GapMind for Amino acid biosynthesis

 

Alignments for a candidate for glyA in Lentibacillus jeotgali Grbi

Align Serine hydroxymethyltransferase; SHMT; Serine methylase; EC 2.1.2.1 (characterized)
to candidate WP_010531577.1 ON01_RS13415 serine hydroxymethyltransferase

Query= SwissProt::P39148
         (415 letters)



>NCBI__GCF_000224785.1:WP_010531577.1
          Length = 411

 Score =  619 bits (1596), Expect = 0.0
 Identities = 301/410 (73%), Positives = 348/410 (84%)

Query: 1   MKHLPAQDEQVFNAIKNERERQQTKIELIASENFVSEAVMEAQGSVLTNKYAEGYPGKRY 60
           M HL   D +VF AI++E+ RQQ KIELIASENFVSEAVMEA GSV+TNKYAEGYP KRY
Sbjct: 1   MDHLKQTDHEVFEAIQDEKTRQQDKIELIASENFVSEAVMEAMGSVMTNKYAEGYPSKRY 60

Query: 61  YGGCEHVDVVEDIARDRAKEIFGAEHVNVQPHSGAQANMAVYFTILEQGDTVLGMNLSHG 120
           YGGCEHVDVVE++ARDRAKE+FGA+H NVQPHSGAQANMAVYF++L  GDT+LGMNL+HG
Sbjct: 61  YGGCEHVDVVENLARDRAKELFGADHANVQPHSGAQANMAVYFSVLNPGDTILGMNLNHG 120

Query: 121 GHLTHGSPVNFSGVQYNFVEYGVDKETQYIDYDDVREKALAHKPKLIVAGASAYPRTIDF 180
           GHLTHGSPVNFSG  YN V+YGVD ET+ +DYD V E+A   +PKLI+AGASAY R IDF
Sbjct: 121 GHLTHGSPVNFSGKLYNVVDYGVDDETEKLDYDAVLERAKEEQPKLIIAGASAYSREIDF 180

Query: 181 KKFREIADEVGAYFMVDMAHIAGLVAAGLHPNPVPYADFVTTTTHKTLRGPRGGMILCRE 240
            KFREIADEVGAY +VDMAHIAGLVAAGLH NPV +ADFVTTTTHKTLRGPRGGMILC+E
Sbjct: 181 SKFREIADEVGAYLLVDMAHIAGLVAAGLHQNPVEHADFVTTTTHKTLRGPRGGMILCKE 240

Query: 241 EFGKKIDKSIFPGIQGGPLMHVIAAKAVSFGEVLQDDFKTYAQNVISNAKRLAEALTKEG 300
           E  K IDK++FP +QGGPLMHVIAAKAVSF E L DDFKTYA+ +I NAK L++ALT EG
Sbjct: 241 EHAKLIDKNVFPRMQGGPLMHVIAAKAVSFKEALTDDFKTYAKQIIQNAKALSDALTNEG 300

Query: 301 IQLVSGGTDNHLILVDLRSLGLTGKVAEHVLDEIGITSNKNAIPYDPEKPFVTSGIRLGT 360
           +++VSGGTDNHL+L+D+  L LTGKVAE+VLD IGIT+NKN IP+D E PFVTSG+R+GT
Sbjct: 301 LRVVSGGTDNHLLLLDVTPLNLTGKVAENVLDNIGITANKNTIPFDQESPFVTSGMRMGT 360

Query: 361 AAVTSRGFDGDALEEVGAIIALALKNHEDEGKLEEARQRVAALTDKFPLY 410
           AAVT+RGF    ++E+ +IIAL LKNHEDE  L EA +RV  LT  F +Y
Sbjct: 361 AAVTTRGFKEPEMKEIASIIALVLKNHEDENVLREAEERVQTLTGNFAIY 410


Lambda     K      H
   0.317    0.136    0.388 

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: 632
Number of extensions: 20
Number of successful extensions: 1
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: 415
Length of database: 411
Length adjustment: 31
Effective length of query: 384
Effective length of database: 380
Effective search space:   145920
Effective search space used:   145920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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