GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21715 in Rhodobacter viridis JA737

Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate WP_110804905.1 C8J30_RS06530 amino acid ABC transporter permease

Query= reanno::pseudo5_N2C3_1:AO356_00475
         (220 letters)



>NCBI__GCF_003217355.1:WP_110804905.1
          Length = 262

 Score =  130 bits (326), Expect = 3e-35
 Identities = 78/220 (35%), Positives = 116/220 (52%), Gaps = 14/220 (6%)

Query: 14  FDTLLAGLGLGLSLALVSIAIGCVIGLAMAFALLSKHRVLRVLASVYVTVIRNTPILVLI 73
           F TL  G+G+ + + L + A   V+GL +A A LS+H + R LA  Y  VIR  PI+V++
Sbjct: 37  FATLSKGIGITVFVTLFAFAGALVLGLVLAVASLSRHLIWRQLARFYTEVIRGVPIIVML 96

Query: 74  LLIYFAL-------------PSLGIR-LDKLPSFVITLSLYAGAYLTEVFRGGLLSIHKG 119
           L + FAL             P   +R    L   V+ L L   A+L EVFR GLLS+ +G
Sbjct: 97  LYVAFALVPAVVAGWNALGLPEASVRDFPLLARAVLALILAYAAFLAEVFRAGLLSVERG 156

Query: 120 QREAGLAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARK 179
           Q EA  A+GL  W     +  P   R VLP L N+F+++ KD+SL + + V ++T   + 
Sbjct: 157 QIEAAKALGLNGWLRFRLIIFPQAFRTVLPPLGNDFVAMVKDSSLVSVLGVADITQLGKV 216

Query: 180 INVESYRVIETWLVTTALYVAACYLIAMVLRYFEQRLAIR 219
               ++R  ET+ V   +Y+A    +++ LR  E  L  R
Sbjct: 217 TAAGNFRYFETYNVVALIYLAMTVTLSLALRKLEAHLRKR 256


Lambda     K      H
   0.329    0.142    0.414 

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: 175
Number of extensions: 15
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: 220
Length of database: 262
Length adjustment: 23
Effective length of query: 197
Effective length of database: 239
Effective search space:    47083
Effective search space used:    47083
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: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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