GapMind for Amino acid biosynthesis

 

Alignments for a candidate for glyA in Phaeobacter inhibens BS107

Align Serine hydroxymethyltransferase 2; SHMT 2; Serine methylase 2; EC 2.1.2.1 (characterized)
to candidate GFF1172 PGA1_c11870 serine hydroxymethyltransferase GlyA

Query= SwissProt::Q3JGP5
         (424 letters)



>FitnessBrowser__Phaeo:GFF1172
          Length = 432

 Score =  575 bits (1481), Expect = e-168
 Identities = 285/419 (68%), Positives = 337/419 (80%), Gaps = 1/419 (0%)

Query: 7   FFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEGYPGK 66
           FF+QSLAERD  + G+I  EL RQ+ ++ELIASENIVS AV++AQG+VLTNKYAEGYPG+
Sbjct: 11  FFTQSLAERDPELFGSITDELGRQRDEIELIASENIVSAAVMEAQGTVLTNKYAEGYPGR 70

Query: 67  RYYGGCEFADEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTVLGMSLD 126
           RYYGGC++ D  E LAI+R K+LF+   ANVQP+SG+QAN  V  AL KPGDT+LGM L 
Sbjct: 71  RYYGGCQYVDVAENLAIDRAKKLFDCEFANVQPNSGSQANQGVFQALIKPGDTILGMDLA 130

Query: 127 AGGHLTHGAKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFSAYPRKL 186
           +GGHLTHGA+P  SGKWFNA+ YGV  +  LIDYDQ+EALA +H+P LIIAG SA PR +
Sbjct: 131 SGGHLTHGARPNQSGKWFNAVHYGVREEDCLIDYDQIEALAVEHQPKLIIAGGSAIPRVI 190

Query: 187 DFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRGGFVLT 246
           DFARFR IAD VGA L VDMAH AG++AAG H +P  HAHV T+TTHKTLRGPRGG +LT
Sbjct: 191 DFARFREIADKVGAYLHVDMAHFAGLVAAGEHPSPFPHAHVATTTTHKTLRGPRGGMILT 250

Query: 247 NDEEIAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQALGDVLK 306
           ND +IAKK+NSA+FPG+QGGPLMHVIA KAVAFGEAL  +FK Y  +V ANA AL D L 
Sbjct: 251 NDADIAKKVNSAIFPGIQGGPLMHVIAAKAVAFGEALRPEFKDYQKQVRANAVALSDQLI 310

Query: 307 AGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPTITSGIR 366
            GG+D+VTGGTD H++LVDLRPKG+ G  V++AL RA IT NKNGIPFDPEKPT+TSGIR
Sbjct: 311 KGGLDIVTGGTDTHVMLVDLRPKGVTGNIVDKALGRAHITTNKNGIPFDPEKPTVTSGIR 370

Query: 367 LGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHAT-EQRVRREIFALCERFPIY 424
           LGTPAGTTRGFG AEFRE+  LI+EV + L  N E  +AT E  VR ++ ALC RFP+Y
Sbjct: 371 LGTPAGTTRGFGEAEFREIADLIIEVVDGLAANGEDGNATVEASVREKVAALCARFPLY 429


Lambda     K      H
   0.318    0.136    0.391 

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: 651
Number of extensions: 29
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: 424
Length of database: 432
Length adjustment: 32
Effective length of query: 392
Effective length of database: 400
Effective search space:   156800
Effective search space used:   156800
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: 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:

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