GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Echinicola vietnamensis KMM 6221, DSM 17526

Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate Echvi_0124 Echvi_0124 Aspartate/tyrosine/aromatic aminotransferase

Query= BRENDA::Q8YTF2
         (403 letters)



>FitnessBrowser__Cola:Echvi_0124
          Length = 386

 Score =  264 bits (674), Expect = 4e-75
 Identities = 137/381 (35%), Positives = 213/381 (55%), Gaps = 2/381 (0%)

Query: 6   ITPADRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPK 65
           I PA R+  +  Y F++     A+ + +G  +I++G+G+PD      V +A   +   P 
Sbjct: 2   IAPAHRLANVKEYYFSKKLREVARLKAEGHPIINMGIGSPDLPPHPSVTEALNHSSAQPT 61

Query: 66  NHGYPPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVL 125
           +HGY  ++G  + R AI ++Y + Y V L P  E LP++GSKE + H+++AY+NPGD VL
Sbjct: 62  SHGYQSYQGIPALREAIASFYQKHYAVSLSPTDEILPMMGSKEAIMHISLAYLNPGDKVL 121

Query: 126 VPSPAYPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGA 185
           +P+P YP +     + G       LK EN WL D+  + E      K+++ NYP  PTGA
Sbjct: 122 IPNPGYPTYSSVTELVGAKAVYYDLKEENQWLPDIGQLEELAQSGIKLMWINYPHMPTGA 181

Query: 186 TAPREFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTY 245
            A RE  E +V FA+K++ILLV+D  Y+ +      P S+L I GAKDI +E ++LSKT+
Sbjct: 182 NASREALEALVTFAKKHQILLVNDNPYSFILTQ--SPISILSIDGAKDIALELNSLSKTF 239

Query: 246 NMAGWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTR 305
           NM GWRVG + G    +Q +  +K+N+D G+F  +Q  A  AL L   +  ++   Y  R
Sbjct: 240 NMPGWRVGMLCGQASYLQEVLKVKSNMDSGMFLGIQEGAIAALNLDQRWFDQMDAIYHKR 299

Query: 306 RDFLIQGLGELGWDVPKTKATMYLWVKCPVGMGSTDFALNLLQQTGVVVTPGNAFGVAGE 365
           R+ + +    +G    +  A M++W K       +     LL +  + +TPG+ FG  G 
Sbjct: 300 REAVWKLAERVGAICERNSAGMFVWAKLATQTTPSALVDKLLYENHIFITPGDIFGSNGH 359

Query: 366 GYVRISLIADCDRLGEALDRI 386
           GY+R SL    + + EA DR+
Sbjct: 360 GYIRFSLCVPENLIQEAFDRV 380


Lambda     K      H
   0.321    0.140    0.427 

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: 410
Number of extensions: 16
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: 403
Length of database: 386
Length adjustment: 31
Effective length of query: 372
Effective length of database: 355
Effective search space:   132060
Effective search space used:   132060
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: 50 (23.9 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