GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Salinicoccus carnicancri Crm

Align aspartate transaminase; EC 2.6.1.1 (characterized)
to candidate WP_017548955.1 C792_RS0108030 pyridoxal phosphate-dependent aminotransferase

Query= CharProtDB::CH_004890
         (393 letters)



>NCBI__GCF_000330705.1:WP_017548955.1
          Length = 395

 Score =  452 bits (1163), Expect = e-132
 Identities = 218/389 (56%), Positives = 285/389 (73%), Gaps = 1/389 (0%)

Query: 1   MKLAKRVSALTPSTTLAITAKAKELKAAGHDVIGLGAGEPDFNTPQHIIDAAVRSMNEGH 60
           M+++ R+  +TPS TLAITAK+++LKA G DVIGLGAGEPDFNTP  IID A  S+  G 
Sbjct: 1   MQISDRIKNVTPSQTLAITAKSRDLKAQGVDVIGLGAGEPDFNTPDEIIDKAYESLKAGK 60

Query: 61  TKYTPSGGLAELKNSIAEKFKRDQNIEYKPSQIIVCTGAKHALYTLFQVILDEEDEVIIP 120
           TKYT + G+ ELK++I  K ++D  + Y+PS++ V  GAKH LY LFQ  L+  DEVIIP
Sbjct: 61  TKYTAAAGIPELKSAIINKMEKDHGLVYEPSEVFVGNGAKHVLYNLFQATLNPGDEVIIP 120

Query: 121 TPYWVSYPEQVKLAGGKPVYVEGLEENHFKISPEQLKNAITEKTKAIVINSPSNPTGVMY 180
            PYWVSY EQVKLAGG PV +   E   FK++PE +   +T+KT+ +++NSPSNP+G++Y
Sbjct: 121 VPYWVSYTEQVKLAGGNPVIMPTDESTSFKVTPEIIDGFLTDKTRMLLLNSPSNPSGMVY 180

Query: 181 TEEELSALGEVCLEHDILIVSDEIYEKLTYGGKKHVSIAQLSDRLKEQTVIINGVSKSHS 240
           T EEL AL     E D+++V+DEIYE L Y   +H+SIA LS+R+KE T +INGVSKSH+
Sbjct: 181 TREELEALAAYIEEKDLIVVADEIYETLVY-DSEHISIASLSNRMKENTFVINGVSKSHA 239

Query: 241 MTGWRIGYAAGSEDIIKAMTNLASHSTSNPTSIAQYGAIAAYNGPSEPLEEMREAFEHRL 300
           MTGWRIGY  G+  ++KAMT+L SHSTSNP + +Q+ AIAAY        E    F  R 
Sbjct: 240 MTGWRIGYCCGNSGVVKAMTDLTSHSTSNPVTPSQWAAIAAYEMDDSFTREYNRTFHERR 299

Query: 301 NTIYAKLIEIPGFSCVKPEGAFYLFPNAKEAAQSCGFKDVDEFVKALLEEEKVAIVPGSG 360
           +  Y KL+EIP  +C+KP+GAFYLFPN  E A+ CGF  VD FV A+LEE  VA+VPGSG
Sbjct: 300 DAAYEKLMEIPYITCIKPQGAFYLFPNFSECAERCGFDSVDAFVNAVLEEVYVAVVPGSG 359

Query: 361 FGSPENVRLSYATSLDLLEEAIERIKRFV 389
           FGSP+N+RLSY+ S++ + EA+ERI++FV
Sbjct: 360 FGSPDNIRLSYSLSIEDMNEALERIRKFV 388


Lambda     K      H
   0.313    0.131    0.370 

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: 534
Number of extensions: 23
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: 393
Length of database: 395
Length adjustment: 31
Effective length of query: 362
Effective length of database: 364
Effective search space:   131768
Effective search space used:   131768
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 26 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