GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davA in Marinobacter adhaerens HP15

Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate GFF2120 HP15_2074 carbon-nitrogen hydrolase family protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1170
         (264 letters)



>FitnessBrowser__Marino:GFF2120
          Length = 307

 Score =  103 bits (257), Expect = 4e-27
 Identities = 88/284 (30%), Positives = 133/284 (46%), Gaps = 36/284 (12%)

Query: 14  DVAGNLQRLQQLALEA--KGADLLVLPEMFLTGYNIGVDAVSV--LAEVYNGESAQQVAR 69
           D A +L   ++L  EA   GA+L++L E+  T Y    +  SV  LAE   G ++++++ 
Sbjct: 22  DKAASLATTEKLVREAVASGANLVILQELHATLYFCQTEETSVFELAEPIPGPTSKRLSD 81

Query: 70  IAKAAGIAILYGYPERTEDGQIYNAVQLIDSDGERVCNYRKTHLFGDLDH---------- 119
           +A+  GI ++    ER  +G  +N   + + DG     YRK H+  D             
Sbjct: 82  LARELGIVLVGSIFERRMNGVYHNTAVVFEKDGSLAGLYRKMHIPDDPGFYEKFYFTPGD 141

Query: 120 SMFSAGSDEFPIVELNGWKLGFLICYDLEFPENARRLALAGAELILVPTANMIPFDFVAD 179
           + F+ G   F  ++ +  +LG L+C+D  +PE AR +ALAGAE+++ PTA  I +D   D
Sbjct: 142 AQFNDGRSGFTPIDTSVGRLGVLVCWDQWYPEAARLMALAGAEILIYPTA--IGWDVTDD 199

Query: 180 -----------VTV-RARAFENQCYVAYANYCGHEGD-------IHYCGQSSIAAPDGSR 220
                      VTV R  A  N   V   N  G E D       I + G S I  P G  
Sbjct: 200 PDEQARQLDAWVTVQRGHAVANNLPVVAPNRVGTEPDPSGHSDGIRFWGNSFICGPQGEL 259

Query: 221 IAQA-GLDESLIVGELDRQLMVDSRAANRYLLDRRPELYGELNK 263
           +A+     E ++   LDR      R    YL DRR + YG++ K
Sbjct: 260 LARGDDSSECILAVTLDRSRSESVRRIWPYLRDRRIDAYGDILK 303


Lambda     K      H
   0.321    0.139    0.411 

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: 179
Number of extensions: 12
Number of successful extensions: 4
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: 307
Length adjustment: 26
Effective length of query: 238
Effective length of database: 281
Effective search space:    66878
Effective search space used:    66878
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 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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