GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuD in Herbaspirillum seropedicae SmR1

Align Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) (characterized)
to candidate HSERO_RS21960 HSERO_RS21960 glutamine amidotransferase

Query= reanno::pseudo6_N2E2:Pf6N2E2_4510
         (258 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS21960 HSERO_RS21960 glutamine
           amidotransferase
          Length = 378

 Score =  108 bits (271), Expect = 1e-28
 Identities = 72/183 (39%), Positives = 99/183 (54%), Gaps = 12/183 (6%)

Query: 54  DILDALDGILLTGSPSNVEPFHYQGPASAPGTAHDPARDATTLPLIRAAVDAGIPVLGIC 113
           D    LDG++L G  ++V P  Y   A+ P  + D  RD   L L+   ++AG PVLGIC
Sbjct: 187 DYAKHLDGLVLQGG-ADVSPQSYAQSATRPEWSGDRVRDMYELELLHEFIEAGKPVLGIC 245

Query: 114 RGFQEMNVAFGGSLHQKV-HEVGTFIDHREDDTQAVDVQY-GPAHAVHIQPGGVLAGLGL 171
           RG Q +NVAFGG+L+Q +  +V T I H       V+ QY    H +H   G  LA L  
Sbjct: 246 RGCQLINVAFGGTLYQDIATDVPTAIPH-------VNEQYDSNYHTLHFPQGSSLANLLK 298

Query: 172 PQRIEVNSIHSQGIERLAPGLRAEAVA-PDGLIEAVSVPGGKAFALGVQWHPEWEVSSNP 230
            +   VNSIH Q +  L   L  EAV+ PD ++EA+       F +G+QWHPE+  + +P
Sbjct: 299 AENAVVNSIHHQAVRDLGRDLSVEAVSGPDQIVEAIRYRKA-PFVMGLQWHPEFHRAGSP 357

Query: 231 HYL 233
             L
Sbjct: 358 ELL 360


Lambda     K      H
   0.319    0.136    0.413 

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: 291
Number of extensions: 14
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: 258
Length of database: 378
Length adjustment: 27
Effective length of query: 231
Effective length of database: 351
Effective search space:    81081
Effective search space used:    81081
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 (21.7 bits)
S2: 48 (23.1 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