GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Pf6N2E2_5402 in Pseudomonas stutzeri RCH2

Align ABC transporter for D-Alanine, periplasmic substrate-binding component (characterized)
to candidate GFF3104 Psest_3163 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain

Query= reanno::pseudo6_N2E2:Pf6N2E2_5402
         (343 letters)



>lcl|FitnessBrowser__psRCH2:GFF3104 Psest_3163 ABC-type amino acid
           transport/signal transduction systems, periplasmic
           component/domain
          Length = 342

 Score =  548 bits (1413), Expect = e-161
 Identities = 271/340 (79%), Positives = 302/340 (88%), Gaps = 1/340 (0%)

Query: 4   LKSTLAVMTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVGIDA 63
           +KSTLAV+ AA++LG+SG AQAGATLDAVQKKGFVQCG+SDGLPGFS  D+ GK  GID 
Sbjct: 4   VKSTLAVLGAASLLGISGLAQAGATLDAVQKKGFVQCGISDGLPGFSFADAKGKYQGIDV 63

Query: 64  DFCRAVAAAVFGDATKVKFSQLNAKERFTALQSGEIDMLSRNSTMTSSRDAGMGLKFPGF 123
           D CRAVAAAVFGDA+KVK+S L AKERFTALQSGE+D+LSRN+T TSSRDA MGL F G 
Sbjct: 64  DICRAVAAAVFGDASKVKYSPLTAKERFTALQSGEVDVLSRNTTWTSSRDAAMGLNFTG- 122

Query: 124 ITYYDGIGFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITFDTSD 183
           +TYYDG GFL N +LGV SAKELDGAT+CIQAGTTTELN+SDYFRANG KYTPIT+DTSD
Sbjct: 123 VTYYDGQGFLVNKELGVSSAKELDGATVCIQAGTTTELNLSDYFRANGHKYTPITYDTSD 182

Query: 184 ESAKSLESGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDDEWLAI 243
           ESAKSLESGRCDVLTSD+SQL+AQR KLA P DYVVLPE ISKEPLGP VR GD+EW  I
Sbjct: 183 ESAKSLESGRCDVLTSDQSQLYAQRIKLAKPADYVVLPEVISKEPLGPAVRQGDEEWFDI 242

Query: 244 VRWTGYALLNAEEAGVTSKNVEAEAKSTKNPDVARMLGADGEYGKDLKLPKDWVVQIVKQ 303
           VRWT +A+LNAEE GVTS NVE  AKSTKNPDVAR+LGA+GEYGKDLKLPKDW VQIVKQ
Sbjct: 243 VRWTLFAMLNAEELGVTSANVEEMAKSTKNPDVARLLGAEGEYGKDLKLPKDWAVQIVKQ 302

Query: 304 VGNYGEMFERNLGKGTPLEIDRGLNALWNAGGIQYAPPVR 343
           VGNYGE+F+RN+G G+ L+I+RGLNALWN GG+QYAPPVR
Sbjct: 303 VGNYGEIFDRNVGAGSELKIERGLNALWNNGGLQYAPPVR 342


Lambda     K      H
   0.315    0.133    0.383 

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: 506
Number of extensions: 19
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: 343
Length of database: 342
Length adjustment: 29
Effective length of query: 314
Effective length of database: 313
Effective search space:    98282
Effective search space used:    98282
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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