GapMind for Amino acid biosynthesis

 

Aligments for a candidate for leuA in Herbaspirillum seropedicae SmR1

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate HSERO_RS04700 HSERO_RS04700 2-isopropylmalate synthase

Query= BRENDA::P9WQB3
         (644 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS04700 HSERO_RS04700
           2-isopropylmalate synthase
          Length = 575

 Score =  498 bits (1283), Expect = e-145
 Identities = 279/621 (44%), Positives = 374/621 (60%), Gaps = 76/621 (12%)

Query: 42  PVNRYRPFAEEVEPIRLRNRTWPDRVIDRAPLWCAVDLRDGNQALIDPMSPARKRRMFDL 101
           P  +YR  A    P+ L +R WP R + +AP W + DLRDGNQAL +PM+  RK R+F  
Sbjct: 5   PSQKYRAIA----PVDLPDRRWPSRTLRQAPTWLSTDLRDGNQALFEPMNRERKLRLFHE 60

Query: 102 LVRMGYKEIEVGFPSASQTDFDFVREIIEQGAIPDDVTIQVLTQCRPELIERTFQACSGA 161
           LVR+G+KEIEVGFP+AS+ DF+ VR +I++  IPDDVT  V+TQ R +LI  T ++ +GA
Sbjct: 61  LVRIGFKEIEVGFPAASRIDFETVRHLIDEHLIPDDVTPMVMTQLRADLITETVKSVAGA 120

Query: 162 PRAIVHFYNSTSILQRRVVFRANRAEVQAIATDGARKCVEQAAKYPGTQWRFEYSPESYT 221
            R IVHFYN+ +   R +VF  +  ++  +  D         A +P T+W  +YSPE++ 
Sbjct: 121 RRVIVHFYNAIAPAWREIVFGMSVPQIITLVEDHIALFRRLTAVHPETEWILQYSPETFC 180

Query: 222 GTELEYAKQVCDAVGEVIAPTPERPIIFNLPATVEMTTPNVYADSIEWMSRNLANRESVI 281
             ELE + +VC+A        P R +I NLP TVE++TPNV+AD IEWM R L  RE +I
Sbjct: 181 MAELEVSLEVCNAAIRAWDAGPRRRMIINLPTTVEVSTPNVFADQIEWMDRRLERREHLI 240

Query: 282 LSLHPHNDRGTAVAAAELGFAAGADRIEGCLFGNGERTGNVCLVTLGLNLFSRGVDPQID 341
           LS+HPHNDRGTAVA AE    AGA R+EGCLFGNGER+GNV +VTL LNL+++G+ P +D
Sbjct: 241 LSVHPHNDRGTAVACAEQAMLAGAQRVEGCLFGNGERSGNVDVVTLALNLYTQGIAPGLD 300

Query: 342 FSNIDEIRRTVEYCNQLPVHERHPYGGDLVYTAFSGSHQDAINKGLDAMKLDADAADCDV 401
           FS+I  + R  E C  LP+H RHPY GDLV+TAFSGSHQDAI KG  A + DA       
Sbjct: 301 FSDIAALARVAEECTALPIHPRHPYVGDLVFTAFSGSHQDAIAKGFAAQRPDAP------ 354

Query: 402 DDMLWQVPYLPIDPRDVGRTYEAVIRVNSQSGKGGVAYIMKTDHGLSLPRRLQIEFSQVI 461
               W+VPYLPIDP D+GRTY++++RVNSQSGKGG+A++++ DH +++PRR+Q+EFS ++
Sbjct: 355 ----WRVPYLPIDPTDLGRTYDSIVRVNSQSGKGGIAFLLQRDHHITMPRRMQVEFSAIV 410

Query: 462 QKIAEGTAGEGGEVSPKEMWDAFAEEYLAPVR-------------PLER----IRQHVDA 504
           Q +A+ +     E++ + +WD F   YLAPV+              LE+     R H   
Sbjct: 411 QALADASE---TELTSEHLWDVFERTYLAPVQASPDFSDRTSLAPALEQRRFIYRSHCLH 467

Query: 505 ADDDGGTTSITATVKINGVETEISGSGNGPLAAFVHALADVGFDVAVLDYYEHAM--SAG 562
              DG    +        V T + GSGNGP+AA V AL   G  + +  Y E ++    G
Sbjct: 468 PHPDGERIVLELADTEGNVRT-VEGSGNGPIAATVAAL---GLALRIDSYEERSLGVGVG 523

Query: 563 DDAQAAAYVEASVTIASPAQPGEAGRHASDPVTIASPAQPGEAGRHASDPVTSKTVWGVG 622
            DAQA A VEA    A P  PG                                  +GVG
Sbjct: 524 ADAQALAIVEA----ALPTVPGSR--------------------------------FGVG 547

Query: 623 IAPSITTASLRAVVSAVNRAA 643
              +ITTAS+ AV+SA +R A
Sbjct: 548 RHENITTASIMAVLSAASRFA 568


Lambda     K      H
   0.317    0.133    0.399 

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: 948
Number of extensions: 47
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 644
Length of database: 575
Length adjustment: 37
Effective length of query: 607
Effective length of database: 538
Effective search space:   326566
Effective search space used:   326566
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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 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