GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ltaE in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_02468 H281DRAFT_02468 serine hydroxymethyltransferase

Query= curated2:D3DKC4
         (427 letters)



>FitnessBrowser__Burk376:H281DRAFT_02468
          Length = 424

 Score =  472 bits (1215), Expect = e-138
 Identities = 243/413 (58%), Positives = 302/413 (73%), Gaps = 6/413 (1%)

Query: 4   LFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGG 63
           L   D  +  AI+KE ERQ   +ELIASEN  S AV+EAQGSV+TNKYAEG P KRYYGG
Sbjct: 12  LATRDQAVRGAILKELERQQSQVELIASENIVSRAVLEAQGSVLTNKYAEGYPGKRYYGG 71

Query: 64  CEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHL 123
           CE+VD  E LA+ER K LF+A+ ANVQPHSG QAN AV +A++KPGDT++GM L  GGHL
Sbjct: 72  CEYVDEIETLALERIKQLFNAKFANVQPHSGAQANGAVMLALVKPGDTVLGMSLDAGGHL 131

Query: 124 THGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKL 183
           THGAK   SGK +NAV YGV+ +T LIDYDQ+  LA++HKP L++ G SAYPR +D+ +L
Sbjct: 132 THGAKPAMSGKWFNAVQYGVNRDTLLIDYDQIEELAQQHKPALLIAGFSAYPRALDFKRL 191

Query: 184 REIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKE-F 242
           R IADSVGA LMVDMAH AG+IA G + NPV +AH VTSTTHKTLRGPR GF+L   E  
Sbjct: 192 RAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRGGFVLTNDEDI 251

Query: 243 AKDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFK 302
           AK I+ +VFPG+QGGPLMHVIA KAVAF EA+   FK Y   V+ANA+ L E     G  
Sbjct: 252 AKKINSAVFPGLQGGPLMHVIAGKAVAFGEALQPGFKTYIDNVLANAQALGEVLKAGGVD 311

Query: 303 VVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPA 362
           +V+GGTD+H++L+DLR  GL G +VE+AL +A IT NKN +PFD   P  TSG+RLGTPA
Sbjct: 312 LVTGGTDNHLLLVDLRPKGLKGNQVEQALERAGITCNKNGIPFDTEKPTITSGVRLGTPA 371

Query: 363 MTTRGMKEDQMRIIARLISKVIKNI-----GDEKVIEYVRQEVIEMCEQFPLY 410
            TTRG   ++ R + RLI +V+ ++     G     + VR+E+  +CE+FP+Y
Sbjct: 372 GTTRGFGVNEFRDVGRLIVEVLDSLRDHPEGHAATEQRVRREIFALCERFPIY 424


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: 595
Number of extensions: 26
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: 424
Length adjustment: 32
Effective length of query: 395
Effective length of database: 392
Effective search space:   154840
Effective search space used:   154840
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 Sep 17 2021. The underlying query database was built on Sep 17 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