AA+AG++    YG     +GF+ G+KAFT
Sbjct: 185 RACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFT 244

Query: 238 AAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRP 297
           AAV GGIG++ GA++GG++LG+ EA+ S Y+ T         Y D+ +F +LI++L + P
Sbjct: 245 AAVLGGIGSIPGAMIGGLILGIAEALSSAYLST--------EYKDVVSFALLILVLLVMP 296

Query: 298 SGLLG 302
           +G+LG
Sbjct: 297 TGILG 301


Lambda     K      H
   0.327    0.142    0.419 

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: 248
Number of extensions: 10
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: 309
Length of database: 308
Length adjustment: 27
Effective length of query: 282
Effective length of database: 281
Effective search space:    79242
Effective search space used:    79242
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 (21.7 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