Alignments for a candidate for glyA in Sinorhizobium medicae WSM419

GapMind for Amino acid biosynthesis

Alignments for a candidate for glyA in Sinorhizobium medicae WSM419

Align serine hydroxymethyltransferase subunit (EC 2.1.2.1) (characterized)
to candidate WP_011975013.1 SMED_RS04060 serine hydroxymethyltransferase

Query= metacyc::MONOMER-4244
         (434 letters)



>NCBI__GCF_000017145.1:WP_011975013.1
          Length = 431

 Score =  606 bits (1562), Expect = e-178
 Identities = 298/420 (70%), Positives = 343/420 (81%), Gaps = 1/420 (0%)

Query: 15  FFKSHVSETDPDIFSAIQKEFGRQQHEIELIASENIVSQAVLDAAGSVLTNKYAEGYPGK 74
           FF   ++++DPDIF AI+KE GRQ+HEIELIASENIVS+AVL+A GS++TNKYAEGYPGK
Sbjct: 9   FFARSLADSDPDIFGAIEKELGRQRHEIELIASENIVSRAVLEAQGSIMTNKYAEGYPGK 68

Query: 75  RYYGGCQYVDIVEDIAIDRAKKLFNCEFANVQPNSGSQANQGVFNALAQPGDTILGLSLA 134
           RYYGGCQYVDI E++AI+RAKKLF   FANVQPNSGSQ NQ VF AL QPGDT +GL L 
Sbjct: 69  RYYGGCQYVDIAEELAIERAKKLFGVGFANVQPNSGSQMNQAVFLALLQPGDTFMGLDLN 128

Query: 135 AGGHLTHGAPVNQSGKWFKAVHYMVKPDSHLIDMDEVRKLAQEHKPRIIIAGGSAYPRKI 194
           +GGHLTHG+PVN SGKWF  V Y V+ D HL+DMD+V K A+EHKP++IIAGG+AY R  
Sbjct: 129 SGGHLTHGSPVNMSGKWFNVVSYGVREDDHLLDMDDVAKKAREHKPKLIIAGGTAYSRIW 188

Query: 195 DFAAFRAIADEVGAIFLVDMAHFAGLVAAGLIPSPFPHAHVVTTTTHKTLRGPRGGMILT 254
           D+  FR IADEVGA  +VDMAH AGLVA    PSPFPH HV TTTTHK+LRGPRGGMILT
Sbjct: 189 DWKRFREIADEVGAWLMVDMAHIAGLVAGDQHPSPFPHCHVATTTTHKSLRGPRGGMILT 248

Query: 255 NDADIAKKINSAIFPGIQGGPLMHVIAGKAVAFGEALRPDFKVYIKQVMDNARALGEVLV 314
           ND +IAKKINSA+FPG+QGGPLMHVIA KAVAFGEAL+P FK Y  QV+ NAR L + L 
Sbjct: 249 NDEEIAKKINSAVFPGLQGGPLMHVIAAKAVAFGEALQPSFKDYAAQVVKNARTLADTLK 308

Query: 315 QNGFALVSGGTDTHLVLVDLRPKKLTGTKAEKALGRANITCNKNGIPFDPEKPMVTSGIR 374
            NG  +VSGGTD HL+LVDLR K  TG +AE ALGRA +TCNKNGIPFDPEKP VTSG+R
Sbjct: 309 ANGLDIVSGGTDNHLMLVDLRKKNATGKRAEAALGRAYVTCNKNGIPFDPEKPFVTSGVR 368

Query: 375 LGSPAGTTRGFGVAEFQEIGRLISEVLDGV-AKNGEDGNGAVEAAVKAKAIALCDRFPIY 433
           LG+PAGTTRGF  AEF+EIG LI EVLDG+ A N ++GN AVEA V+ K + L  RFP+Y
Sbjct: 369 LGTPAGTTRGFKEAEFKEIGELIVEVLDGLKAANSDEGNAAVEAGVREKVMKLTGRFPMY 428


Lambda     K      H
   0.319    0.136    0.396 

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: 619
Number of extensions: 20
Number of successful extensions: 2
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: 434
Length of database: 431
Length adjustment: 32
Effective length of query: 402
Effective length of database: 399
Effective search space:   160398
Effective search space used:   160398
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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Protein sequences (fasta format)
Organisms (tab-delimited)
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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
the source code
instructions for running GapMind on your computer
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