GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Methanosarcina mazei Go1

Align Aromatic-amino-acid aminotransferase 2; ARAT-II; AROAT; EC 2.6.1.57 (characterized)
to candidate WP_048038594.1 MM_RS12280 pyridoxal phosphate-dependent aminotransferase

Query= SwissProt::H3ZPU1
         (389 letters)



>NCBI__GCF_000007065.1:WP_048038594.1
          Length = 370

 Score =  288 bits (738), Expect = 1e-82
 Identities = 157/380 (41%), Positives = 246/380 (64%), Gaps = 16/380 (4%)

Query: 4   SDRLEMVNPSEIRKLFDLAQGIEGIISLGIGEPDFDTPEHIKEYAKEALDKGLTHYSPNI 63
           S+ +  ++ S IRK+F+ A      I+LG+G+PDFDTP+HIK  A +A+++G T Y+   
Sbjct: 7   SENVSRIDTSGIRKIFEAAGS--NAINLGLGQPDFDTPDHIKAAAIKAINEGFTGYTAGP 64

Query: 64  GILELREAVAEKFKKHNGIDADPKTQIMITVGTNQQILMGLATFLKDNEEVLIPSPMFVS 123
           GI ELREA+++KFK+ N     P+ +I++T G ++ + + L   L   +EVLI +P FVS
Sbjct: 65  GIPELREALSQKFKEENCFSVSPQ-EIIVTSGASEALTIALTALLNRGDEVLISNPGFVS 123

Query: 124 YAPAVILAGGKPVEVPTYEENEFRLSVDELEKYVTPKTRALIINTPNNPTGAVLTKKDLE 183
           Y     +  GK V VP  E+    +  +++ + +TPKT+A+I+N+P+NPTGAV ++ D++
Sbjct: 124 YNALTEMLYGKVVNVPLGED--LTMKPEDVLERITPKTKAIILNSPSNPTGAVSSRADIK 181

Query: 184 EIADFAVEHDLMILSDEVYEYFVYDGVKNYSIASLDGMFERTITMNGFSKTFAMTGWRLG 243
            +A+ A +H + I+SDEVYEYF+Y+G ++ S AS     +  +T+N  SK++AMTGWRLG
Sbjct: 182 ALAEIADDHRITIISDEVYEYFIYEG-EHVSPASYS---DNVVTVNATSKSYAMTGWRLG 237

Query: 244 FLAAPEWVVEKMVRFQMYNATCPVTFIQYAAAKALRDERSWQAVEEMRREYERRRNLVWK 303
           +LAA    + +M++   Y   C  +  Q AA  A+   +   +V  MR E+ +RR+++ K
Sbjct: 238 YLAARNEYISQMLKVHQYIQACANSIAQKAAYAAVTGPK--DSVSAMREEFRKRRDVLVK 295

Query: 304 RLNEMGLPTVKPKGAFYIFPRIKDTGLSSKEFSELMIKEAKVVVVPGSAFGQAGEGYVRI 363
            LN++G+    PKGAFY FPR+     +S E +  MI    VVVVPG+AFG  G+GY+RI
Sbjct: 296 GLNDLGMECALPKGAFYAFPRVS----NSAEVASKMISNG-VVVVPGTAFGSEGDGYIRI 350

Query: 364 SYATAYEKLEEAMDRMEKVL 383
           SYA + + +E+++  MEKVL
Sbjct: 351 SYAASMKDIEKSLSIMEKVL 370


Lambda     K      H
   0.318    0.135    0.387 

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: 352
Number of extensions: 16
Number of successful extensions: 6
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: 389
Length of database: 370
Length adjustment: 30
Effective length of query: 359
Effective length of database: 340
Effective search space:   122060
Effective search space used:   122060
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 25 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