Alignments for a candidate for ilvI in Leptospirillum ferrooxidans C2-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Leptospirillum ferrooxidans C2-3

Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_014449473.1 LFE_RS06695 thiamine pyrophosphate-binding protein

Query= curated2:Q7U5G1
         (617 letters)



>NCBI__GCF_000284315.1:WP_014449473.1
          Length = 563

 Score =  235 bits (600), Expect = 3e-66
 Identities = 179/550 (32%), Positives = 275/550 (50%), Gaps = 31/550 (5%)

Query: 27  LMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHAADAYARATG 86
           +++ L   GV  IFG PG  I  + ++L I  S   V  +++RHE+AG  AA A A+ +G
Sbjct: 9   IVEFLAEMGVRQIFGIPGDTIDSLMESLRIQSS---VHFVVMRHEEAGAFAASAQAKLSG 65

Query: 87  KVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAFQETDIFGITLPIV 146
           K+ VC G  GPGA +L+ G+  A +D VP++ ITGQ+PR  IGT   QE D   +   + 
Sbjct: 66  KLAVCVGCQGPGAIHLLNGLYDAALDHVPVLAITGQIPRDEIGTGRPQEIDQLRLFGDVA 125

Query: 147 KHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFNYVPVEPGSVIPGGF- 205
            ++  VR P +L ++++QA   A   R G   + IP DV +      P  P  +    F 
Sbjct: 126 VYNQEVRSPENLEAVLSQAVRKALVLR-GVAHLSIPSDVMRLP---APPRPPEITKDHFA 181

Query: 206 HQP--EPPLDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQLPVTTTLMG 263
           H+    PPL   + A  +++++A R  +  G G   A A   L  L+ R   P+  T   
Sbjct: 182 HRSILHPPLSEILRAG-EILDRASRVTILYGEGVRRAEA--PLLDLSWRLGAPLVHTTRS 238

Query: 264 KGAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDDRVTGKLDTFAPRARVVHF 323
           K          +G +G+ G+  AN AV   D L+ VG+ F  R     + +  R  +V  
Sbjct: 239 KDILPSLHPSVMGGIGLMGSRSANHAVQNSDALLVVGSDFAFR-----EYYPERVPIVQV 293

Query: 324 EIDPAEIGKNRKADVAVLGDLGLSLARMVEISLQRTAEPRT-AAWLERINT--WKDRYPL 380
           EIDP+ IG+    +V +LG+     AR V  +L      RT A++L+R+ T   K+R   
Sbjct: 294 EIDPSRIGRRVPVEVGLLGE-----AREVLPALTEQVHKRTDASFLDRMRTEREKEREGY 348

Query: 381 TIPPAEGAIYPQEVLLAVRDLAP-DAIVTTDVGQHQMWAAQHLR-NGPRGWISSAGLGTM 438
                +G ++P E+   + D AP D I   D G   +W    L   G + ++ S+ LG++
Sbjct: 349 QRSKQDGLLHPGELTRMIGDRAPDDTIFLFDAGTVTVWGNNCLNIRGSQRFLWSSNLGSL 408

Query: 439 GFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVKVVIVNNHWQGMVRQ 498
           GF +PAA+GA+ A  +R VV + GD    M + +L T   Y LP+ +V+ NN     + +
Sbjct: 409 GFALPAAIGAKFAYRERPVVAMTGDGGFGMLLGDLATAVRYSLPMVIVVYNNGSYQFI-E 467

Query: 499 WQESFYDERYSASDMLNGMPDFIALARSFGVDGVKITDRELLHRDLAAALQSPTPTMIDV 558
           ++E         + + N  PDF+AL+R+FG DG  +   E +   L AA  S  P +ID 
Sbjct: 468 YEEEAEGNPVFGTKLTN--PDFVALSRAFGGDGASVRSMEDVPAALEAAFASKVPFVIDA 525

Query: 559 HVRRGENCYP 568
            V   E   P
Sbjct: 526 FVNPNELYIP 535


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: 875
Number of extensions: 48
Number of successful extensions: 5
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: 563
Length adjustment: 37
Effective length of query: 580
Effective length of database: 526
Effective search space:   305080
Effective search space used:   305080
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 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:

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 2024 update 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 original 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