GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ltaE in Phaeobacter inhibens BS107

Align Serine hydroxymethyltransferase; SHMT; Serine methylase; EC 2.1.2.1; L-threonine/L-allo-threonine aldolase; EC 4.1.2.48 (uncharacterized)
to candidate GFF1172 PGA1_c11870 serine hydroxymethyltransferase GlyA

Query= curated2:D3DKC4
         (427 letters)



>FitnessBrowser__Phaeo:GFF1172
          Length = 432

 Score =  501 bits (1289), Expect = e-146
 Identities = 251/415 (60%), Positives = 316/415 (76%), Gaps = 7/415 (1%)

Query: 4   LFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGG 63
           L   D E++ +I  E  RQ   +ELIASEN  S AVMEAQG+V+TNKYAEG P +RYYGG
Sbjct: 16  LAERDPELFGSITDELGRQRDEIELIASENIVSAAVMEAQGTVLTNKYAEGYPGRRYYGG 75

Query: 64  CEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHL 123
           C++VD+AE+LAI+RAK LFD E ANVQP+SG+QAN  V+ A++KPGDTI+GMDL+ GGHL
Sbjct: 76  CQYVDVAENLAIDRAKKLFDCEFANVQPNSGSQANQGVFQALIKPGDTILGMDLASGGHL 135

Query: 124 THGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKL 183
           THGA+ N SGK +NAV+YGV  E  LIDYDQ+  LA EH+PKLI+ G SA PRVID+A+ 
Sbjct: 136 THGARPNQSGKWFNAVHYGVREEDCLIDYDQIEALAVEHQPKLIIAGGSAIPRVIDFARF 195

Query: 184 REIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCK-KEF 242
           REIAD VGAYL VDMAH+AGL+A G +P+P P+AH  T+TTHKTLRGPR G IL    + 
Sbjct: 196 REIADKVGAYLHVDMAHFAGLVAAGEHPSPFPHAHVATTTTHKTLRGPRGGMILTNDADI 255

Query: 243 AKDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFK 302
           AK ++ ++FPGIQGGPLMHVIAAKAVAF EA+  EFK+Y +QV ANA  L+++ IK G  
Sbjct: 256 AKKVNSAIFPGIQGGPLMHVIAAKAVAFGEALRPEFKDYQKQVRANAVALSDQLIKGGLD 315

Query: 303 VVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPA 362
           +V+GGTD+H++L+DLR  G+TG  V++ALG+A+IT NKN +PFDP  P  TSGIRLGTPA
Sbjct: 316 IVTGGTDTHVMLVDLRPKGVTGNIVDKALGRAHITTNKNGIPFDPEKPTVTSGIRLGTPA 375

Query: 363 MTTRGMKEDQMRIIARLISKVIKNI------GDEKVIEYVRQEVIEMCEQFPLYP 411
            TTRG  E + R IA LI +V+  +      G+  V   VR++V  +C +FPLYP
Sbjct: 376 GTTRGFGEAEFREIADLIIEVVDGLAANGEDGNATVEASVREKVAALCARFPLYP 430


Lambda     K      H
   0.319    0.136    0.395 

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: 613
Number of extensions: 22
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: 427
Length of database: 432
Length adjustment: 32
Effective length of query: 395
Effective length of database: 400
Effective search space:   158000
Effective search space used:   158000
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: 51 (24.3 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 (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