GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Herbaspirillum seropedicae SmR1

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

Query= CharProtDB::CH_024500
         (309 letters)



>FitnessBrowser__HerbieS:HSERO_RS03330
          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 Apr 09 2024. The underlying query database was built on Apr 09 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