GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Synechococcus elongatus PCC 7942

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate Synpcc7942_1029 Synpcc7942_1029 branched-chain amino acid aminotransferase

Query= BRENDA::P0AB80
         (309 letters)



>FitnessBrowser__SynE:Synpcc7942_1029
          Length = 304

 Score =  181 bits (459), Expect = 2e-50
 Identities = 105/301 (34%), Positives = 165/301 (54%), Gaps = 13/301 (4%)

Query: 8   YIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGP---VVFRHREHMQRLHDS 64
           Y +F G++V + +A++ + +HALHYGT  F G+R     + P   ++FR   H QRL  S
Sbjct: 7   YAFFRGQLVPFPEAQLSIATHALHYGTGAFGGLRGIPDPENPDRVLLFRLDRHCQRLSQS 66

Query: 65  AKIYRFPVSQSIDELMEACRDVIRKNNLT-SAYIRPLIFVGDVGMGVNPPAGYSTDVIIA 123
           AK   F +S   +E+ +A    ++KN  + S YIRP ++  D+G+          D  I 
Sbjct: 67  AKFLHFELSA--EEIFKAIEAFVQKNQPSQSFYIRPFVYTSDLGIAPRLH-NIEKDFFIY 123

Query: 124 AFPWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEG 183
               G YL  E    G+   +SSW R    ++P   K  G Y++S L  +EA   G+ E 
Sbjct: 124 GLQLGDYLSPE----GVSCRISSWYRQEDRSLPLRGKISGAYIASSLAKTEAVASGFDEA 179

Query: 184 IALDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLS 243
           I ++  G + E  G NLF V++G L TP +    L GITRD++I++A++LGI V ++ + 
Sbjct: 180 ILMNSQGKVCEATGMNLFMVRNGRLITPGYDQDILEGITRDSVIRVAQDLGIPVDQRPID 239

Query: 244 RESLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWGW 303
           +  L++ADEVF+SGTAA++TPV+ V+       R  P+T +I+Q    +  G       W
Sbjct: 240 KSELFIADEVFLSGTAAKVTPVKQVENYLTPCDR--PITDQIRQQLTLITEGRLAAYQDW 297

Query: 304 L 304
           +
Sbjct: 298 V 298


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: 235
Number of extensions: 10
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: 304
Length adjustment: 27
Effective length of query: 282
Effective length of database: 277
Effective search space:    78114
Effective search space used:    78114
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 Aug 03 2021. The underlying query database was built on Aug 03 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