GapMind for Amino acid biosynthesis

 

Aligments for a candidate for tyrB in Herbaspirillum seropedicae SmR1

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate HSERO_RS03330 HSERO_RS03330 branched-chain amino acid aminotransferase

Query= BRENDA::P0AB80
         (309 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS03330 HSERO_RS03330
           branched-chain amino acid aminotransferase
          Length = 306

 Score =  278 bits (712), Expect = 9e-80
 Identities = 140/299 (46%), Positives = 195/299 (65%), Gaps = 2/299 (0%)

Query: 9   IWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKIY 68
           IW +GE++ W DA VHV++H LHYG  VFEG+R Y +  G  +FR +EH +RL +SAKI+
Sbjct: 10  IWKDGELIDWRDATVHVLTHTLHYGMGVFEGVRAYKTPDGTAIFRLQEHTRRLRNSAKIF 69

Query: 69  RFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAFPWG 128
           +  V    D L +A R V+R+N L S YIRPLI++G   +GV+   G    V +AA+ WG
Sbjct: 70  QMEVPYDHDTLAQAQRQVVRENQLESCYIRPLIWIGSEKLGVS-AKGNQIHVAVAAWSWG 128

Query: 129 AYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALDV 188
           AYLG + L +GI    SS++R   N     AKA G Y++S+L   EA   GY E + LD 
Sbjct: 129 AYLGEDGLNKGIRVKTSSFSRHHVNVSLVRAKACGYYINSILANQEALADGYDEALLLDT 188

Query: 189 NGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESLY 248
            GY+SEG+GEN+F VK+G ++TP   +S L GITRDA++ +A++LGIEV E+ ++R+ +Y
Sbjct: 189 EGYVSEGSGENVFIVKNGKIYTPDL-ASCLDGITRDAVLTMARDLGIEVIEKRITRDEMY 247

Query: 249 LADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWGWLDQV 307
            ADE F +GTAAEITP+R +D   +G G  GPVT+++Q  FF +  G       WL  V
Sbjct: 248 CADEAFFTGTAAEITPIRELDRRVIGSGARGPVTEKLQTLFFDVVAGRAPQYKHWLTLV 306


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: 299
Number of extensions: 13
Number of successful extensions: 3
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: 306
Length adjustment: 27
Effective length of query: 282
Effective length of database: 279
Effective search space:    78678
Effective search space used:    78678
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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