GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tpiA in Methanosarcina barkeri Fusaro

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_011308470.1 MBAR_RS18885 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>NCBI__GCF_000195895.1:WP_011308470.1
          Length = 413

 Score =  255 bits (652), Expect = 2e-72
 Identities = 161/409 (39%), Positives = 248/409 (60%), Gaps = 34/409 (8%)

Query: 4   MTIRDVDLKGKRVIMRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVILLSHLGR 62
           +T+ DV L  KRV++RVDFN P+ D G + DD +I++ LPT++ +LE  +KV+L+SH GR
Sbjct: 11  LTMSDVVLDNKRVLVRVDFNSPMDDNGNILDDKKIKSHLPTLQ-SLEH-SKVVLMSHQGR 68

Query: 63  PKGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPG 122
           P  E     +L   AK  +ELLG+EV +   +     + A++ L +GE+LLLENTRF+  
Sbjct: 69  PGDEDYT--TLEAHAKLATELLGREVTYEDDIFSSCARNAIKSLAQGEILLLENTRFNAE 126

Query: 123 ETKNDP-------ELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEI 175
           E  N P       ++ K    L D+ +NDAF  +HR+  S VG  + +PSVAG LM+KEI
Sbjct: 127 EITNRPPEKQAKSQMVKKLYPLFDLFINDAFSVSHRSQCSVVGFTEVLPSVAGILMDKEI 186

Query: 176 KFLSKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEK--ADRILIGGAMMFTFLKALG--- 230
             L K     E P + +LGGAK +D I  I+N++++  AD+IL  G +   F+ A+G   
Sbjct: 187 TGLDKALKCREHPAIFILGGAKANDSIKAISNILKRAGADKILTTGVVATIFMMAMGVDV 246

Query: 231 KEVGSSRVEE----DKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDG 286
            EV    +E+    D+I +A +LL   K+   +I++P D      +  G E++ V +D  
Sbjct: 247 SEVNRKFIEDKKYMDQISIASKLL---KDYSGKIIVPQDVA----LNSGGERQEVEVDK- 298

Query: 287 IPEGWMGL-DIGPETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEK 345
           I +G + + DIG ETIE + + L +AK  V++GP G+FE+D+F  GT ++  A A    +
Sbjct: 299 IKKGNLPIADIGRETIENYSKYLKEAKLCVFHGPTGIFELDNFRLGTDELLKAAA----Q 354

Query: 346 GAITVVGGGDSAAAVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394
            + +V GGG +  A+++ GL  KFSH+S GGGAS+ ++ G+ LPGI ++
Sbjct: 355 ASYSVAGGGHTLDAIDQLGLGSKFSHISMGGGASITYISGEPLPGITAL 403


Lambda     K      H
   0.317    0.137    0.386 

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: 41
Number of successful extensions: 8
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: 654
Length of database: 413
Length adjustment: 35
Effective length of query: 619
Effective length of database: 378
Effective search space:   233982
Effective search space used:   233982
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: 52 (24.6 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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