GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysT in Sinorhizobium fredii NGR234

Align methanogen homoaconitase (EC 4.2.1.114) (characterized)
to candidate WP_012709627.1 NGR_RS26830 3-isopropylmalate dehydratase large subunit

Query= BRENDA::Q58409
         (420 letters)



>NCBI__GCF_000018545.1:WP_012709627.1
          Length = 469

 Score =  233 bits (595), Expect = 7e-66
 Identities = 152/437 (34%), Positives = 228/437 (52%), Gaps = 46/437 (10%)

Query: 26  VDLAMTHDGTTPLAYKALKEMSDSVWNPDKIVVAFDHNVPPNTVKAA----EMQKLALEF 81
           +D  + H+ T+P A++ L+     V  P+K +   DHNVP +  +      E  ++ +E 
Sbjct: 29  IDRHLVHEVTSPQAFEGLRMAGRKVRAPEKTLAVVDHNVPTSPDRHLGIKNEESRIQVEA 88

Query: 82  VKR----FGIKNFHKGG--EGICHQILAEN-YVLPNMFVAGGDSHTCTHGAFGAFATGFG 134
           + R    FG++ + +    +GI H +  E  + LP M +  GDSHT THGAFGA A G G
Sbjct: 89  LARNAADFGVEYYSENDKRQGIVHIVGPEQGFTLPGMTIVCGDSHTSTHGAFGALAHGIG 148

Query: 135 ATDMAYIYATGETWIKVPKTIRVDIVGK-NENVSAKDIVLRVCKEIGRRGATYMAIEYGG 193
            +++ ++ AT     K  K + V + G+    V+AKDI+L +  EIG  G T   IE+ G
Sbjct: 149 TSEVEHVLATQTLIQKKAKNMLVRVDGQLPPGVTAKDIILAIIGEIGTAGGTGHVIEFAG 208

Query: 194 EVVKNMDMDGRLTLCNMAIEMGGKTGVIEADEITYDYLK-KERGLSDEDIAKLKKERITV 252
           E ++++ M+GR+T+CNM IE G + G+I  DE T+DY+K K R    +          T+
Sbjct: 209 EAIRSLSMEGRMTICNMTIEGGARAGLIAPDETTFDYIKDKPRAPKGKAWDMALDYWKTL 268

Query: 253 NRDEANYYKEIEI-DITDMEE--------------QVAVPHHPD---------------- 281
           + DE  +Y  I + D  D+                Q AVP+  D                
Sbjct: 269 HTDEGAHYDRIVVLDAADLPPIVSWGSSPEDVISVQGAVPNPDDIQEETKRASKWRALDY 328

Query: 282 -NVKPISDVEGTEINQVFIGSCTNGRLSDLREAAKYLKGREVHKDVKLIVIPASKKVFLQ 340
             +KP + +    +++VFIGSCTNGR+ DLR  AK ++GR+V   V  +++P S  V  Q
Sbjct: 329 MGLKPGTKITDIAVDRVFIGSCTNGRIEDLRAVAKVVEGRKVASTVSAMIVPGSGLVKEQ 388

Query: 341 ALKEGIIDIFVKAGAMICTPGCGPCLGAHQGVLAEGEICLSTTNRNFKGRMGHINSYIYL 400
           A  EG+  IF +AG     PGC  CL  +   L  GE C ST+NRNF+GR G      +L
Sbjct: 389 AEAEGLDKIFKEAGFDWREPGCSMCLAMNDDRLKPGERCASTSNRNFEGRQG-FKGRTHL 447

Query: 401 ASPKIAAISAVKGYITN 417
            SP +AA +AV G+  +
Sbjct: 448 VSPAMAAAAAVAGHFVD 464


Lambda     K      H
   0.318    0.136    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: 488
Number of extensions: 19
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: 420
Length of database: 469
Length adjustment: 32
Effective length of query: 388
Effective length of database: 437
Effective search space:   169556
Effective search space used:   169556
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: 51 (24.3 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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