GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Synechococcus elongatus PCC 7942

Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate Synpcc7942_2495 Synpcc7942_2495 integral membrane protein of the ABC-type Nat permease for neutral amino acids NatD

Query= ecocyc::LIVH-MONOMER
         (308 letters)



>FitnessBrowser__SynE:Synpcc7942_2495
          Length = 313

 Score =  202 bits (515), Expect = 6e-57
 Identities = 118/313 (37%), Positives = 182/313 (58%), Gaps = 14/313 (4%)

Query: 8   FLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMG-- 65
           +LQ + NG+ +G  YAL A+GYT+V+ I+G+INFAHG V+ +G+Y+++ ++         
Sbjct: 3   WLQPLINGLAIGGVYALFALGYTLVFSILGVINFAHGAVFTLGAYLTYALVGGRFSFNGL 62

Query: 66  IDTGWLLVAAGFVGAIVIAS--AYGWS--IERVAYRPVRNSKR--LIALISAIGMSIFLQ 119
           +    L  +  F  A+++ S  A G S  IE+VA+RP+R  +   L+ LIS++G+++F+ 
Sbjct: 63  LANAALPFSLPFALALLLGSLLAGGASLLIEQVAFRPLRRRQADPLLTLISSLGVAVFIV 122

Query: 120 NYVSLTEGSRDVALPSLFNGQWV----VGHSENFSASITTMQAVIWIVTFLAMLALTIFI 175
           N + +  G+     PS   G       +G S+     I T+Q ++++V       LT  I
Sbjct: 123 NLIQILVGAEIYTFPSNIYGDLPSAINLGSSDR-PIQIRTVQIILFVVAIAMFSLLTWLI 181

Query: 176 RYSRMGRACRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIG 235
             +R+G A +A AED   ASLLGI+ DR I LTF +   +  +AG L+G    +  PY G
Sbjct: 182 NGTRVGHALKAVAEDATTASLLGIDPDRYIRLTFFLSGVLGGLAGTLVGTSVSITGPYFG 241

Query: 236 FMAGMKAFTAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVM 295
              G+K  +  VLGG+G+IPG + GGL+LG+AEA      S  Y+D V+FALL  +LL+ 
Sbjct: 242 IAYGLKGLSVMVLGGLGNIPGTIAGGLLLGLAEAWVPPQWS-GYRDAVAFALLFAMLLIR 300

Query: 296 PTGILGRPEVEKV 308
           P G+  R   EKV
Sbjct: 301 PQGLFSRARTEKV 313


Lambda     K      H
   0.328    0.141    0.410 

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: 274
Number of extensions: 13
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: 308
Length of database: 313
Length adjustment: 27
Effective length of query: 281
Effective length of database: 286
Effective search space:    80366
Effective search space used:    80366
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