GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ltaE in Bacillus altitudinis 41KF2b

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 WP_026050167.1 BA79_RS08870 serine hydroxymethyltransferase

Query= curated2:D3DKC4
         (427 letters)



>NCBI__GCF_000691145.1:WP_026050167.1
          Length = 415

 Score =  520 bits (1339), Expect = e-152
 Identities = 252/413 (61%), Positives = 318/413 (76%)

Query: 1   MRHLFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRY 60
           M+HL   DA++++AI  E +RQ   +ELIASENF S AVMEAQGSV+TNKYAEG P KRY
Sbjct: 1   MKHLPEQDAQVFKAIQLERKRQQDKIELIASENFVSEAVMEAQGSVLTNKYAEGYPGKRY 60

Query: 61  YGGCEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHG 120
           YGGCE VD+ ED+A +RAK +F AE+ NVQPHSG QANMAVY  +L+ GDT++GM+LSHG
Sbjct: 61  YGGCEHVDVVEDIARDRAKEIFGAEYVNVQPHSGAQANMAVYFTILEHGDTVLGMNLSHG 120

Query: 121 GHLTHGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDW 180
           GHLTHG+ VNFSG  YN V YGV  ET  IDY  +   A+EHKPKLIV GASAYPR ID+
Sbjct: 121 GHLTHGSPVNFSGVQYNFVEYGVDKETQHIDYQDVLEKAREHKPKLIVAGASAYPRQIDF 180

Query: 181 AKLREIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKK 240
            K REIAD VGAY MVDMAH AGL+A G++PNPVPYA FVT+TTHKTLRGPR G ILC++
Sbjct: 181 KKFREIADEVGAYFMVDMAHIAGLVAAGLHPNPVPYADFVTTTTHKTLRGPRGGMILCRE 240

Query: 241 EFAKDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEG 300
           EF K IDKS+FPGIQGGPLMHVI+AKAV+F E ++ +FK YA+ V+ NA+ LAE  + E 
Sbjct: 241 EFGKKIDKSIFPGIQGGPLMHVISAKAVSFGEVLNGDFKTYAQNVIDNAKQLAETLLSED 300

Query: 301 FKVVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGT 360
            ++VSGGTD+H+VL+DLR  G+TG+  E  L +  ITVNKNA+P+DP  P  TSG+R+GT
Sbjct: 301 IQLVSGGTDNHLVLIDLRSLGITGKIAENVLDEIGITVNKNAIPYDPEKPFVTSGVRVGT 360

Query: 361 PAMTTRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLYPEL 413
            A+T+RG  ++ M+ +  +I+  +K+  DE  +E  ++ V ++  +FPLY EL
Sbjct: 361 AAVTSRGFDQEAMKEVGSIIALALKHHEDEAKLEEAKKRVSDLTARFPLYHEL 413


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: 606
Number of extensions: 25
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: 427
Length of database: 415
Length adjustment: 32
Effective length of query: 395
Effective length of database: 383
Effective search space:   151285
Effective search space used:   151285
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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