GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ltaE in Echinicola vietnamensis KMM 6221, DSM 17526

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 Echvi_1188 Echvi_1188 Glycine/serine hydroxymethyltransferase

Query= curated2:D3DKC4
         (427 letters)



>FitnessBrowser__Cola:Echvi_1188
          Length = 422

 Score =  459 bits (1182), Expect = e-134
 Identities = 232/419 (55%), Positives = 302/419 (72%), Gaps = 16/419 (3%)

Query: 8   DAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEFV 67
           D  I++ I KE +RQ   +ELIASENFTS  VMEA GSV+TNKYAEGLP KRYYGGCE V
Sbjct: 4   DQVIFDLIQKEEDRQKRGIELIASENFTSKQVMEAAGSVLTNKYAEGLPKKRYYGGCEVV 63

Query: 68  DIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTHGA 127
           D  E +AI+RAK LF A  ANVQPHSG QAN AV++A L PGD I+G DLSHGGHLTHG+
Sbjct: 64  DDIEQIAIDRAKELFGATWANVQPHSGAQANAAVFLACLNPGDHILGFDLSHGGHLTHGS 123

Query: 128 KVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREIA 187
            VNFSGK Y   +YGV  ET +ID D++   A+E KPKLI+ GASAY R  D+A+ REIA
Sbjct: 124 PVNFSGKNYKPHFYGVEEETGIIDMDKVAEKAREVKPKLIICGASAYSRDWDYARFREIA 183

Query: 188 DSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKEF----- 242
           D VGA L+ D++H AGLIA G+  +P+ + H VT+TTHKTLRG R G I+ +++F     
Sbjct: 184 DEVGALLLADISHPAGLIARGLLKDPLEHCHIVTTTTHKTLRGTRGGLIMMREDFDNPFG 243

Query: 243 -----------AKDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARV 291
                       + +D +VFPG+QGGPL H+IAAKA+AF+EA+S E+ EY  QV  NA +
Sbjct: 244 IKNPKGELRKMTQLLDSAVFPGMQGGPLEHIIAAKAIAFQEALSDEYMEYILQVKKNASI 303

Query: 292 LAEEFIKEGFKVVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPV 351
           +A+ F+++G+K++SGGTD+H++L+DLR+  L+G+  EE LGK +IT+NKN VPFD   P 
Sbjct: 304 MADAFVEKGYKLISGGTDNHLMLIDLRNKDLSGKIAEETLGKVDITINKNMVPFDTRSPF 363

Query: 352 KTSGIRLGTPAMTTRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410
            TSG+R+GT A+T+RG+KE +M  I  LI + + N  DE  +  ++QEV +   QFPLY
Sbjct: 364 VTSGMRVGTAAITSRGLKEQEMTKIVDLIDRALMNHEDEAALAKIKQEVNDWMVQFPLY 422


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: 572
Number of extensions: 31
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: 427
Length of database: 422
Length adjustment: 32
Effective length of query: 395
Effective length of database: 390
Effective search space:   154050
Effective search space used:   154050
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