Alignments for a candidate for ilvI in Methylocapsa acidiphila B2

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Methylocapsa acidiphila B2

Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_026607721.1 METAC_RS0115265 thiamine pyrophosphate-binding protein

Query= curated2:Q7U5G1
         (617 letters)



>NCBI__GCF_000427445.1:WP_026607721.1
          Length = 574

 Score =  222 bits (566), Expect = 3e-62
 Identities = 174/556 (31%), Positives = 258/556 (46%), Gaps = 29/556 (5%)

Query: 23  GAAALMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHAADAYA 82
           G   ++DAL   GVD +F  PGG + P   AL   ++   +K I+   E    + AD YA
Sbjct: 4   GTDFILDALASEGVDHLFMVPGGLVDPFLPALGRQKA---LKPIVAAQEGGAVYMADGYA 60

Query: 83  RATGKVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAFQET-----D 137
           RA+GK G      GPG TN VT +A AQ D  P+++++G+V     G   FQ+      D
Sbjct: 61  RASGKFGAALCIGGPGFTNTVTAVAAAQTDGSPVLLLSGEVATLVEGLGMFQDASPLTLD 120

Query: 138 IFGITLPIVKHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKD--VGQEQFNYVPV 195
              +  PIV+ S  V +P +L  I   A L   +   GPV + +P D  + +   +YVP+
Sbjct: 121 DVSVLKPIVRMSSSVDNPKNLPHIFKHAMLQLRTKPSGPVHLSLPSDCQIAELSVDYVPI 180

Query: 196 EPGSVIPGGFHQPEPPLDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQL 255
           +P  V P                  D      R  +  G G   A A  +LR  AE +++
Sbjct: 181 DPTLVDPAPLSLSGAEAAFRHFTGADGGRPPIRIAILAGAGVEHAYAAKALRQFAELWRI 240

Query: 256 PVTTTLMGKGAFDENDALSVGMLGMHGTAYANFAVTEC--DLLIAVGARFDDRVTGKLDT 313
           PV TTL  KG F E+  LS+G+ G  GT +A  A+ +   DLLI + +  ++R T     
Sbjct: 241 PVATTLRAKGVFPEDHVLSLGVFGYGGTHHARMALLDAPPDLLIVLASGLNERDTMHWSL 300

Query: 314 FAPRARVVHFEIDPAEIGKNRKADVAVLGDLG------LSLARMVEISLQRTAEPRTAAW 367
               +  +   +  A IG +  A   V+GD G      L    +++ SL  T+     AW
Sbjct: 301 QLAPSATICVNLAAANIGMH-SAGGGVVGDCGAFLRYLLDRTDVLDASLG-TSRAAREAW 358

Query: 368 LERINTWKDRYPLTIPPAEGA-IYPQEVLLAVRDLAP-DAIVTTDVGQHQMWAAQHLRN- 424
           L  I        +    ++   I+P  ++  +R   P D ++  D G H+ +A  +  + 
Sbjct: 359 LSEIRATPRLQDVEHCASDAVPIHPARIIAELRRAFPRDGVLLVDSGAHRAFAGHYWESY 418

Query: 425 GPRGWISSAGLGTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVK 484
            PR +IS+  LG MG+ +PAA G Q A P R+V  + GD  + MN  E+ T A YGLP+ 
Sbjct: 419 EPRTYISATNLGPMGWAIPAAAGVQCAQPQRRVAVVTGDGCMGMNGIEVATAARYGLPIL 478

Query: 485 VVIVNNHWQGMVRQWQESFYDERYSASDMLNGMP--DFIALARSFGVDGVKITDRELLHR 542
            V+VNN   G V  W  +   +     D L  +P  D+   ARS G  G  + +   L  
Sbjct: 479 FVVVNNAALGNV--WLRA--HKLGPVPDELTRLPDHDWAGFARSLGCRGETVREPGDLAG 534

Query: 543 DLAAALQSPTPTMIDV 558
             A  L    P +IDV
Sbjct: 535 AFARGLAGEGPCLIDV 550


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: 953
Number of extensions: 66
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: 574
Length adjustment: 37
Effective length of query: 580
Effective length of database: 537
Effective search space:   311460
Effective search space used:   311460
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 Apr 10 2024. The underlying query database was built on Apr 09 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis