GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08235 in Synechococcus elongatus PCC 7942

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate Synpcc7942_2495 Synpcc7942_2495 integral membrane protein of the ABC-type Nat permease for neutral amino acids NatD

Query= reanno::azobra:AZOBR_RS08235
         (301 letters)



>FitnessBrowser__SynE:Synpcc7942_2495
          Length = 313

 Score =  191 bits (485), Expect = 2e-53
 Identities = 117/317 (36%), Positives = 179/317 (56%), Gaps = 25/317 (7%)

Query: 4   FLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFV--ALI--TFLAIGS 59
           +LQ LINGL++G +Y L A+GYT+V+ I+G+INFAHG ++ +GA++  AL+   F   G 
Sbjct: 3   WLQPLINGLAIGGVYALFALGYTLVFSILGVINFAHGAVFTLGAYLTYALVGGRFSFNGL 62

Query: 60  LGITWVPLAL---LVMLVASMLFTAVYGWTVERIAYRPLR--SSPRLAPLISAIGMSIFL 114
           L    +P +L   L +L+ S+L        +E++A+RPLR   +  L  LIS++G+++F+
Sbjct: 63  LANAALPFSLPFALALLLGSLLAGGA-SLLIEQVAFRPLRRRQADPLLTLISSLGVAVFI 121

Query: 115 QNYVQILQGARSKPLQPILPG------NLTLMDGAVSVSYVRLATIVITIALMYGFTQLI 168
            N +QIL GA        + G      NL   D  + +  V++   V+ IA+    T LI
Sbjct: 122 VNLIQILVGAEIYTFPSNIYGDLPSAINLGSSDRPIQIRTVQIILFVVAIAMFSLLTWLI 181

Query: 169 TRTSLGRAQRACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIG 228
             T +G A +A  +D   A LLG++ DR I LTF +   L  +AG +V     +   Y G
Sbjct: 182 NGTRVGHALKAVAEDATTASLLGIDPDRYIRLTFFLSGVLGGLAGTLVGTSVSITGPYFG 241

Query: 229 FLAGVKAFTAAVLGGIGSLPGAMLGGVVIGLIEAF----WSGYMGSEWKDVATFTILVLV 284
              G+K  +  VLGG+G++PG + GG+++GL EA+    WSGY     +D   F +L  +
Sbjct: 242 IAYGLKGLSVMVLGGLGNIPGTIAGGLLLGLAEAWVPPQWSGY-----RDAVAFALLFAM 296

Query: 285 LIFRPTGLLGRPEIEKV 301
           L+ RP GL  R   EKV
Sbjct: 297 LLIRPQGLFSRARTEKV 313


Lambda     K      H
   0.329    0.144    0.425 

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: 327
Number of extensions: 16
Number of successful extensions: 6
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: 301
Length of database: 313
Length adjustment: 27
Effective length of query: 274
Effective length of database: 286
Effective search space:    78364
Effective search space used:    78364
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