Aligments for a candidate for gly1 in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Aligments for a candidate for gly1 in Phaeobacter inhibens BS107

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

Query= SwissProt::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 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 (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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for Amino acid biosynthesis