GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2396 in Pseudomonas fluorescens FW300-N2C3

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate AO356_05320 AO356_05320 leucine ABC transporter substrate-binding protein

Query= uniprot:A0A165KTD4
         (375 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_05320
          Length = 375

 Score =  199 bits (505), Expect = 1e-55
 Identities = 125/368 (33%), Positives = 191/368 (51%), Gaps = 9/368 (2%)

Query: 6   KLTVVAAIAAAAGVASAQ--EQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVT 63
           +++ + A    AGVAS       +KIG   P +G  A YG    +GA+MAIE++NA+G  
Sbjct: 7   QISKLFAAMVLAGVASHSFAADTIKIGIAGPKTGPVAQYGDMQFSGAKMAIEQINAKGGV 66

Query: 64  IGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPH 123
            G + +  E    DDA DPKQ  A A K+ +  V  VVGHL S +T PAS +Y D G+  
Sbjct: 67  DGKQLVAVEY---DDACDPKQAVAVANKVVNDGVKFVVGHLCSSSTQPASDIYEDEGVIM 123

Query: 124 VTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVAD 183
           +T AAT+P++T  GYK  FR I  D+A G     Y  D +K K VA++ D+  YG+G+A 
Sbjct: 124 ITPAATSPDITARGYKMIFRTIGLDSAQGPAAGNYIADHVKPKIVAVLHDKQQYGEGIAS 183

Query: 184 VFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQL 243
             KKT   KG+KV   +       DF +++  +K  N D ++YGG  P+ G +LRQ ++ 
Sbjct: 184 AVKKTLEGKGVKVAVFEGVNAGDKDFSSMIAKLKQANVDFVYYGGYHPELGLILRQSQEK 243

Query: 244 GMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQ 303
           G+   K+ G +G+    I+++   AK     +      S  + P   A    + AK  + 
Sbjct: 244 GL-KAKFMGPEGVGNDSISQI---AKESSEGLLVTLPKSFDQDPANVALADAFKAKKEDP 299

Query: 304 FQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAIT 363
              +   +Y A  +I DA+K A S D       +   +FK  T  ++F+  G++K+    
Sbjct: 300 SGPFVFPSYSAVTVIADAIKAAKSEDAGKVAEAIHAGTFKTPTGDLSFDAKGDLKDFKFV 359

Query: 364 LYVYKDGK 371
           +Y +  GK
Sbjct: 360 VYEWHFGK 367


Lambda     K      H
   0.315    0.131    0.375 

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: 405
Number of extensions: 18
Number of successful extensions: 3
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: 375
Length of database: 375
Length adjustment: 30
Effective length of query: 345
Effective length of database: 345
Effective search space:   119025
Effective search space used:   119025
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: 50 (23.9 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