GapMind for catabolism of small carbon sources

 

Aligments for a candidate for putA in Sinorhizobium meliloti 1021

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate SMa2213 SMa2213 aldehyde dehydrogenase

Query= BRENDA::Q9K9B2
         (515 letters)



>lcl|FitnessBrowser__Smeli:SMa2213 SMa2213 aldehyde dehydrogenase
          Length = 494

 Score =  251 bits (640), Expect = 6e-71
 Identities = 154/439 (35%), Positives = 229/439 (52%), Gaps = 18/439 (4%)

Query: 67  VSKANQDLAEKAIQSADEAFQT--WRNVNPEERANILVKAAAIIRRRKHEFSAWLVHEAG 124
           V + N + A++A+++A  AF    W  ++P ER  I+ + AA+I       +   V + G
Sbjct: 38  VPRGNAEDADRAVRAAHRAFSQGPWGKMHPTERGRIIQRFAALIEEHADALADIEVRDNG 97

Query: 125 KPWKEADADTAEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYTPMGVTVTISPWNFA 184
           +   E          +  YYA    ++        +P       + P+GV V I PWN  
Sbjct: 98  RLLAEMTHQIRYIPRWYHYYAGFADKIEGTLHPCDKPALSFSR-HEPLGVCVGIVPWNAP 156

Query: 185 LAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINYVPGSGAEVGDY 244
           L +    A   +  GNT+V+KPA  T   A K +E++E AG P GVIN V G G EVG+ 
Sbjct: 157 LLLFSLKAAPALAAGNTLVMKPAEFTSATALKLMELVEKAGFPTGVINVVTGYGPEVGEP 216

Query: 245 LVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDTVVVDRDADLDLA 304
           LV HP T  + FTGS   G  LY  AA        +KRV +E+GGK   +V  DADLD A
Sbjct: 217 LVTHPLTRHVGFTGSTKTGAHLYSLAA------KDVKRVSLELGGKSPNIVFGDADLDNA 270

Query: 305 AESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPTNRDNYMGPVID 364
              ++   FG  GQ C AGSR ++H+ ++DE LEK     K   +GDP   +  +GP+ +
Sbjct: 271 VRGVVGGIFGAVGQTCIAGSRLLVHRSIHDEFLEKLAVFTKTARIGDPRKVETQIGPIAN 330

Query: 365 EKAFEKIMSYIEIGKKEGR--LMTGGEGD---SSTGFFIQPTIIADLDPEAVIMQEEIFG 419
              FEK++ YI+I ++EG   ++ GG  D     TG+FI+PTI A +  +  I +EE+FG
Sbjct: 331 SMQFEKVLGYIDIARREGAELILGGGRPDLEECGTGYFIEPTIFAGVSNDMRIAREEVFG 390

Query: 420 PVVAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGNLYFNRNCTGAIV 479
           PV++    ++ + AL IAN++E+GL   V T +     +       G+++ N   T   +
Sbjct: 391 PVLSAIVFDEPEEALAIANDSEFGLGAGVWTSDMRLALKMSERLEAGSVWVN---TYRDI 447

Query: 480 GY-HPFGGFKMSGTDSKAG 497
            Y  PFGG+K SG   + G
Sbjct: 448 SYTTPFGGYKKSGIGRENG 466


Lambda     K      H
   0.316    0.134    0.388 

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: 619
Number of extensions: 29
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: 515
Length of database: 494
Length adjustment: 34
Effective length of query: 481
Effective length of database: 460
Effective search space:   221260
Effective search space used:   221260
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 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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, or view the source code.

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