GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Methanospirillum lacunae Ki8-1

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_109969613.1 DK846_RS14130 acetylornithine transaminase

Query= BRENDA::P42588
         (459 letters)



>NCBI__GCF_003173355.1:WP_109969613.1
          Length = 384

 Score =  235 bits (600), Expect = 2e-66
 Identities = 154/389 (39%), Positives = 221/389 (56%), Gaps = 41/389 (10%)

Query: 71  GSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLA 130
           GS  T+ D  G++++D + G  + + GH +P VV A+  Q A+    S     P +  LA
Sbjct: 28  GSGCTVTDADGKQYLDLVAGIAVCSTGHCHPKVVKAIAEQAAELIHCSNLFYVPHQGALA 87

Query: 131 KTLAALT--PGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGAL 188
           K L  ++  PG  K +FF NSG E++E ALKLA+      G+  FIA  G FHG+++G+L
Sbjct: 88  KKLVEISGLPGNAK-AFFSNSGAEAMEGALKLARIRT---GRKEFIACEGGFHGRTMGSL 143

Query: 189 SATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVIL 248
           + T K   R+PFMPL P    VP+G+++A++ A+ E      + AAVILEPIQGEGGVI+
Sbjct: 144 ACTHKPAIREPFMPLQPFTSFVPYGDVQALKGAITE------ETAAVILEPIQGEGGVII 197

Query: 249 PPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMP 308
           PPPGYL  VR++CD  G L+I+DEVQ+GMGRTG  FA + E + PDI+ +AKA+  G  P
Sbjct: 198 PPPGYLKQVREICDAKGVLLIVDEVQSGMGRTGHWFAFQEEGIHPDIITMAKAMASG-FP 256

Query: 309 IGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLD 368
           +GA +A E     L      H +TF G P+ACAAALA+I+V + + LP +   KG+    
Sbjct: 257 MGAIVAREG----LEFGKSEHGSTFAGGPIACAAALASIDV-IGKVLP-EVAAKGERFRA 310

Query: 369 GFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAK---TI 425
               L           R KG+++ I   D+           ++   V G L N      +
Sbjct: 311 ALAHL---------NPRVKGLMIGITIGDH-------CADVQKECAVHGLLVNCAAHGNL 354

Query: 426 RIEPPLTLT---IEQCELVIKAARKALAA 451
           R+ PPLT+T   I++   +I AA    A+
Sbjct: 355 RLVPPLTITNAEIDKATGIINAAVSKFAS 383


Lambda     K      H
   0.320    0.135    0.393 

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: 448
Number of extensions: 26
Number of successful extensions: 5
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: 459
Length of database: 384
Length adjustment: 32
Effective length of query: 427
Effective length of database: 352
Effective search space:   150304
Effective search space used:   150304
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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 (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