GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Ruegeria conchae TW15

Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_010443464.1 G7G_RS0121085 acetolactate synthase large subunit

Query= curated2:Q7U5G1
         (617 letters)



>NCBI__GCF_000192475.1:WP_010443464.1
          Length = 557

 Score =  233 bits (594), Expect = 2e-65
 Identities = 170/549 (30%), Positives = 267/549 (48%), Gaps = 34/549 (6%)

Query: 27  LMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHAADAYARATG 86
           L+ AL   GV+ IF  PG   L + ++L  ++    ++ +L RHEQ     A  Y R TG
Sbjct: 18  LVAALEAEGVEYIFAVPGEENLDVLESLRTSK----IELVLTRHEQGAAFMAATYGRLTG 73

Query: 87  KVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAFQETDIFGITLPIV 146
           K GVC  T GPGATN  T  A A +  +P+++ITGQ P        FQ  DI G+  PI 
Sbjct: 74  KAGVCMATLGPGATNFATPAAYAHLGGMPLIMITGQKPIKKSKQGQFQIVDIVGLFDPIC 133

Query: 147 KHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFNYVPVEPGSVIPGGFH 206
           K S  +     + S++ +AF +A   RPG VL+++P+D+  E+ +   +EP        H
Sbjct: 134 KMSKQIVHGNTIPSLIREAFRVAQEERPGAVLLELPEDIAAEETSEHVLEP--------H 185

Query: 207 QPEPPL--DAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQLPVTTTLMGK 264
           Q    +  DA +  A ++I  A+ PLL +G GA    A  +L       Q+P   T MGK
Sbjct: 186 QRHYAVAGDAVLTEAAEMIRAARMPLLLLGAGANRKHARSALSKFVNDTQIPFFNTQMGK 245

Query: 265 GAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDDRVTGKLDTFAPRARVVHFE 324
           G  DE   L +G   +    Y + A+   DL+I VG    ++    ++      +V+H  
Sbjct: 246 GVVDERSELFLGTAALSDGDYLHCAIERADLIINVGHDVVEKPPFFMEEGG--TKVIHVN 303

Query: 325 IDPAEIGKNRKADVAVLGDLGLSLARMVEISLQRTAEPRTAAWLERINTWKDRYPLTIPP 384
              A++ +     V V+GDL  S++++ E  LQ   E    ++ +R+    D     +  
Sbjct: 304 YKAAQVDQVYFPQVEVVGDLAQSISKLGEF-LQGPLE-FDRSYFQRVKNETD-----LHT 356

Query: 385 AEGA------IYPQEVLLAVRDLAPDA-IVTTDVGQHQMWAAQHLR-NGPRGWISSAGLG 436
           +EGA      + PQ  +   R +  D  I+  D G +++W A++ +   P   +    L 
Sbjct: 357 SEGADDPRFPVIPQRFVSDTRKVMGDCDIIALDNGIYKIWYARNYQAYQPNTVLLDNALA 416

Query: 437 TMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVKVVIVNNHWQGMV 496
           TMG G+P+AM A    P+R+V+ I GD   +MN QE+ T    GL + V ++N+   GM+
Sbjct: 417 TMGAGLPSAMMAAKLYPERRVMAICGDGGFMMNSQEIETAVRLGLNLVVTVLNDSSYGMI 476

Query: 497 RQWQESFYDERYSASDMLNGMPDFIALARSFGVDGVKITDRELLHRDLAAALQSPTPTMI 556
           R W++S         +  N  PDF+  A S+G  G ++   E L      A ++    +I
Sbjct: 477 R-WKQSHAGFDDWGLEFKN--PDFVQYANSYGATGHRVERTEDLVPTFEKAFEAGGVHLI 533

Query: 557 DVHVRRGEN 565
           D+ V   EN
Sbjct: 534 DLPVDYSEN 542


Lambda     K      H
   0.320    0.136    0.414 

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: 726
Number of extensions: 34
Number of successful extensions: 6
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: 617
Length of database: 557
Length adjustment: 37
Effective length of query: 580
Effective length of database: 520
Effective search space:   301600
Effective search space used:   301600
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: 53 (25.0 bits)

This GapMind analysis is from Jul 26 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