GapMind for Amino acid biosynthesis

 

Aligments for a candidate for argI in Pedobacter sp. GW460-11-11-14-LB5

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate CA265_RS14660 CA265_RS14660 aspartate carbamoyltransferase

Query= BRENDA::Q51742
         (315 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS14660 CA265_RS14660 aspartate
           carbamoyltransferase
          Length = 311

 Score =  116 bits (290), Expect = 8e-31
 Identities = 99/318 (31%), Positives = 159/318 (50%), Gaps = 31/318 (9%)

Query: 5   LAGRDLLCLQDYTAEEIWTILETAKMFKIWQKIGKPHRL---LEGKTLAMIFQKPSTRTR 61
           L+ R LL ++D    +I  I ETA  FK  + I +P +    L   T+A IF + STRT+
Sbjct: 8   LSTRHLLGIKDINRNDIELIFETADNFK--EVINRPIKKVPSLRDITIANIFFENSTRTK 65

Query: 62  VSFEVAMAHLGGHALYLNAQDLQLRRGETIADTAR-VLSRYVDAIMARVYDHKDVEDLAK 120
           +SFE+A   L    +   A    + +GET+ DT   +LS  VD ++ R       + L+K
Sbjct: 66  LSFELAEKRLSADVVNFAASSSSVSKGETLIDTVNNILSMKVDMVVMRHPYAGAGQFLSK 125

Query: 121 YATVPVIN-GLSDFSHPCQALADYMTIWEKKGTIKGVKVVYVGD--GNNVAHSLMIAGTK 177
           +    ++N G     HP QAL D  +I +K G + G KVV VGD   + VA S ++   +
Sbjct: 126 HVKAQIVNAGDGAHEHPTQALLDAFSIRQKLGDVAGKKVVIVGDILHSRVAISNILCLQR 185

Query: 178 LGADVVVATPEGYEPDEKVIKWAEQNAAESGGSFELLHDPVKAVKDADVIYTDVWASMGQ 237
           LGA+V+V  P    P         ++  + G   E  H+ +KA+      + DV   +  
Sbjct: 186 LGAEVMVCGPTTLIP---------KHIHQLGVKVE--HNLIKALN-----WCDVANMLRI 229

Query: 238 EAEAEE------RRKIFRPFQVNKDLVKHAKPDYMFMHCLPAHRGEEVTDDVIDSPNSVV 291
           + E ++       R+    + +NK ++ +   + + MH  P +RG E+T DV DS  S++
Sbjct: 230 QLERQDIKYFPSLREYAMMYGLNKQILDNLDKEIIVMHPGPINRGVEITSDVADSKQSII 289

Query: 292 WDQAENRLHAQKAVLALV 309
            +Q EN +  + AVL L+
Sbjct: 290 LEQVENGVAVRMAVLYLL 307


Lambda     K      H
   0.319    0.134    0.400 

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: 7
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: 315
Length of database: 311
Length adjustment: 27
Effective length of query: 288
Effective length of database: 284
Effective search space:    81792
Effective search space used:    81792
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: 48 (23.1 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 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, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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