GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21219 in Phaeobacter inhibens BS107

Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate GFF1303 PGA1_c13190 ABC transporter permease protein

Query= reanno::Smeli:SM_b21219
         (281 letters)



>FitnessBrowser__Phaeo:GFF1303
          Length = 276

 Score =  140 bits (353), Expect = 3e-38
 Identities = 91/270 (33%), Positives = 148/270 (54%), Gaps = 11/270 (4%)

Query: 14  ASALLLAVVILAPVAWLLIMSISPAADLSAKPLAWWPSDIDLSRYRTLLSAVENSAGAAF 73
           A A  + ++I  P+ W ++ S    A   + P  +   D  L  Y    S V+  +   +
Sbjct: 15  ALAWAVGLLIFFPILWTILTSFKTEAQAISDPPVFLFFDWTLENY----SVVQERSD--Y 68

Query: 74  IASLLNSIKVAGMATLAAVVVAVPAAWAVSRTPAVAWS--LYAVIATYMLPPVALAVPLY 131
           +  L NS+ +AG +T+  +++AVPAAW+++  P+      L  +++T MLP V +  P+Y
Sbjct: 69  MRFLWNSVIIAGGSTILGIIIAVPAAWSMAFVPSKRTKDILLWMLSTKMLPAVGVLYPIY 128

Query: 132 MGLAYFGLLNSVFGLALVYLTILAPFTTWLLKSGFDSIPREIESAAMIDGARL-DQILRI 190
           +     GLL++ FGL +V + I  P   W+L + F  IP EI  AA +DGA L ++IL +
Sbjct: 129 ILFIKMGLLDNRFGLVVVLMLINLPIIVWMLYTYFKEIPGEILEAARMDGATLKEEILYV 188

Query: 191 LTLPLAAPVMATSALFAFLLAWDEFFYALLFTSDQRAKTLTVAIADLAGGRVSDYGLIAT 250
           LT P+A P +A++ L   +LAW+E F+ L  T+  +A  LT  IA  +      Y  ++ 
Sbjct: 189 LT-PMAIPGIASTLLLNIILAWNEAFWTLNLTA-AKAAPLTAFIASYSSPEGLFYAKLSA 246

Query: 251 AGVLAALPPVLIGLIMQRALISGLTSGGVK 280
           A  +A  P +++G   Q+ L+SGLT G VK
Sbjct: 247 ASTMAIAPILILGWFSQKQLVSGLTFGAVK 276


Lambda     K      H
   0.325    0.136    0.402 

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: 222
Number of extensions: 13
Number of successful extensions: 2
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: 281
Length of database: 276
Length adjustment: 25
Effective length of query: 256
Effective length of database: 251
Effective search space:    64256
Effective search space used:    64256
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 47 (22.7 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