GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Thermocrinis albus DSM 14484

Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate WP_041434172.1 THAL_RS02350 branched-chain-amino-acid transaminase

Query= CharProtDB::CH_024500
         (309 letters)



>NCBI__GCF_000025605.1:WP_041434172.1
          Length = 305

 Score =  221 bits (563), Expect = 2e-62
 Identities = 122/305 (40%), Positives = 182/305 (59%), Gaps = 8/305 (2%)

Query: 7   DYIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCY--DSHKGPVVFRHREHMQRLHDS 64
           +Y +F G +V  E+AK+ + +++ HYGT+VFEGIR Y  + H    +   REH QRL  +
Sbjct: 2   EYAFFEGRIVPIEEAKISIKTNSFHYGTAVFEGIRAYWNEEHHQLYILFAREHYQRLLAN 61

Query: 65  AKIYRFPVSQSIDELMEACRDVIRKNNLT-SAYIRPLIFVGDVGMGVNPPAGYSTDVIIA 123
            +     +  S+D+L+    +++RKNN+    YIRP+ +  D+ +      G++ ++ I 
Sbjct: 62  CRAMFMELPYSVDDLVNITVELLRKNNIKHDVYIRPIAYFKDLAL-TPKLIGFTPEIAIY 120

Query: 124 AFPWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEG 183
            + +G YL      +GI    SSW R   N+IP+  K  G Y++S L  +EA   GY E 
Sbjct: 121 TYSFGRYLDTS---KGIRVKTSSWIRNDDNSIPSRWKVAGAYVNSALAKTEAILAGYDEA 177

Query: 184 IALDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAK-ELGIEVREQVL 242
           I L+ NG+++EG+GEN+F V+   + TPP     L GITR A+IKL K EL +EV E+ +
Sbjct: 178 IMLNQNGFVAEGSGENIFLVRGRKVVTPPCWDHILEGITRSAVIKLIKNELVLEVEERSI 237

Query: 243 SRESLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWG 302
           SR  LY ADEVF++GTAAEITPV  +D  ++G G  GP+T+ +Q+ +F    G  E   G
Sbjct: 238 SRSELYSADEVFLTGTAAEITPVVEIDNRKIGSGDIGPITRELQKIYFDAVRGNIERYKG 297

Query: 303 WLDQV 307
           WL  V
Sbjct: 298 WLTPV 302


Lambda     K      H
   0.319    0.136    0.413 

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: 253
Number of extensions: 13
Number of successful extensions: 4
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: 309
Length of database: 305
Length adjustment: 27
Effective length of query: 282
Effective length of database: 278
Effective search space:    78396
Effective search space used:    78396
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: 48 (23.1 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