GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davA in Pseudomonas simiae WCS417

Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate GFF2084 PS417_10630 hydratase

Query= reanno::pseudo6_N2E2:Pf6N2E2_4777
         (264 letters)



>FitnessBrowser__WCS417:GFF2084
          Length = 295

 Score = 86.3 bits (212), Expect = 7e-22
 Identities = 89/283 (31%), Positives = 140/283 (49%), Gaps = 30/283 (10%)

Query: 2   RVALYQCPPLP--LDPAGNLHRLHQVALEAR--GADVLVLPEMFMTGYNIGV--DAVNVL 55
           RVA+ Q  P     + + NLH+   +A EA   GA+++VLPE+   GY      DA +  
Sbjct: 9   RVAVIQLDPQVGMNNRSSNLHQSLALATEAANGGANLIVLPELTNCGYFFSSRQDAFDHA 68

Query: 56  AEVYNGEWAQQIARIAKAAGLAIVYGYPERGEDG-QIYNAVQLIDAQGERLANYRKSHLF 114
             +  GE  +     A    + +V G  E   DG Q++N   L+   G  +  YRK+HL+
Sbjct: 69  ELIPGGESVRAWIDFACKHQVYLVTGLCEI--DGMQLFNTAVLLGPDGF-IGKYRKAHLW 125

Query: 115 GDLDHAMFSAGDAALPIVELNGWKLGLLICYDLEFPENARRLALAGAELI--------LV 166
            +L+   F+ GD   P+ E    ++GLLIC+D+ FPE  R L+  GA++I          
Sbjct: 126 -NLEKLWFTPGDTGFPVFETPIGRIGLLICWDIWFPEVPRILSQQGADIICSLNNWVWTP 184

Query: 167 PTANMQPYEFIADVTVRARAIENQCFVAYANYCGHEGELQYCGQSSIAAPNG-SRPALAG 225
           P    +  + +A       A  N  F+A A+  G E E +Y G S IA  NG    A+A 
Sbjct: 185 PPLFDEAGKCMASYLTMTAAHVNNVFIAAASRIGEEREARYLGCSLIAGTNGWPIGAVAS 244

Query: 226 LD-EALIVAELDRQLMDDSRAA--YNYLH----DRRPELYDDL 261
            + + ++ A++D   +  +R+A  +N L+    DRR +LYD +
Sbjct: 245 ANRQEILFADVD---ITSARSAPIWNSLNDLQRDRRIDLYDQM 284


Lambda     K      H
   0.321    0.139    0.419 

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: 194
Number of extensions: 12
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: 264
Length of database: 295
Length adjustment: 26
Effective length of query: 238
Effective length of database: 269
Effective search space:    64022
Effective search space used:    64022
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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