GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gbuA in Pseudomonas putida KT2440

Align Guanidinobutyrase; GBase; EC 3.5.3.7; D-arginase; EC 3.5.3.10 (uncharacterized)
to candidate PP_2196 PP_2196 agmatinase

Query= curated2:Q8KZT5
         (353 letters)



>lcl|FitnessBrowser__Putida:PP_2196 PP_2196 agmatinase
          Length = 311

 Score =  237 bits (605), Expect = 3e-67
 Identities = 132/311 (42%), Positives = 182/311 (58%), Gaps = 16/311 (5%)

Query: 23  YAGAATYARLPRLDQVSKADVTVVGVPFDSGVSYRPGARFGANHVREAS-RLLRPYNPAW 81
           YAG  +++R      +   DV V GVPFD+  S RPGARFG   +R AS +     +  W
Sbjct: 15  YAGVVSFSRRRYSRDLRGVDVVVSGVPFDTATSNRPGARFGPRAIRAASVQQAWARHWPW 74

Query: 82  DVSPFENIQVADAGDMAVNPFNINEAIETIQQNALDLTANGSKLVTLGGDHTIALPLLRA 141
              PF+++ V D GD   +        ++I+ +A  +   G  ++TLGGDH I+ PLL+A
Sbjct: 75  AFDPFDHLAVIDYGDCPFDSGTPQSVPDSIEAHAEHILQAGCAMLTLGGDHFISYPLLKA 134

Query: 142 AAERAGEPIAMLHFDAHLDTWDTYFGAEYTHGTPFRRAVEEGILDTEAISHVGTRGPLYG 201
            A R G P+A++HFDAH DTW    G    HGT F  A  EG++D      +G R     
Sbjct: 135 HARRHG-PLALIHFDAHSDTWPDEAGKRIDHGTMFWHAAREGLVDPAHSVQIGLR----- 188

Query: 202 KKDLDDDHRFGFGIVTSADVYYQGVLETVAKIRDRIGNRPLYISVDIDVLDPAHAPGTGT 261
                +D   GF I+ +  V+ QG    +A IR R+G RP+Y++ DID LDPA+APGTGT
Sbjct: 189 ---TTNDDSQGFAILDARQVHRQGTEAVIAAIRQRVGERPVYLTFDIDCLDPAYAPGTGT 245

Query: 262 PEAGGITSRELLEIIRGFRGMNLVGADVVEVAPAYDHAEITGVAGSHVAYELVTLMADNA 321
           P  GG+++ + LEI+ G RG+NLVG D+VEVAPAYDHA+IT +AG+ +A E++ L A   
Sbjct: 246 PVCGGLSTVQALEILGGLRGINLVGMDLVEVAPAYDHADITALAGATLAMEMLCLYA--- 302

Query: 322 VEGDRHGAPNG 332
               RH   NG
Sbjct: 303 ---ARHKVDNG 310


Lambda     K      H
   0.318    0.137    0.402 

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: 387
Number of extensions: 29
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: 353
Length of database: 311
Length adjustment: 28
Effective length of query: 325
Effective length of database: 283
Effective search space:    91975
Effective search space used:    91975
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 (21.7 bits)
S2: 49 (23.5 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 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.

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