GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Herbaspirillum seropedicae SmR1

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate HSERO_RS23725 HSERO_RS23725 peptidase M20

Query= curated2:Q5NM04
         (376 letters)



>FitnessBrowser__HerbieS:HSERO_RS23725
          Length = 414

 Score = 74.7 bits (182), Expect = 4e-18
 Identities = 98/403 (24%), Positives = 167/403 (41%), Gaps = 43/403 (10%)

Query: 6   DPVDLAARLIACKSVTPSDDGAMNIMADALKSAGF----TVHLLTKGQAPD---GPVTNL 58
           + V +  +LI   + TP  + A +  A A   AG+      H++   Q  D     +TNL
Sbjct: 20  EEVGVLQQLIRIPTDTPPGNNAPHADAVAELVAGWGWAAEKHVVPAQQVADYGMQSITNL 79

Query: 59  IAIR--GEGYPHLAYAGHSDVVPAGQGWSSDPFTPTIKDGYLVGRGAVDMKSSVAAFIAA 116
           I  R  G+G P LA   H DVVP G+GW+ DP+   I DG + GR A   KS  A+++ A
Sbjct: 80  IVRRPYGDGGPTLALNAHGDVVPPGEGWTHDPYGGEIADGRIYGRAAAVSKSDFASYLFA 139

Query: 117 ASRY----TEHKGTLSLLITGDEEGPATFGTPAIIEWLNEQSI-KPDYCLVGEPTSVERL 171
                      +G + L  T DEE    FG      WL EQ + +PDY L          
Sbjct: 140 TRALEAVGASLRGGVELHFTYDEE----FGGLLGPGWLLEQKLTRPDYVLAA------GF 189

Query: 172 GDTVKNGRRGSVNMWIEVEGIQGHVAYPDRACNPIPVLARIISDLESWV-----LDKGDQ 226
              V       +   I V G   H + P+   + +     I++ +   +     +     
Sbjct: 190 SYNVVTAHNACLQFEITVHGRATHGSMPETGHDALQAATAILNAIYGALPGLKEIRSAIP 249

Query: 227 WFQPSNLEVTSIECDNKATNVIPALAKAQLNIRFNALHKGAELVDSLKK----RVAAIDP 282
                 + V  I+     TNV+P     +++ R       +++   ++K     VA +  
Sbjct: 250 GITHPTMIVGRID-GGTNTNVVPGKVVLKMDRRMIPEEDPSQVEAGVRKLIEDAVAGLPG 308

Query: 283 -KARVKAAISGEAFVTEEG--VLTDTISAAIAKNTGITPSLSTSGGTSDARFLTKL-CPV 338
            +  ++  +   A     G   L +++     +  G T + + S   +DAR   +   PV
Sbjct: 309 IRVEIRRLLLARALRPLPGHEKLVESLLRNAREVMGETLTTNGSALYTDARLYGEQGIPV 368

Query: 339 VEFG-----LVNATMHKVDEKASVEDIRQLSRIDEDIIKSFLG 376
           V FG     L+ +   + DE  +++D+R+ +++   ++  FLG
Sbjct: 369 VLFGAGPRTLMESNAKQADENLALDDLRKATKVVALMLLDFLG 411


Lambda     K      H
   0.316    0.133    0.389 

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: 354
Number of extensions: 15
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 376
Length of database: 414
Length adjustment: 31
Effective length of query: 345
Effective length of database: 383
Effective search space:   132135
Effective search space used:   132135
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: 41 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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